effect of media research paper

• A-Z Publications

Annual Review of Psychology

Volume 67, 2016, review article, media effects: theory and research.

• Patti M. Valkenburg 1 , Jochen Peter 1 , and Joseph B. Walther 2
• View Affiliations Hide Affiliations Affiliations: 1 Amsterdam School of Communication Research, University of Amsterdam, Amsterdam 1012 WX, The Netherlands; email: [email protected] , [email protected] 2 Wee Kim Wee School of Communication and Information, Nanyang Technological University, 637718 Singapore; email: [email protected]
• Vol. 67:315-338 (Volume publication date January 2016) https://doi.org/10.1146/annurev-psych-122414-033608
• First published as a Review in Advance on August 19, 2015
• © Annual Reviews

This review analyzes trends and commonalities among prominent theories of media effects. On the basis of exemplary meta-analyses of media effects and bibliometric studies of well-cited theories, we identify and discuss five features of media effects theories as well as their empirical support. Each of these features specifies the conditions under which media may produce effects on certain types of individuals. Our review ends with a discussion of media effects in newer media environments. This includes theories of computer-mediated communication, the development of which appears to share a similar pattern of reformulation from unidirectional, receiver-oriented views, to theories that recognize the transactional nature of communication. We conclude by outlining challenges and promising avenues for future research.

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• Article Type: Review Article

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Effects of social media use on psychological well-being: a mediated model.

• 1 School of Finance and Economics, Jiangsu University, Zhenjiang, China
• 2 Research Unit of Governance, Competitiveness, and Public Policies (GOVCOPP), Center for Economics and Finance (cef.up), School of Economics and Management, University of Porto, Porto, Portugal
• 3 Department of Business Administration, Sukkur Institute of Business Administration (IBA) University, Sukkur, Pakistan
• 4 CETYS Universidad, Tijuana, Mexico
• 5 Department of Business Administration, Al-Quds University, Jerusalem, Israel
• 6 Business School, Shandong University, Weihai, China

The growth in social media use has given rise to concerns about the impacts it may have on users' psychological well-being. This paper's main objective is to shed light on the effect of social media use on psychological well-being. Building on contributions from various fields in the literature, it provides a more comprehensive study of the phenomenon by considering a set of mediators, including social capital types (i.e., bonding social capital and bridging social capital), social isolation, and smartphone addiction. The paper includes a quantitative study of 940 social media users from Mexico, using structural equation modeling (SEM) to test the proposed hypotheses. The findings point to an overall positive indirect impact of social media usage on psychological well-being, mainly due to the positive effect of bonding and bridging social capital. The empirical model's explanatory power is 45.1%. This paper provides empirical evidence and robust statistical analysis that demonstrates both positive and negative effects coexist, helping to reconcile the inconsistencies found so far in the literature.

Introduction

The use of social media has grown substantially in recent years ( Leong et al., 2019 ; Kemp, 2020 ). Social media refers to “the websites and online tools that facilitate interactions between users by providing them opportunities to share information, opinions, and interest” ( Swar and Hameed, 2017 , p. 141). Individuals use social media for many reasons, including entertainment, communication, and searching for information. Notably, adolescents and young adults are spending an increasing amount of time on online networking sites, e-games, texting, and other social media ( Twenge and Campbell, 2019 ). In fact, some authors (e.g., Dhir et al., 2018 ; Tateno et al., 2019 ) have suggested that social media has altered the forms of group interaction and its users' individual and collective behavior around the world.

Consequently, there are increased concerns regarding the possible negative impacts associated with social media usage addiction ( Swar and Hameed, 2017 ; Kircaburun et al., 2020 ), particularly on psychological well-being ( Chotpitayasunondh and Douglas, 2016 ; Jiao et al., 2017 ; Choi and Noh, 2019 ; Chatterjee, 2020 ). Smartphones sometimes distract their users from relationships and social interaction ( Chotpitayasunondh and Douglas, 2016 ; Li et al., 2020a ), and several authors have stressed that the excessive use of social media may lead to smartphone addiction ( Swar and Hameed, 2017 ; Leong et al., 2019 ), primarily because of the fear of missing out ( Reer et al., 2019 ; Roberts and David, 2020 ). Social media usage has been associated with anxiety, loneliness, and depression ( Dhir et al., 2018 ; Reer et al., 2019 ), social isolation ( Van Den Eijnden et al., 2016 ; Whaite et al., 2018 ), and “phubbing,” which refers to the extent to which an individual uses, or is distracted by, their smartphone during face-to-face communication with others ( Chotpitayasunondh and Douglas, 2016 ; Jiao et al., 2017 ; Choi and Noh, 2019 ; Chatterjee, 2020 ).

However, social media use also contributes to building a sense of connectedness with relevant others ( Twenge and Campbell, 2019 ), which may reduce social isolation. Indeed, social media provides several ways to interact both with close ties, such as family, friends, and relatives, and weak ties, including coworkers, acquaintances, and strangers ( Chen and Li, 2017 ), and plays a key role among people of all ages as they exploit their sense of belonging in different communities ( Roberts and David, 2020 ). Consequently, despite the fears regarding the possible negative impacts of social media usage on well-being, there is also an increasing number of studies highlighting social media as a new communication channel ( Twenge and Campbell, 2019 ; Barbosa et al., 2020 ), stressing that it can play a crucial role in developing one's presence, identity, and reputation, thus facilitating social interaction, forming and maintaining relationships, and sharing ideas ( Carlson et al., 2016 ), which consequently may be significantly correlated to social support ( Chen and Li, 2017 ; Holliman et al., 2021 ). Interestingly, recent studies (e.g., David et al., 2018 ; Bano et al., 2019 ; Barbosa et al., 2020 ) have suggested that the impact of smartphone usage on psychological well-being depends on the time spent on each type of application and the activities that users engage in.

Hence, the literature provides contradictory cues regarding the impacts of social media on users' well-being, highlighting both the possible negative impacts and the social enhancement it can potentially provide. In line with views on the need to further investigate social media usage ( Karikari et al., 2017 ), particularly regarding its societal implications ( Jiao et al., 2017 ), this paper argues that there is an urgent need to further understand the impact of the time spent on social media on users' psychological well-being, namely by considering other variables that mediate and further explain this effect.

One of the relevant perspectives worth considering is that provided by social capital theory, which is adopted in this paper. Social capital theory has previously been used to study how social media usage affects psychological well-being (e.g., Bano et al., 2019 ). However, extant literature has so far presented only partial models of associations that, although statistically acceptable and contributing to the understanding of the scope of social networks, do not provide as comprehensive a vision of the phenomenon as that proposed within this paper. Furthermore, the contradictory views, suggesting both negative (e.g., Chotpitayasunondh and Douglas, 2016 ; Van Den Eijnden et al., 2016 ; Jiao et al., 2017 ; Whaite et al., 2018 ; Choi and Noh, 2019 ; Chatterjee, 2020 ) and positive impacts ( Carlson et al., 2016 ; Chen and Li, 2017 ; Twenge and Campbell, 2019 ) of social media on psychological well-being, have not been adequately explored.

Given this research gap, this paper's main objective is to shed light on the effect of social media use on psychological well-being. As explained in detail in the next section, this paper explores the mediating effect of bonding and bridging social capital. To provide a broad view of the phenomenon, it also considers several variables highlighted in the literature as affecting the relationship between social media usage and psychological well-being, namely smartphone addiction, social isolation, and phubbing. The paper utilizes a quantitative study conducted in Mexico, comprising 940 social media users, and uses structural equation modeling (SEM) to test a set of research hypotheses.

This article provides several contributions. First, it adds to existing literature regarding the effect of social media use on psychological well-being and explores the contradictory indications provided by different approaches. Second, it proposes a conceptual model that integrates complementary perspectives on the direct and indirect effects of social media use. Third, it offers empirical evidence and robust statistical analysis that demonstrates that both positive and negative effects coexist, helping resolve the inconsistencies found so far in the literature. Finally, this paper provides insights on how to help reduce the potential negative effects of social media use, as it demonstrates that, through bridging and bonding social capital, social media usage positively impacts psychological well-being. Overall, the article offers valuable insights for academics, practitioners, and society in general.

The remainder of this paper is organized as follows. Section Literature Review presents a literature review focusing on the factors that explain the impact of social media usage on psychological well-being. Based on the literature review, a set of hypotheses are defined, resulting in the proposed conceptual model, which includes both the direct and indirect effects of social media usage on psychological well-being. Section Research Methodology explains the methodological procedures of the research, followed by the presentation and discussion of the study's results in section Results. Section Discussion is dedicated to the conclusions and includes implications, limitations, and suggestions for future research.

Literature Review

Putnam (1995 , p. 664–665) defined social capital as “features of social life – networks, norms, and trust – that enable participants to act together more effectively to pursue shared objectives.” Li and Chen (2014 , p. 117) further explained that social capital encompasses “resources embedded in one's social network, which can be assessed and used for instrumental or expressive returns such as mutual support, reciprocity, and cooperation.”

Putnam (1995 , 2000) conceptualized social capital as comprising two dimensions, bridging and bonding, considering the different norms and networks in which they occur. Bridging social capital refers to the inclusive nature of social interaction and occurs when individuals from different origins establish connections through social networks. Hence, bridging social capital is typically provided by heterogeneous weak ties ( Li and Chen, 2014 ). This dimension widens individual social horizons and perspectives and provides extended access to resources and information. Bonding social capital refers to the social and emotional support each individual receives from his or her social networks, particularly from close ties (e.g., family and friends).

Overall, social capital is expected to be positively associated with psychological well-being ( Bano et al., 2019 ). Indeed, Williams (2006) stressed that interaction generates affective connections, resulting in positive impacts, such as emotional support. The following sub-sections use the lens of social capital theory to explore further the relationship between the use of social media and psychological well-being.

Social Media Use, Social Capital, and Psychological Well-Being

The effects of social media usage on social capital have gained increasing scholarly attention, and recent studies have highlighted a positive relationship between social media use and social capital ( Brown and Michinov, 2019 ; Tefertiller et al., 2020 ). Li and Chen (2014) hypothesized that the intensity of Facebook use by Chinese international students in the United States was positively related to social capital forms. A longitudinal survey based on the quota sampling approach illustrated the positive effects of social media use on the two social capital dimensions ( Chen and Li, 2017 ). Abbas and Mesch (2018) argued that, as Facebook usage increases, it will also increase users' social capital. Karikari et al. (2017) also found positive effects of social media use on social capital. Similarly, Pang (2018) studied Chinese students residing in Germany and found positive effects of social networking sites' use on social capital, which, in turn, was positively associated with psychological well-being. Bano et al. (2019) analyzed the 266 students' data and found positive effects of WhatsApp use on social capital forms and the positive effect of social capital on psychological well-being, emphasizing the role of social integration in mediating this positive effect.

Kim and Kim (2017) stressed the importance of having a heterogeneous network of contacts, which ultimately enhances the potential social capital. Overall, the manifest and social relations between people from close social circles (bonding social capital) and from distant social circles (bridging social capital) are strengthened when they promote communication, social support, and the sharing of interests, knowledge, and skills, which are shared with other members. This is linked to positive effects on interactions, such as acceptance, trust, and reciprocity, which are related to the individuals' health and psychological well-being ( Bekalu et al., 2019 ), including when social media helps to maintain social capital between social circles that exist outside of virtual communities ( Ellison et al., 2007 ).

Grounded on the above literature, this study proposes the following hypotheses:

H1a: Social media use is positively associated with bonding social capital.

H1b: Bonding social capital is positively associated with psychological well-being.

H2a: Social media use is positively associated with bridging social capital.

H2b: Bridging social capital is positively associated with psychological well-being.

Social Media Use, Social Isolation, and Psychological Well-Being

Social isolation is defined as “a deficit of personal relationships or being excluded from social networks” ( Choi and Noh, 2019 , p. 4). The state that occurs when an individual lacks true engagement with others, a sense of social belonging, and a satisfying relationship is related to increased mortality and morbidity ( Primack et al., 2017 ). Those who experience social isolation are deprived of social relationships and lack contact with others or involvement in social activities ( Schinka et al., 2012 ). Social media usage has been associated with anxiety, loneliness, and depression ( Dhir et al., 2018 ; Reer et al., 2019 ), and social isolation ( Van Den Eijnden et al., 2016 ; Whaite et al., 2018 ). However, some recent studies have argued that social media use decreases social isolation ( Primack et al., 2017 ; Meshi et al., 2020 ). Indeed, the increased use of social media platforms such as Facebook, WhatsApp, Instagram, and Twitter, among others, may provide opportunities for decreasing social isolation. For instance, the improved interpersonal connectivity achieved via videos and images on social media helps users evidence intimacy, attenuating social isolation ( Whaite et al., 2018 ).

Chappell and Badger (1989) stated that social isolation leads to decreased psychological well-being, while Choi and Noh (2019) concluded that greater social isolation is linked to increased suicide risk. Schinka et al. (2012) further argued that, when individuals experience social isolation from siblings, friends, family, or society, their psychological well-being tends to decrease. Thus, based on the literature cited above, this study proposes the following hypotheses:

H3a: Social media use is significantly associated with social isolation.

H3b: Social isolation is negatively associated with psychological well-being.

Social Media Use, Smartphone Addiction, Phubbing, and Psychological Well-Being

Smartphone addiction refers to “an individuals' excessive use of a smartphone and its negative effects on his/her life as a result of his/her inability to control his behavior” ( Gökçearslan et al., 2018 , p. 48). Regardless of its form, smartphone addiction results in social, medical, and psychological harm to people by limiting their ability to make their own choices ( Chotpitayasunondh and Douglas, 2016 ). The rapid advancement of information and communication technologies has led to the concept of social media, e-games, and also to smartphone addiction ( Chatterjee, 2020 ). The excessive use of smartphones for social media use, entertainment (watching videos, listening to music), and playing e-games is more common amongst people addicted to smartphones ( Jeong et al., 2016 ). In fact, previous studies have evidenced the relationship between social use and smartphone addiction ( Salehan and Negahban, 2013 ; Jeong et al., 2016 ; Swar and Hameed, 2017 ). In line with this, the following hypotheses are proposed:

H4a: Social media use is positively associated with smartphone addiction.

H4b: Smartphone addiction is negatively associated with psychological well-being.

While smartphones are bringing individuals closer, they are also, to some extent, pulling people apart ( Tonacci et al., 2019 ). For instance, they can lead to individuals ignoring others with whom they have close ties or physical interactions; this situation normally occurs due to extreme smartphone use (i.e., at the dinner table, in meetings, at get-togethers and parties, and in other daily activities). This act of ignoring others is called phubbing and is considered a common phenomenon in communication activities ( Guazzini et al., 2019 ; Chatterjee, 2020 ). Phubbing is also referred to as an act of snubbing others ( Chatterjee, 2020 ). This term was initially used in May 2012 by an Australian advertising agency to describe the “growing phenomenon of individuals ignoring their families and friends who were called phubbee (a person who is a recipients of phubbing behavior) victim of phubber (a person who start phubbing her or his companion)” ( Chotpitayasunondh and Douglas, 2018 ). Smartphone addiction has been found to be a determinant of phubbing ( Kim et al., 2018 ). Other recent studies have also evidenced the association between smartphones and phubbing ( Chotpitayasunondh and Douglas, 2016 ; Guazzini et al., 2019 ; Tonacci et al., 2019 ; Chatterjee, 2020 ). Vallespín et al. (2017 ) argued that phubbing behavior has a negative influence on psychological well-being and satisfaction. Furthermore, smartphone addiction is considered responsible for the development of new technologies. It may also negatively influence individual's psychological proximity ( Chatterjee, 2020 ). Therefore, based on the above discussion and calls for the association between phubbing and psychological well-being to be further explored, this study proposes the following hypotheses:

H5: Smartphone addiction is positively associated with phubbing.

H6: Phubbing is negatively associated with psychological well-being.

Indirect Relationship Between Social Media Use and Psychological Well-Being

Beyond the direct hypotheses proposed above, this study investigates the indirect effects of social media use on psychological well-being mediated by social capital forms, social isolation, and phubbing. As described above, most prior studies have focused on the direct influence of social media use on social capital forms, social isolation, smartphone addiction, and phubbing, as well as the direct impact of social capital forms, social isolation, smartphone addiction, and phubbing on psychological well-being. Very few studies, however, have focused on and evidenced the mediating role of social capital forms, social isolation, smartphone addiction, and phubbing derived from social media use in improving psychological well-being ( Chen and Li, 2017 ; Pang, 2018 ; Bano et al., 2019 ; Choi and Noh, 2019 ). Moreover, little is known about smartphone addiction's mediating role between social media use and psychological well-being. Therefore, this study aims to fill this gap in the existing literature by investigating the mediation of social capital forms, social isolation, and smartphone addiction. Further, examining the mediating influence will contribute to a more comprehensive understanding of social media use on psychological well-being via the mediating associations of smartphone addiction and psychological factors. Therefore, based on the above, we propose the following hypotheses (the conceptual model is presented in Figure 1 ):

H7: (a) Bonding social capital; (b) bridging social capital; (c) social isolation; and (d) smartphone addiction mediate the relationship between social media use and psychological well-being.

Figure 1 . Conceptual model.

Research Methodology

Sample procedure and online survey.

This study randomly selected students from universities in Mexico. We chose University students for the following reasons. First, students are considered the most appropriate sample for e-commerce studies, particularly in the social media context ( Oghazi et al., 2018 ; Shi et al., 2018 ). Second, University students are considered to be frequent users and addicted to smartphones ( Mou et al., 2017 ; Stouthuysen et al., 2018 ). Third, this study ensured that respondents were experienced, well-educated, and possessed sufficient knowledge of the drawbacks of social media and the extreme use of smartphones. A total sample size of 940 University students was ultimately achieved from the 1,500 students contacted, using a convenience random sampling approach, due both to the COVID-19 pandemic and budget and time constraints. Additionally, in order to test the model, a quantitative empirical study was conducted, using an online survey method to collect data. This study used a web-based survey distributed via social media platforms for two reasons: the COVID-19 pandemic; and to reach a large number of respondents ( Qalati et al., 2021 ). Furthermore, online surveys are considered a powerful and authenticated tool for new research ( Fan et al., 2021 ), while also representing a fast, simple, and less costly approach to collecting data ( Dutot and Bergeron, 2016 ).

Data Collection Procedures and Respondent's Information

Data were collected by disseminating a link to the survey by e-mail and social network sites. Before presenting the closed-ended questionnaire, respondents were assured that their participation would remain voluntary, confidential, and anonymous. Data collection occurred from July 2020 to December 2020 (during the pandemic). It should be noted that, because data were collected during the pandemic, this may have had an influence on the results of the study. The reason for choosing a six-month lag time was to mitigate common method bias (CMB) ( Li et al., 2020b ). In the present study, 1,500 students were contacted via University e-mail and social applications (Facebook, WhatsApp, and Instagram). We sent a reminder every month for 6 months (a total of six reminders), resulting in 940 valid responses. Thus, 940 (62.6% response rate) responses were used for hypotheses testing.

Table 1 reveals that, of the 940 participants, three-quarters were female (76.4%, n = 719) and nearly one-quarter (23.6%, n = 221) were male. Nearly half of the participants (48.8%, n = 459) were aged between 26 and 35 years, followed by 36 to 35 years (21.9%, n = 206), <26 (20.3%, n = 191), and over 45 (8.9%, n = 84). Approximately two-thirds (65%, n = 611) had a bachelor's degree or above, while one-third had up to 12 years of education. Regarding the daily frequency of using the Internet, nearly half (48.6%, n = 457) of the respondents reported between 5 and 8 h a day, and over one-quarter (27.2%) 9–12 h a day. Regarding the social media platforms used, over 38.5 and 39.6% reported Facebook and WhatsApp, respectively. Of the 940 respondents, only 22.1% reported Instagram (12.8%) and Twitter (9.2%). It should be noted, however, that the sample is predominantly female and well-educated.

Table 1 . Respondents' characteristics.

Measurement Items

The study used five-point Likert scales (1 = “strongly disagree;” 5 = “strongly agree”) to record responses.

Social Media Use

Social media use was assessed using four items adapted from Karikari et al. (2017) . Sample items include “Social media is part of my everyday activity,” “Social media has become part of my daily life,” “I would be sorry if social media shut down,” and “I feel out of touch, when I have not logged onto social media for a while.” The adapted items had robust reliability and validity (CA = 783, CR = 0.857, AVE = 0.600).

Social Capital

Social capital was measured using a total of eight items, representing bonding social capital (four items) and bridging social capital (four items) adapted from Chan (2015) . Sample construct items include: bonging social capital (“I am willing to spend time to support general community activities,” “I interact with people who are quite different from me”) and bridging social capital (“My social media community is a good place to be,” “Interacting with people on social media makes me want to try new things”). The adapted items had robust reliability and validity [bonding social capital (CA = 0.785, CR = 0.861, AVE = 0.608) and bridging social capital (CA = 0.834, CR = 0.883, AVE = 0.601)].

Social Isolation

Social isolation was assessed using three items from Choi and Noh (2019) . Sample items include “I do not have anyone to play with,” “I feel alone from people,” and “I have no one I can trust.” This adapted scale had substantial reliability and validity (CA = 0.890, CR = 0.928, AVE = 0.811).

Smartphone Addiction

Smartphone addiction was assessed using five items taken from Salehan and Negahban (2013) . Sample items include “I am always preoccupied with my mobile,” “Using my mobile phone keeps me relaxed,” and “I am not able to control myself from frequent use of mobile phones.” Again, these adapted items showed substantial reliability and validity (CA = 903, CR = 0.928, AVE = 0.809).

Phubbing was assessed using four items from Chotpitayasunondh and Douglas (2018) . Sample items include: “I have conflicts with others because I am using my phone” and “I would rather pay attention to my phone than talk to others.” This construct also demonstrated significant reliability and validity (CA = 770, CR = 0.894, AVE = 0.809).

Psychological Well-Being

Psychological well-being was assessed using five items from Jiao et al. (2017) . Sample items include “I lead a purposeful and meaningful life with the help of others,” “My social relationships are supportive and rewarding in social media,” and “I am engaged and interested in my daily on social media.” This study evidenced that this adapted scale had substantial reliability and validity (CA = 0.886, CR = 0.917, AVE = 0.688).

Data Analysis

Based on the complexity of the association between the proposed construct and the widespread use and acceptance of SmartPLS 3.0 in several fields ( Hair et al., 2019 ), we utilized SEM, using SmartPLS 3.0, to examine the relationships between constructs. Structural equation modeling is a multivariate statistical analysis technique that is used to investigate relationships. Further, it is a combination of factor and multivariate regression analysis, and is employed to explore the relationship between observed and latent constructs.

SmartPLS 3.0 “is a more comprehensive software program with an intuitive graphical user interface to run partial least square SEM analysis, certainly has had a massive impact” ( Sarstedt and Cheah, 2019 ). According to Ringle et al. (2015) , this commercial software offers a wide range of algorithmic and modeling options, improved usability, and user-friendly and professional support. Furthermore, Sarstedt and Cheah (2019) suggested that structural equation models enable the specification of complex interrelationships between observed and latent constructs. Hair et al. (2019) argued that, in recent years, the number of articles published using partial least squares SEM has increased significantly in contrast to covariance-based SEM. In addition, partial least squares SEM using SmartPLS is more appealing for several scholars as it enables them to predict more complex models with several variables, indicator constructs, and structural paths, instead of imposing distributional assumptions on the data ( Hair et al., 2019 ). Therefore, this study utilized the partial least squares SEM approach using SmartPLS 3.0.

Common Method Bias (CMB) Test

This study used the Kaiser–Meyer–Olkin (KMO) test to measure the sampling adequacy and ensure data suitability. The KMO test result was 0.874, which is greater than an acceptable threshold of 0.50 ( Ali Qalati et al., 2021 ; Shrestha, 2021 ), and hence considered suitable for explanatory factor analysis. Moreover, Bartlett's test results demonstrated a significance level of 0.001, which is considered good as it is below the accepted threshold of 0.05.

The term CMB is associated with Campbell and Fiske (1959) , who highlighted the importance of CMB and identified that a portion of variance in the research may be due to the methods employed. It occurs when all scales of the study are measured at the same time using a single questionnaire survey ( Podsakoff and Organ, 1986 ); subsequently, estimates of the relationship among the variables might be distorted by the impacts of CMB. It is considered a serious issue that has a potential to “jeopardize” the validity of the study findings ( Tehseen et al., 2017 ). There are several reasons for CMB: (1) it mainly occurs due to response “tendencies that raters can apply uniformity across the measures;” and (2) it also occurs due to similarities in the wording and structure of the survey items that produce similar results ( Jordan and Troth, 2019 ). Harman's single factor test and a full collinearity approach were employed to ensure that the data was free from CMB ( Tehseen et al., 2017 ; Jordan and Troth, 2019 ; Ali Qalati et al., 2021 ). Harman's single factor test showed a single factor explained only 22.8% of the total variance, which is far below the 50.0% acceptable threshold ( Podsakoff et al., 2003 ).

Additionally, the variance inflation factor (VIF) was used, which is a measure of the amount of multicollinearity in a set of multiple regression constructs and also considered a way of detecting CMB ( Hair et al., 2019 ). Hair et al. (2019) suggested that the acceptable threshold for the VIF is 3.0; as the computed VIFs for the present study ranged from 1.189 to 1.626, CMB is not a key concern (see Table 2 ). Bagozzi et al. (1991) suggested a correlation-matrix procedure to detect CMB. Common method bias is evident if correlation among the principle constructs is >0.9 ( Tehseen et al., 2020 ); however, no values >0.9 were found in this study (see section Assessment of Measurement Model). This study used a two-step approach to evaluate the measurement model and the structural model.

Table 2 . Common method bias (full collinearity VIF).

Assessment of Measurement Model

Before conducting the SEM analysis, the measurement model was assessed to examine individual item reliability, internal consistency, and convergent and discriminant validity. Table 3 exhibits the values of outer loading used to measure an individual item's reliability ( Hair et al., 2012 ). Hair et al. (2017) proposed that the value for each outer loading should be ≥0.7; following this principle, two items of phubbing (PHUB3—I get irritated if others ask me to get off my phone and talk to them; PHUB4—I use my phone even though I know it irritated others) were removed from the analysis Hair et al. (2019) . According to Nunnally (1978) , Cronbach's alpha values should exceed 0.7. The threshold values of constructs in this study ranged from 0.77 to 0.903. Regarding internal consistency, Bagozzi and Yi (1988) suggested that composite reliability (CR) should be ≥0.7. The coefficient value for CR in this study was between 0.857 and 0.928. Regarding convergent validity, Fornell and Larcker (1981) suggested that the average variance extracted (AVE) should be ≥0.5. Average variance extracted values in this study were between 0.60 and 0.811. Finally, regarding discriminant validity, according to Fornell and Larcker (1981) , the square root of the AVE for each construct should exceed the inter-correlations of the construct with other model constructs. That was the case in this study, as shown in Table 4 .

Table 3 . Study measures, factor loading, and the constructs' reliability and convergent validity.

Table 4 . Discriminant validity and correlation.

Hence, by analyzing the results of the measurement model, it can be concluded that the data are adequate for structural equation estimation.

Assessment of the Structural Model

This study used the PLS algorithm and a bootstrapping technique with 5,000 bootstraps as proposed by Hair et al. (2019) to generate the path coefficient values and their level of significance. The coefficient of determination ( R 2 ) is an important measure to assess the structural model and its explanatory power ( Henseler et al., 2009 ; Hair et al., 2019 ). Table 5 and Figure 2 reveal that the R 2 value in the present study was 0.451 for psychological well-being, which means that 45.1% of changes in psychological well-being occurred due to social media use, social capital forms (i.e., bonding and bridging), social isolation, smartphone addiction, and phubbing. Cohen (1998) proposed that R 2 values of 0.60, 0.33, and 0.19 are considered substantial, moderate, and weak. Following Cohen's (1998) threshold values, this research demonstrates a moderate predicting power for psychological well-being among Mexican respondents ( Table 6 ).

Table 5 . Summary of path coefficients and hypothesis testing.

Figure 2 . Structural model.

Table 6 . Strength of the model (Predictive relevance, coefficient of determination, and model fit indices).

Apart from the R 2 measure, the present study also used cross-validated redundancy measures, or effect sizes ( q 2 ), to assess the proposed model and validate the results ( Ringle et al., 2012 ). Hair et al. (2019) suggested that a model exhibiting an effect size q 2 > 0 has predictive relevance ( Table 6 ). This study's results evidenced that it has a 0.15 <0.29 <0.35 (medium) predictive relevance, as 0.02, 0.15, and 0.35 are considered small, medium, and large, respectively ( Cohen, 1998 ). Regarding the goodness-of-fit indices, Hair et al. (2019) suggested the standardized root mean square residual (SRMR) to evaluate the goodness of fit. Standardized root mean square is an absolute measure of fit: a value of zero indicates perfect fit and a value <0.08 is considered good fit ( Hair et al., 2019 ). This study exhibits an adequate model fitness level with an SRMR value of 0.063 ( Table 6 ).

Table 5 reveals that all hypotheses of the study were accepted base on the criterion ( p -value < 0.05). H1a (β = 0.332, t = 10.283, p = 0.001) was confirmed, with the second most robust positive and significant relationship (between social media use and bonding social capital). In addition, this study evidenced a positive and significant relationship between bonding social capital and psychological well-being (β = 0.127, t = 4.077, p = 0.001); therefore, H1b was accepted. Regarding social media use and bridging social capital, the present study found the most robust positive and significant impact (β = 0.439, t = 15.543, p = 0.001); therefore, H2a was accepted. The study also evidenced a positive and significant association between bridging social capital and psychological well-being (β = 0.561, t = 20.953, p = 0.001); thus, H2b was accepted. The present study evidenced a significant effect of social media use on social isolation (β = 0.145, t = 4.985, p = 0.001); thus, H3a was accepted. In addition, this study accepted H3b (β = −0.051, t = 2.01, p = 0.044). Furthermore, this study evidenced a positive and significant effect of social media use on smartphone addiction (β = 0.223, t = 6.241, p = 0.001); therefore, H4a was accepted. Furthermore, the present study found that smartphone addiction has a negative significant influence on psychological well-being (β = −0.068, t = 2.387, p = 0.017); therefore, H4b was accepted. Regarding the relationship between smartphone addiction and phubbing, this study found a positive and significant effect of smartphone addiction on phubbing (β = 0.244, t = 7.555, p = 0.001); therefore, H5 was accepted. Furthermore, the present research evidenced a positive and significant influence of phubbing on psychological well-being (β = 0.137, t = 4.938, p = 0.001); therefore, H6 was accepted. Finally, the study provides interesting findings on the indirect effect of social media use on psychological well-being ( t -value > 1.96 and p -value < 0.05); therefore, H7a–d were accepted.

Furthermore, to test the mediating analysis, Preacher and Hayes's (2008) approach was used. The key characteristic of an indirect relationship is that it involves a third construct, which plays a mediating role in the relationship between the independent and dependent constructs. Logically, the effect of A (independent construct) on C (the dependent construct) is mediated by B (a third variable). Preacher and Hayes (2008) suggested the following: B is a construct acting as a mediator if A significantly influences B, A significantly accounts for variability in C, B significantly influences C when controlling for A, and the influence of A on C decreases significantly when B is added simultaneously with A as a predictor of C. According to Matthews et al. (2018) , if the indirect effect is significant while the direct insignificant, full mediation has occurred, while if both direct and indirect effects are substantial, partial mediation has occurred. This study evidenced that there is partial mediation in the proposed construct ( Table 5 ). Following Preacher and Hayes (2008) this study evidenced that there is partial mediation in the proposed construct, because the relationship between independent variable (social media use) and dependent variable (psychological well-being) is significant ( p -value < 0.05) and indirect effect among them after introducing mediator (bonding social capital, bridging social capital, social isolation, and smartphone addiction) is also significant ( p -value < 0.05), therefore it is evidenced that when there is a significant effect both direct and indirect it's called partial mediation.

The present study reveals that the social and psychological impacts of social media use among University students is becoming more complex as there is continuing advancement in technology, offering a range of affordable interaction opportunities. Based on the 940 valid responses collected, all the hypotheses were accepted ( p < 0.05).

H1a finding suggests that social media use is a significant influencing factor of bonding social capital. This implies that, during a pandemic, social media use enables students to continue their close relationships with family members, friends, and those with whom they have close ties. This finding is in line with prior work of Chan (2015) and Ellison et al. (2007) , who evidenced that social bonding capital is predicted by Facebook use and having a mobile phone. H1b findings suggest that, when individuals believe that social communication can help overcome obstacles to interaction and encourage more virtual self-disclosure, social media use can improve trust and promote the establishment of social associations, thereby enhancing well-being. These findings are in line with those of Gong et al. (2021) , who also witnessed the significant effect of bonding social capital on immigrants' psychological well-being, subsequently calling for the further evidence to confirm the proposed relationship.

The findings of the present study related to H2a suggest that students are more likely to use social media platforms to receive more emotional support, increase their ability to mobilize others, and to build social networks, which leads to social belongingness. Furthermore, the findings suggest that social media platforms enable students to accumulate and maintain bridging social capital; further, online classes can benefit students who feel shy when participating in offline classes. This study supports the previous findings of Chan (2015) and Karikari et al. (2017) . Notably, the present study is not limited to a single social networking platform, taking instead a holistic view of social media. The H2b findings are consistent with those of Bano et al. (2019) , who also confirmed the link between bonding social capital and psychological well-being among University students using WhatsApp as social media platform, as well as those of Chen and Li (2017) .

The H3a findings suggest that, during the COVID-19 pandemic when most people around the world have had limited offline or face-to-face interaction and have used social media to connect with families, friends, and social communities, they have often been unable to connect with them. This is due to many individuals avoiding using social media because of fake news, financial constraints, and a lack of trust in social media; thus, the lack both of offline and online interaction, coupled with negative experiences on social media use, enhances the level of social isolation ( Hajek and König, 2021 ). These findings are consistent with those of Adnan and Anwar (2020) . The H3b suggests that higher levels of social isolation have a negative impact on psychological well-being. These result indicating that, consistent with Choi and Noh (2019) , social isolation is negatively and significantly related to psychological well-being.

The H4a results suggests that substantial use of social media use leads to an increase in smartphone addiction. These findings are in line with those of Jeong et al. (2016) , who stated that the excessive use of smartphones for social media, entertainment (watching videos, listening to music), and playing e-games was more likely to lead to smartphone addiction. These findings also confirm the previous work of Jeong et al. (2016) , Salehan and Negahban (2013) , and Swar and Hameed (2017) . The H4b results revealed that a single unit increase in smartphone addiction results in a 6.8% decrease in psychological well-being. These findings are in line with those of Tangmunkongvorakul et al. (2019) , who showed that students with higher levels of smartphone addiction had lower psychological well-being scores. These findings also support those of Shoukat (2019) , who showed that smartphone addiction inversely influences individuals' mental health.

This suggests that the greater the smartphone addiction, the greater the phubbing. The H5 findings are in line with those of Chatterjee (2020) , Chotpitayasunondh and Douglas (2016) , Guazzini et al. (2019) , and Tonacci et al. (2019) , who also evidenced a significant impact of smartphone addiction and phubbing. Similarly, Chotpitayasunondh and Douglas (2018) corroborated that smartphone addiction is the main predictor of phubbing behavior. However, these findings are inconsistent with those of Vallespín et al. (2017 ), who found a negative influence of phubbing.

The H6 results suggests that phubbing is one of the significant predictors of psychological well-being. Furthermore, these findings suggest that, when phubbers use a cellphone during interaction with someone, especially during the current pandemic, and they are connected with many family members, friends, and relatives; therefore, this kind of action gives them more satisfaction, which simultaneously results in increased relaxation and decreased depression ( Chotpitayasunondh and Douglas, 2018 ). These findings support those of Davey et al. (2018) , who evidenced that phubbing has a significant influence on adolescents and social health students in India.

The findings showed a significant and positive effect of social media use on psychological well-being both through bridging and bonding social capital. However, a significant and negative effect of social media use on psychological well-being through smartphone addiction and through social isolation was also found. Hence, this study provides evidence that could shed light on the contradictory contributions in the literature suggesting both positive (e.g., Chen and Li, 2017 ; Twenge and Campbell, 2019 ; Roberts and David, 2020 ) and negative (e.g., Chotpitayasunondh and Douglas, 2016 ; Jiao et al., 2017 ; Choi and Noh, 2019 ; Chatterjee, 2020 ) effects of social media use on psychological well-being. This study concludes that the overall impact is positive, despite some degree of negative indirect impact.

Theoretical Contributions

This study's findings contribute to the current literature, both by providing empirical evidence for the relationships suggested by extant literature and by demonstrating the relevance of adopting a more complex approach that considers, in particular, the indirect effect of social media on psychological well-being. As such, this study constitutes a basis for future research ( Van Den Eijnden et al., 2016 ; Whaite et al., 2018 ) aiming to understand the impacts of social media use and to find ways to reduce its possible negative impacts.

In line with Kim and Kim (2017) , who stressed the importance of heterogeneous social networks in improving social capital, this paper suggests that, to positively impact psychological well-being, social media usage should be associated both with strong and weak ties, as both are important in building social capital, and hence associated with its bonding and bridging facets. Interestingly, though, bridging capital was shown as having the greatest impact on psychological well-being. Thus, the importance of wider social horizons, the inclusion in different groups, and establishing new connections ( Putnam, 1995 , 2000 ) with heterogeneous weak ties ( Li and Chen, 2014 ) are highlighted in this paper.

Practical Contributions

These findings are significant for practitioners, particularly those interested in dealing with the possible negative impacts of social media use on psychological well-being. Although social media use is associated with factors that negatively impact psychological well-being, particularly smartphone addiction and social isolation, these negative impacts can be lessened if the connections with both strong and weak ties are facilitated and featured by social media. Indeed, social media platforms offer several features, from facilitating communication with family, friends, and acquaintances, to identifying and offering access to other people with shared interests. However, it is important to access heterogeneous weak ties ( Li and Chen, 2014 ) so that social media offers access to wider sources of information and new resources, hence enhancing bridging social capital.

Limitations and Directions for Future Studies

This study is not without limitations. For example, this study used a convenience sampling approach to reach to a large number of respondents. Further, this study was conducted in Mexico only, limiting the generalizability of the results; future research should therefore use a cross-cultural approach to investigate the impacts of social media use on psychological well-being and the mediating role of proposed constructs (e.g., bonding and bridging social capital, social isolation, and smartphone addiction). The sample distribution may also be regarded as a limitation of the study because respondents were mainly well-educated and female. Moreover, although Internet channels represent a particularly suitable way to approach social media users, the fact that this study adopted an online survey does not guarantee a representative sample of the population. Hence, extrapolating the results requires caution, and study replication is recommended, particularly with social media users from other countries and cultures. The present study was conducted in the context of mainly University students, primarily well-educated females, via an online survey on in Mexico; therefore, the findings represent a snapshot at a particular time. Notably, however, the effect of social media use is increasing due to COVID-19 around the globe and is volatile over time.

Two of the proposed hypotheses of this study, namely the expected negative impacts of social media use on social isolation and of phubbing on psychological well-being, should be further explored. One possible approach is to consider the type of connections (i.e., weak and strong ties) to explain further the impact of social media usage on social isolation. Apparently, the prevalence of weak ties, although facilitating bridging social capital, may have an adverse impact in terms of social isolation. Regarding phubbing, the fact that the findings point to a possible positive impact on psychological well-being should be carefully addressed, specifically by psychology theorists and scholars, in order to identify factors that may help further understand this phenomenon. Other suggestions for future research include using mixed-method approaches, as qualitative studies could help further validate the results and provide complementary perspectives on the relationships between the considered variables.

Data Availability Statement

The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation.

Ethics Statement

The studies involving human participants were reviewed and approved by Jiangsu University. The patients/participants provided their written informed consent to participate in this study.

Author Contributions

All authors listed have made a substantial, direct and intellectual contribution to the work, and approved it for publication.

This study is supported by the National Statistics Research Project of China (2016LY96).

Conflict of Interest

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

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Keywords: smartphone addiction, social isolation, bonding social capital, bridging social capital, phubbing, social media use

Citation: Ostic D, Qalati SA, Barbosa B, Shah SMM, Galvan Vela E, Herzallah AM and Liu F (2021) Effects of Social Media Use on Psychological Well-Being: A Mediated Model. Front. Psychol. 12:678766. doi: 10.3389/fpsyg.2021.678766

Received: 10 March 2021; Accepted: 25 May 2021; Published: 21 June 2021.

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Copyright © 2021 Ostic, Qalati, Barbosa, Shah, Galvan Vela, Herzallah and Liu. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY) . The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

*Correspondence: Sikandar Ali Qalati, sidqalati@gmail.com ; 5103180243@stmail.ujs.edu.cn ; Esthela Galvan Vela, esthela.galvan@cetys.mx

† ORCID: Dragana Ostic orcid.org/0000-0002-0469-1342 Sikandar Ali Qalati orcid.org/0000-0001-7235-6098 Belem Barbosa orcid.org/0000-0002-4057-360X Esthela Galvan Vela orcid.org/0000-0002-8778-3989 Feng Liu orcid.org/0000-0001-9367-049X

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2.2 Media Effects Theories

Learning objectives.

• Identify the basic theories of media effects.
• Explain the uses of various media effects theories.

Early media studies focused on the use of mass media in propaganda and persuasion. However, journalists and researchers soon looked to behavioral sciences to help figure out the effect of mass media and communications on society. Scholars have developed many different approaches and theories to figure this out. You can refer to these theories as you research and consider the media’s effect on culture.

Widespread fear that mass-media messages could outweigh other stabilizing cultural influences, such as family and community, led to what is known as the direct effects model of media studies. This model assumed that audiences passively accepted media messages and would exhibit predictable reactions in response to those messages. For example, following the radio broadcast of War of the Worlds in 1938 (which was a fictional news report of an alien invasion), some people panicked and believed the story to be true.

Challenges to the Direct Effects Theory

The results of the People’s Choice Study challenged this model. Conducted in 1940, the study attempted to gauge the effects of political campaigns on voter choice. Researchers found that voters who consumed the most media had generally already decided for which candidate to vote, while undecided voters generally turned to family and community members to help them decide. The study thus discredited the direct effects model and influenced a host of other media theories (Hanson, 2009). These theories do not necessarily give an all-encompassing picture of media effects but rather work to illuminate a particular aspect of media influence.

Marshall McLuhan’s Influence on Media Studies

During the early 1960s, English professor Marshall McLuhan wrote two books that had an enormous effect on the history of media studies. Published in 1962 and 1964, respectively, the Gutenberg Galaxy and Understanding Media both traced the history of media technology and illustrated the ways these innovations had changed both individual behavior and the wider culture. Understanding Media introduced a phrase that McLuhan has become known for: “The medium is the message.” This notion represented a novel take on attitudes toward media—that the media themselves are instrumental in shaping human and cultural experience.

His bold statements about media gained McLuhan a great deal of attention as both his supporters and critics responded to his utopian views about the ways media could transform 20th-century life. McLuhan spoke of a media-inspired “global village” at a time when Cold War paranoia was at its peak and the Vietnam War was a hotly debated subject. Although 1960s-era utopians received these statements positively, social realists found them cause for scorn. Despite—or perhaps because of—these controversies, McLuhan became a pop culture icon, mentioned frequently in the television sketch-comedy program Laugh-In and appearing as himself in Woody Allen’s film Annie Hall .

The Internet and its accompanying cultural revolution have made McLuhan’s bold utopian visions seem like prophecies. Indeed, his work has received a great deal of attention in recent years. Analysis of McLuhan’s work has, interestingly, not changed very much since his works were published. His supporters point to the hopes and achievements of digital technology and the utopian state that such innovations promise. The current critique of McLuhan, however, is a bit more revealing of the state of modern media studies. Media scholars are much more numerous now than they were during the 1960s, and many of these scholars criticize McLuhan’s lack of methodology and theoretical framework.

Despite his lack of scholarly diligence, McLuhan had a great deal of influence on media studies. Professors at Fordham University have formed an association of McLuhan-influenced scholars. McLuhan’s other great achievement is the popularization of the concept of media studies. His work brought the idea of media effects into the public arena and created a new way for the public to consider the influence of media on culture (Stille, 2000).

Agenda-Setting Theory

In contrast to the extreme views of the direct effects model, the agenda-setting theory of media stated that mass media determine the issues that concern the public rather than the public’s views. Under this theory, the issues that receive the most attention from media become the issues that the public discusses, debates, and demands action on. This means that the media is determining what issues and stories the public thinks about. Therefore, when the media fails to address a particular issue, it becomes marginalized in the minds of the public (Hanson).

When critics claim that a particular media outlet has an agenda, they are drawing on this theory. Agendas can range from a perceived liberal bias in the news media to the propagation of cutthroat capitalist ethics in films. For example, the agenda-setting theory explains such phenomena as the rise of public opinion against smoking. Before the mass media began taking an antismoking stance, smoking was considered a personal health issue. By promoting antismoking sentiments through advertisements, public relations campaigns, and a variety of media outlets, the mass media moved smoking into the public arena, making it a public health issue rather than a personal health issue (Dearing & Rogers, 1996). More recently, coverage of natural disasters has been prominent in the news. However, as news coverage wanes, so does the general public’s interest.

Through a variety of antismoking campaigns, the health risks of smoking became a public agenda.

Quinn Dombrowski – Weapons of mass destruction – CC BY-SA 2.0.

Media scholars who specialize in agenda-setting research study the salience, or relative importance, of an issue and then attempt to understand what causes it to be important. The relative salience of an issue determines its place within the public agenda, which in turn influences public policy creation. Agenda-setting research traces public policy from its roots as an agenda through its promotion in the mass media and finally to its final form as a law or policy (Dearing & Rogers, 1996).

Uses and Gratifications Theory

Practitioners of the uses and gratifications theory study the ways the public consumes media. This theory states that consumers use the media to satisfy specific needs or desires. For example, you may enjoy watching a show like Dancing With the Stars while simultaneously tweeting about it on Twitter with your friends. Many people use the Internet to seek out entertainment, to find information, to communicate with like-minded individuals, or to pursue self-expression. Each of these uses gratifies a particular need, and the needs determine the way in which media is used. By examining factors of different groups’ media choices, researchers can determine the motivations behind media use (Papacharissi, 2009).

A typical uses and gratifications study explores the motives for media consumption and the consequences associated with use of that media. In the case of Dancing With the Stars and Twitter, you are using the Internet as a way to be entertained and to connect with your friends. Researchers have identified a number of common motives for media consumption. These include relaxation, social interaction, entertainment, arousal, escape, and a host of interpersonal and social needs. By examining the motives behind the consumption of a particular form of media, researchers can better understand both the reasons for that medium’s popularity and the roles that the medium fills in society. A study of the motives behind a given user’s interaction with Facebook, for example, could explain the role Facebook takes in society and the reasons for its appeal.

Uses and gratifications theories of media are often applied to contemporary media issues. The analysis of the relationship between media and violence that you read about in preceding sections exemplifies this. Researchers employed the uses and gratifications theory in this case to reveal a nuanced set of circumstances surrounding violent media consumption, as individuals with aggressive tendencies were drawn to violent media (Papacharissi, 2009).

Symbolic Interactionism

Another commonly used media theory, symbolic interactionism , states that the self is derived from and develops through human interaction. This means the way you act toward someone or something is based on the meaning you have for a person or thing. To effectively communicate, people use symbols with shared cultural meanings. Symbols can be constructed from just about anything, including material goods, education, or even the way people talk. Consequentially, these symbols are instrumental in the development of the self.

This theory helps media researchers better understand the field because of the important role the media plays in creating and propagating shared symbols. Because of the media’s power, it can construct symbols on its own. By using symbolic interactionist theory, researchers can look at the ways media affects a society’s shared symbols and, in turn, the influence of those symbols on the individual (Jansson-Boyd, 2010).

One of the ways the media creates and uses cultural symbols to affect an individual’s sense of self is advertising. Advertisers work to give certain products a shared cultural meaning to make them desirable. For example, when you see someone driving a BMW, what do you think about that person? You may assume the person is successful or powerful because of the car he or she is driving. Ownership of luxury automobiles signifies membership in a certain socioeconomic class. Equally, technology company Apple has used advertising and public relations to attempt to become a symbol of innovation and nonconformity. Use of an Apple product, therefore, may have a symbolic meaning and may send a particular message about the product’s owner.

Media also propagate other noncommercial symbols. National and state flags, religious images, and celebrities gain shared symbolic meanings through their representation in the media.

Spiral of Silence

The spiral of silence theory, which states that those who hold a minority opinion silence themselves to prevent social isolation, explains the role of mass media in the formation and maintenance of dominant opinions. As minority opinions are silenced, the illusion of consensus grows, and so does social pressure to adopt the dominant position. This creates a self-propagating loop in which minority voices are reduced to a minimum and perceived popular opinion sides wholly with the majority opinion. For example, prior to and during World War II, many Germans opposed Adolf Hitler and his policies; however, they kept their opposition silent out of fear of isolation and stigma.

Because the media is one of the most important gauges of public opinion, this theory is often used to explain the interaction between media and public opinion. According to the spiral of silence theory, if the media propagates a particular opinion, then that opinion will effectively silence opposing opinions through an illusion of consensus. This theory relates especially to public polling and its use in the media (Papacharissi).

Media Logic

The media logic theory states that common media formats and styles serve as a means of perceiving the world. Today, the deep rooting of media in the cultural consciousness means that media consumers need engage for only a few moments with a particular television program to understand that it is a news show, a comedy, or a reality show. The pervasiveness of these formats means that our culture uses the style and content of these shows as ways to interpret reality. For example, think about a TV news program that frequently shows heated debates between opposing sides on public policy issues. This style of debate has become a template for handling disagreement to those who consistently watch this type of program.

Media logic affects institutions as well as individuals. The modern televangelist has evolved from the adoption of television-style promotion by religious figures, while the utilization of television in political campaigns has led candidates to consider their physical image as an important part of a campaign (Altheide & Snow, 1991).

Cultivation Analysis

The cultivation analysis theory states that heavy exposure to media causes individuals to develop an illusory perception of reality based on the most repetitive and consistent messages of a particular medium. This theory most commonly applies to analyses of television because of that medium’s uniquely pervasive, repetitive nature. Under this theory, someone who watches a great deal of television may form a picture of reality that does not correspond to actual life. Televised violent acts, whether those reported on news programs or portrayed on television dramas, for example, greatly outnumber violent acts that most people encounter in their daily lives. Thus, an individual who watches a great deal of television may come to view the world as more violent and dangerous than it actually is.

Cultivation analysis projects involve a number of different areas for research, such as the differences in perception between heavy and light users of media. To apply this theory, the media content that an individual normally watches must be analyzed for various types of messages. Then, researchers must consider the given media consumer’s cultural background of individuals to correctly determine other factors that are involved in his or her perception of reality. For example, the socially stabilizing influences of family and peer groups influence children’s television viewing and the way they process media messages. If an individual’s family or social life plays a major part in her life, the social messages that she receives from these groups may compete with the messages she receives from television.

Key Takeaways

• The now largely discredited direct effects model of media studies assumes that media audiences passively accept media messages and exhibit predictable reactions in response to those messages.
• Credible media theories generally do not give as much power to the media, such as the agenda-setting theory, or give a more active role to the media consumer, such as the uses and gratifications theory.
• Other theories focus on specific aspects of media influence, such as the spiral of silence theory’s focus on the power of the majority opinion or the symbolic interactionism theory’s exploration of shared cultural symbolism.
• Media logic and cultivation analysis theories deal with how media consumers’ perceptions of reality can be influenced by media messages.

Media theories have a variety of uses and applications. Research one of the following topics and its effect on culture. Examine the topic using at least two of the approaches discussed in this section. Then, write a one-page essay about the topic you’ve selected.

• Internet habits
• Television’s effect on attention span
• Advertising and self-image
• Racial stereotyping in film
• Many of the theories discussed in this section were developed decades ago. Identify how each of these theories can be used today? Do you think these theories are still relevant for modern mass media? Why?

David Altheide and Robert Snow, Media Worlds in the Postjournalism Era (New York: Walter de Gruyter, 1991), 9–11.

Dearing, James and Everett Rogers, Agenda-Setting (Thousand Oaks, CA: Sage, 1996), 4.

Hanson, Ralph. Mass Communication: Living in a Media World (Washington, DC: CQ Press, 2009), 80–81.

Hanson, Ralph. Mass Communication , 92.

Jansson-Boyd, Catherine. Consumer Psychology (New York: McGraw-Hill, 2010), 59–62.

Papacharissi, Zizi. “Uses and Gratifications,” 153–154.

Papacharissi, Zizi. “Uses and Gratifications,” in An Integrated Approach to Communication Theory and Research , ed. Don Stacks and Michael Salwen (New York: Routledge, 2009), 137.

Stille, Alexander. “Marshall McLuhan Is Back From the Dustbin of History; With the Internet, His Ideas Again Seem Ahead of Their Time,” New York Times , October 14, 2000, http://www.nytimes.com/2000/10/14/arts/marshall-mcluhan-back-dustbin-history-with-internet-his-ideas-again-seem-ahead.html .

Understanding Media and Culture Copyright © 2016 by University of Minnesota is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License , except where otherwise noted.

McCarthyism, Media, and Political Repression: Evidence from Hollywood

We study a far-reaching episode of demagoguery in American history. From the late 1940s to 1950s, anti-communist hysteria led by Senator Joseph McCarthy and others gripped the nation. Hundreds of professionals in Hollywood were accused of having ties with the communist. We show that these accusations were not random, targeting those with dissenting views. Actors and screenwriters who were accused suffered a setback in their careers. Beyond the accused, we find that the anti-communist crusade also had a chilling effect on film content, as non-accused filmmakers avoided progressive topics. The decline in progressive films, in turn, made society more conservative.

We are grateful to Desmond Ang, Leah Boustan, Ruben Durante, Shari Eli, James Feigenbaum, Ricard Gill, Pauline Grosjean, Stephan Heblich, Saumitra Jha, Ilyana Kuziemko, Caroline Le Pennec, Kevin Lim, Petra Moser, Suresh Naidu, Nathan Nunn, Sahar Parsa, Daniel I. Rees, Aloysius Siow as well as seminar participants at Princeton University, University of Toronto, University of British Columbia, Simon Fraser University, University of Pittsburgh, University of Hong Kong, Chinese University of Hong Kong, National University of Singapore, Peking University, Lund University, Universidad de Chile, the ASREC Conference, the CNEH Conference, the NBER DAE Spring Meeting, the Mountain West Economic History Conference, and the Southern Economic Association Conference for helpful comments and suggestions. Nishtha Kawatra, Yaqi Liu, Ganesh Manyam, Martin McFarlane, Armaan Nanji, Yibei Wu, and Suning Zhang provided excellent research assistance. The views expressed herein are those of the authors and do not necessarily reflect the views of the National Bureau of Economic Research.

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Social Media and Mental Health: Benefits, Risks, and Opportunities for Research and Practice

John a. naslund.

a Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA

Ameya Bondre

b CareNX Innovations, Mumbai, India

John Torous

c Department of Psychiatry, Beth Israel Deaconess Medical Center, Boston, MA

Kelly A. Aschbrenner

d Department of Psychiatry, Geisel School of Medicine at Dartmouth, Lebanon, NH

Social media platforms are popular venues for sharing personal experiences, seeking information, and offering peer-to-peer support among individuals living with mental illness. With significant shortfalls in the availability, quality, and reach of evidence-based mental health services across the United States and globally, social media platforms may afford new opportunities to bridge this gap. However, caution is warranted, as numerous studies highlight risks of social media use for mental health. In this commentary, we consider the role of social media as a potentially viable intervention platform for offering support to persons with mental disorders, promoting engagement and retention in care, and enhancing existing mental health services. Specifically, we summarize current research on the use of social media among mental health service users, and early efforts using social media for the delivery of evidence-based programs. We also review the risks, potential harms, and necessary safety precautions with using social media for mental health. To conclude, we explore opportunities using data science and machine learning, for example by leveraging social media for detecting mental disorders and developing predictive models aimed at characterizing the aetiology and progression of mental disorders. These various efforts using social media, as summarized in this commentary, hold promise for improving the lives of individuals living with mental disorders.

Introduction

Social media has become a prominent fixture in the lives of many individuals facing the challenges of mental illness. Social media refers broadly to web and mobile platforms that allow individuals to connect with others within a virtual network (such as Facebook, Twitter, Instagram, Snapchat, or LinkedIn), where they can share, co-create, or exchange various forms of digital content, including information, messages, photos, or videos ( Ahmed, Ahmad, Ahmad, & Zakaria, 2019 ). Studies have reported that individuals living with a range of mental disorders, including depression, psychotic disorders, or other severe mental illnesses, use social media platforms at comparable rates as the general population, with use ranging from about 70% among middle-age and older individuals, to upwards of 97% among younger individuals ( Aschbrenner, Naslund, Grinley, et al., 2018 ; M. L. Birnbaum, Rizvi, Correll, Kane, & Confino, 2017 ; Brunette et al., 2019 ; Naslund, Aschbrenner, & Bartels, 2016 ). Other exploratory studies have found that many of these individuals with mental illness appear to turn to social media to share their personal experiences, seek information about their mental health and treatment options, and give and receive support from others facing similar mental health challenges ( Bucci, Schwannauer, & Berry, 2019 ; Naslund, Aschbrenner, Marsch, & Bartels, 2016b ).

Across the United States and globally, very few people living with mental illness have access to adequate mental health services ( Patel et al., 2018 ). The wide reach and near ubiquitous use of social media platforms may afford novel opportunities to address these shortfalls in existing mental health care, by enhancing the quality, availability, and reach of services. Recent studies have explored patterns of social media use, impact of social media use on mental health and wellbeing, and the potential to leverage the popularity and interactive features of social media to enhance the delivery of interventions. However, there remains uncertainty regarding the risks and potential harms of social media for mental health ( Orben & Przybylski, 2019 ), and how best to weigh these concerns against potential benefits.

In this commentary, we summarized current research on the use of social media among individuals with mental illness, with consideration of the impact of social media on mental wellbeing, as well as early efforts using social media for delivery of evidence-based programs for addressing mental health problems. We searched for recent peer reviewed publications in Medline and Google Scholar using the search terms “mental health” or “mental illness” and “social media”, and searched the reference lists of recent reviews and other relevant studies. We reviewed the risks, potential harms, and necessary safety precautions with using social media for mental health. Overall, our goal was to consider the role of social media as a potentially viable intervention platform for offering support to persons with mental disorders, promoting engagement and retention in care, and enhancing existing mental health services, while balancing the need for safety. Given this broad objective, we did not perform a systematic search of the literature and we did not apply specific inclusion criteria based on study design or type of mental disorder.

Social Media Use and Mental Health

In 2020, there are an estimated 3.8 billion social media users worldwide, representing half the global population ( We Are Social, 2020 ). Recent studies have shown that individuals with mental disorders are increasingly gaining access to and using mobile devices, such as smartphones ( Firth et al., 2015 ; Glick, Druss, Pina, Lally, & Conde, 2016 ; Torous, Chan, et al., 2014 ; Torous, Friedman, & Keshavan, 2014 ). Similarly, there is mounting evidence showing high rates of social media use among individuals with mental disorders, including studies looking at engagement with these popular platforms across diverse settings and disorder types. Initial studies from 2015 found that nearly half of a sample of psychiatric patients were social media users, with greater use among younger individuals ( Trefflich, Kalckreuth, Mergl, & Rummel-Kluge, 2015 ), while 47% of inpatients and outpatients with schizophrenia reported using social media, of which 79% reported at least once-a-week usage of social media websites ( Miller, Stewart, Schrimsher, Peeples, & Buckley, 2015 ). Rates of social media use among psychiatric populations have increased in recent years, as reflected in a study with data from 2017 showing comparable rates of social media use (approximately 70%) among individuals with serious mental illness in treatment as compared to low-income groups from the general population ( Brunette et al., 2019 ).

Similarly, among individuals with serious mental illness receiving community-based mental health services, a recent study found equivalent rates of social media use as the general population, even exceeding 70% of participants ( Naslund, Aschbrenner, & Bartels, 2016 ). Comparable findings were demonstrated among middle-age and older individuals with mental illness accessing services at peer support agencies, where 72% of respondents reported using social media ( Aschbrenner, Naslund, Grinley, et al., 2018 ). Similar results, with 68% of those with first episode psychosis using social media daily were reported in another study ( Abdel-Baki, Lal, D.-Charron, Stip, & Kara, 2017 ).

Individuals who self-identified as having a schizophrenia spectrum disorder responded to a survey shared through the National Alliance of Mental Illness (NAMI), and reported that visiting social media sites was one of their most common activities when using digital devices, taking up roughly 2 hours each day ( Gay, Torous, Joseph, Pandya, & Duckworth, 2016 ). For adolescents and young adults ages 12 to 21 with psychotic disorders and mood disorders, over 97% reported using social media, with average use exceeding 2.5 hours per day ( M. L. Birnbaum et al., 2017 ). Similarly, in a sample of adolescents ages 13-18 recruited from community mental health centers, 98% reported using social media, with YouTube as the most popular platform, followed by Instagram and Snapchat ( Aschbrenner et al., 2019 ).

Research has also explored the motivations for using social media as well as the perceived benefits of interacting on these platforms among individuals with mental illness. In the sections that follow (see Table 1 for a summary), we consider three potentially unique features of interacting and connecting with others on social media that may offer benefits for individuals living with mental illness. These include: 1) Facilitate social interaction; 2) Access to a peer support network; and 3) Promote engagement and retention in services.

Summary of potential benefits and challenges with social media for mental health

Facilitate Social Interaction

Social media platforms offer near continuous opportunities to connect and interact with others, regardless of time of day or geographic location. This on demand ease of communication may be especially important for facilitating social interaction among individuals with mental disorders experiencing difficulties interacting in face-to-face settings. For example, impaired social functioning is a common deficit in schizophrenia spectrum disorders, and social media may facilitate communication and interacting with others for these individuals ( Torous & Keshavan, 2016 ). This was suggested in one study where participants with schizophrenia indicated that social media helped them to interact and socialize more easily ( Miller et al., 2015 ). Like other online communication, the ability to connect with others anonymously may be an important feature of social media, especially for individuals living with highly stigmatizing health conditions ( Berger, Wagner, & Baker, 2005 ), such as serious mental disorders ( Highton-Williamson, Priebe, & Giacco, 2015 ).

Studies have found that individuals with serious mental disorders ( Spinzy, Nitzan, Becker, Bloch, & Fennig, 2012 ) as well as young adults with mental illness ( Gowen, Deschaine, Gruttadara, & Markey, 2012 ) appear to form online relationships and connect with others on social media as often as social media users from the general population. This is an important observation because individuals living with serious mental disorders typically have few social contacts in the offline world, and also experience high rates of loneliness ( Badcock et al., 2015 ; Giacco, Palumbo, Strappelli, Catapano, & Priebe, 2016 ). Among individuals receiving publicly funded mental health services who use social media, nearly half (47%) reported using these platforms at least weekly to feel less alone ( Brusilovskiy, Townley, Snethen, & Salzer, 2016 ). In another study of young adults with serious mental illness, most indicated that they used social media to help feel less isolated ( Gowen et al., 2012 ). Interestingly, more frequent use of social media among a sample of individuals with serious mental illness was associated with greater community participation, measured as participation in shopping, work, religious activities or visiting friends and family, as well as greater civic engagement, reflected as voting in local elections ( Brusilovskiy et al., 2016 ).

Emerging research also shows that young people with moderate to severe depressive symptoms appear to prefer communicating on social media rather than in-person ( Rideout & Fox, 2018 ), while other studies have found that some individuals may prefer to seek help for mental health concerns online rather than through in-person encounters ( Batterham & Calear, 2017 ). In a qualitative study, participants with schizophrenia described greater anonymity, the ability to discover that other people have experienced similar health challenges, and reducing fears through greater access to information as important motivations for using the Internet to seek mental health information ( Schrank, Sibitz, Unger, & Amering, 2010 ). Because social media does not require the immediate responses necessary in face-to-face communication, it may overcome deficits with social interaction due to psychotic symptoms that typically adversely affect face-to-face conversations ( Docherty et al., 1996 ). Online social interactions may not require the use of non-verbal cues, particularly in the initial stages of interaction ( Kiesler, Siegel, & McGuire, 1984 ), with interactions being more fluid, and within the control of users, thereby overcoming possible social anxieties linked to in-person interaction ( Indian & Grieve, 2014 ). Furthermore, many individuals with serious mental disorders can experience symptoms including passive social withdrawal, blunted affect and attentional impairment, as well as active social avoidance due to hallucinations or other concerns ( Hansen, Torgalsbøen, Melle, & Bell, 2009 ); thus, potentially reinforcing the relative advantage, as perceived by users, of using social media over in person conversations.

Access to a Peer Support Network

There is growing recognition about the role that social media channels could play in enabling peer support ( Bucci et al., 2019 ; Naslund, Aschbrenner, et al., 2016b ), referred to as a system of mutual giving and receiving where individuals who have endured the difficulties of mental illness can offer hope, friendship, and support to others facing similar challenges ( Davidson, Chinman, Sells, & Rowe, 2006 ; Mead, Hilton, & Curtis, 2001 ). Initial studies exploring use of online self-help forums among individuals with serious mental illnesses have found that individuals with schizophrenia appeared to use these forums for self-disclosure, and sharing personal experiences, in addition to providing or requesting information, describing symptoms, or discussing medication ( Haker, Lauber, & Rössler, 2005 ), while users with bipolar disorder reported using these forums to ask for help from others about their illness ( Vayreda & Antaki, 2009 ). More recently, in a review of online social networking in people with psychosis, Highton-Williamson et al (2015) highlight that an important purpose of such online connections was to establish new friendships, pursue romantic relationships, maintain existing relationships or reconnect with people, and seek online peer support from others with lived experience ( Highton-Williamson et al., 2015 ).

Online peer support among individuals with mental illness has been further elaborated in various studies. In a content analysis of comments posted to YouTube by individuals who self-identified as having a serious mental illness, there appeared to be opportunities to feel less alone, provide hope, find support and learn through mutual reciprocity, and share coping strategies for day-to-day challenges of living with a mental illness ( Naslund, Grande, Aschbrenner, & Elwyn, 2014 ). In another study, Chang (2009) delineated various communication patterns in an online psychosis peer-support group ( Chang, 2009 ). Specifically, different forms of support emerged, including ‘informational support’ about medication use or contacting mental health providers, ‘esteem support’ involving positive comments for encouragement, ‘network support’ for sharing similar experiences, and ‘emotional support’ to express understanding of a peer’s situation and offer hope or confidence ( Chang, 2009 ). Bauer et al. (2013) reported that the main interest in online self-help forums for patients with bipolar disorder was to share emotions with others, allow exchange of information, and benefit by being part of an online social group ( Bauer, Bauer, Spiessl, & Kagerbauer, 2013 ).

For individuals who openly discuss mental health problems on Twitter, a study by Berry et al. (2017) found that this served as an important opportunity to seek support and to hear about the experiences of others ( Berry et al., 2017 ). In a survey of social media users with mental illness, respondents reported that sharing personal experiences about living with mental illness and opportunities to learn about strategies for coping with mental illness from others were important reasons for using social media ( Naslund et al., 2017 ). A computational study of mental health awareness campaigns on Twitter provides further support with inspirational posts and tips being the most shared ( Saha et al., 2019 ). Taken together, these studies offer insights about the potential for social media to facilitate access to an informal peer support network, though more research is necessary to examine how these online interactions may impact intentions to seek care, illness self-management, and clinically meaningful outcomes in offline contexts.

Promote Engagement and Retention in Services

Many individuals living with mental disorders have expressed interest in using social media platforms for seeking mental health information ( Lal, Nguyen, & Theriault, 2018 ), connecting with mental health providers ( M. L. Birnbaum et al., 2017 ), and accessing evidence-based mental health services delivered over social media specifically for coping with mental health symptoms or for promoting overall health and wellbeing ( Naslund et al., 2017 ). With the widespread use of social media among individuals living with mental illness combined with the potential to facilitate social interaction and connect with supportive peers, as summarized above, it may be possible to leverage the popular features of social media to enhance existing mental health programs and services. A recent review by Biagianti et al (2018) found that peer-to-peer support appeared to offer feasible and acceptable ways to augment digital mental health interventions for individuals with psychotic disorders by specifically improving engagement, compliance, and adherence to the interventions, and may also improve perceived social support ( Biagianti, Quraishi, & Schlosser, 2018 ).

Among digital programs that have incorporated peer-to-peer social networking consistent with popular features on social media platforms, a pilot study of the HORYZONS online psychosocial intervention demonstrated significant reductions in depression among patients with first episode psychosis ( Alvarez-Jimenez et al., 2013 ). Importantly, the majority of participants (95%) in this study engaged with the peer-to-peer networking feature of the program, with many reporting increases in perceived social connectedness and empowerment in their recovery process ( Alvarez-Jimenez et al., 2013 ). This moderated online social therapy program is now being evaluated as part of a large randomized controlled trial for maintaining treatment effects from first episode psychosis services ( Alvarez-Jimenez et al., 2019 ).

Other early efforts have demonstrated that use of digital environments with the interactive peer-to-peer features of social media can enhance social functioning and wellbeing in young people at high risk of psychosis ( Alvarez-Jimenez et al., 2018 ). There has also been a recent emergence of several mobile apps to support symptom monitoring and relapse prevention in psychotic disorders. Among these apps, the development of PRIME (Personalized Real-time Intervention for Motivational Enhancement) has involved working closely with young people with schizophrenia to ensure that the design of the app has the look and feel of mainstream social media platforms, as opposed to existing clinical tools ( Schlosser et al., 2016 ). This unique approach to the design of the app is aimed at promoting engagement, and ensuring that the app can effectively improve motivation and functioning through goal setting and promoting better quality of life of users with schizophrenia ( Schlosser et al., 2018 ).

Social media platforms could also be used to promote engagement and participation in in-person services delivered through community mental health settings. For example, the peer-based lifestyle intervention called PeerFIT targets weight loss and improved fitness among individuals living with serious mental illness through a combination of in-person lifestyle classes, exercise groups, and use of digital technologies ( Aschbrenner, Naslund, Shevenell, Kinney, & Bartels, 2016 ; Aschbrenner, Naslund, Shevenell, Mueser, & Bartels, 2016 ). The intervention holds tremendous promise as lack of support is one of the largest barriers toward exercise in patients with serious mental illness ( Firth et al., 2016 ) and it is now possible to use social media to counter such. Specifically, in PeerFIT, a private Facebook group is closely integrated into the program to offer a closed platform where participants can connect with the lifestyle coaches, access intervention content, and support or encourage each other as they work towards their lifestyle goals ( Aschbrenner, Naslund, & Bartels, 2016 ; Naslund, Aschbrenner, Marsch, & Bartels, 2016a ). To date, this program has demonstrate preliminary effectiveness for meaningfully reducing cardiovascular risk factors that contribute to early mortality in this patient group ( Aschbrenner, Naslund, Shevenell, Kinney, et al., 2016 ), while the Facebook component appears to have increased engagement in the program, while allowing participants who were unable to attend in-person sessions due to other health concerns or competing demands to remain connected with the program ( Naslund, Aschbrenner, Marsch, McHugo, & Bartels, 2018 ). This lifestyle intervention is currently being evaluated in a randomized controlled trial enrolling young adults with serious mental illness from a variety of real world community mental health services settings ( Aschbrenner, Naslund, Gorin, et al., 2018 ).

These examples highlight the promise of incorporating the features of popular social media into existing programs, which may offer opportunities to safely promote engagement and program retention, while achieving improved clinical outcomes. This is an emerging area of research, as evidenced by several important effectiveness trials underway ( Alvarez-Jimenez et al., 2019 ; Aschbrenner, Naslund, Gorin, et al., 2018 ), including efforts to leverage online social networking to support family caregivers of individuals receiving first episode psychosis services ( Gleeson et al., 2017 ).

Challenges with Social Media for Mental Health

The science on the role of social media for engaging persons with mental disorders needs a cautionary note on the effects of social media usage on mental health and well being, particularly in adolescents and young adults. While the risks and harms of social media are frequently covered in the popular press and mainstream news reports, careful consideration of the research in this area is necessary. In a review of 43 studies in young people, many benefits of social media were cited, including increased self-esteem, and opportunities for self-disclosure ( Best, Manktelow, & Taylor, 2014 ). Yet, reported negative effects were an increased exposure to harm, social isolation, depressive symptoms and bullying ( Best et al., 2014 ). In the sections that follow (see Table 1 for a summary), we consider three major categories of risk related to use of social media and mental health. These include: 1) Impact on symptoms; 2) Facing hostile interactions; and 3) Consequences for daily life.

Impact on Symptoms

Studies consistently highlight that use of social media, especially heavy use and prolonged time spent on social media platforms, appears to contribute to increased risk for a variety of mental health symptoms and poor wellbeing, especially among young people ( Andreassen et al., 2016 ; Kross et al., 2013 ; Woods & Scott, 2016 ). This may partly be driven by the detrimental effects of screen time on mental health, including increased severity of anxiety and depressive symptoms, which have been well documented ( Stiglic & Viner, 2019 ). Recent studies have reported negative effects of social media use on mental health of young people, including social comparison pressure with others and greater feeling of social isolation after being rejected by others on social media ( Rideout & Fox, 2018 ). In a study of young adults, it was found that negative comparisons with others on Facebook contributed to risk of rumination and subsequent increases in depression symptoms ( Feinstein et al., 2013 ). Still, the cross sectional nature of many screen time and mental health studies makes it challenging to reach causal inferences ( Orben & Przybylski, 2019 ).

Quantity of social media use is also an important factor, as highlighted in a survey of young adults ages 19 to 32, where more frequent visits to social media platforms each week were correlated with greater depressive symptoms ( Lin et al., 2016 ). More time spent using social media is also associated with greater symptoms of anxiety ( Vannucci, Flannery, & Ohannessian, 2017 ). The actual number of platforms accessed also appears to contribute to risk as reflected in another national survey of young adults where use of a large number of social media platforms was associated with negative impact on mental health ( Primack et al., 2017 ). Among survey respondents using between 7 and 11 different social media platforms compared to respondents using only 2 or fewer platforms, there was a 3 times greater odds of having high levels of depressive symptoms and a 3.2 times greater odds of having high levels of anxiety symptoms ( Primack et al., 2017 ).

Many researchers have postulated that worsening mental health attributed to social media use may be because social media replaces face-to-face interactions for young people ( Twenge & Campbell, 2018 ), and may contribute to greater loneliness ( Bucci et al., 2019 ), and negative effects on other aspects of health and wellbeing ( Woods & Scott, 2016 ). One nationally representative survey of US adolescents found that among respondents who reported more time accessing media such as social media platforms or smartphone devices, there was significantly greater depressive symptoms and increased risk of suicide when compared to adolescents who reported spending more time on non-screen activities, such as in-person social interaction or sports and recreation activities ( Twenge, Joiner, Rogers, & Martin, 2018 ). For individuals living with more severe mental illnesses, the effects of social media on psychiatric symptoms have received less attention. One study found that participation in chat rooms may contribute to worsening symptoms in young people with psychotic disorders ( Mittal, Tessner, & Walker, 2007 ), while another study of patients with psychosis found that social media use appeared to predict low mood ( Berry, Emsley, Lobban, & Bucci, 2018 ). These studies highlight a clear relationship between social media use and mental health that may not be present in general population studies ( Orben & Przybylski, 2019 ), and emphasize the need to explore how social media may contribute to symptom severity and whether protective factors may be identified to mitigate these risks.

Facing Hostile Interactions

Popular social media platforms can create potential situations where individuals may be victimized by negative comments or posts. Cyberbullying represents a form of online aggression directed towards specific individuals, such as peers or acquaintances, which is perceived to be most harmful when compared to random hostile comments posted online ( Hamm et al., 2015 ). Importantly, cyberbullying on social media consistently shows harmful impact on mental health in the form of increased depressive symptoms as well as worsening of anxiety symptoms, as evidenced in a review of 36 studies among children and young people ( Hamm et al., 2015 ). Furthermore, cyberbullying disproportionately impacts females as reflected in a national survey of adolescents in the United States, where females were twice as likely to be victims of cyberbullying compared to males ( Alhajji, Bass, & Dai, 2019 ). Most studies report cross-sectional associations between cyberbullying and symptoms of depression or anxiety ( Hamm et al., 2015 ), though one longitudinal study in Switzerland found that cyberbullying contributed to significantly greater depression over time ( Machmutow, Perren, Sticca, & Alsaker, 2012 ).

For youth ages 10 to 17 who reported major depressive symptomatology, there was over 3 times greater odds of facing online harassment in the last year compared to youth who reported mild or no depressive symptoms ( Ybarra, 2004 ). Similarly, in a 2018 national survey of young people, respondents ages 14 to 22 with moderate to severe depressive symptoms were more likely to have had negative experiences when using social media, and in particular, were more likely to report having faced hostile comments, or being “trolled”, from others when compared to respondents without depressive symptoms (31% vs. 14%) ( Rideout & Fox, 2018 ). As these studies depict risks for victimization on social media and the correlation with poor mental health, it is possible that individuals living with mental illness may also experience greater hostility online compared to individuals without mental illness. This would be consistent with research showing greater risk of hostility, including increased violence and discrimination, directed towards individuals living with mental illness in in-person contexts, especially targeted at those with severe mental illnesses ( Goodman et al., 1999 ).

A computational study of mental health awareness campaigns on Twitter reported that while stigmatizing content was rare, it was actually the most spread (re-tweeted) demonstrating that harmful content can travel quickly on social media ( Saha et al., 2019 ). Another study was able to map the spread of social media posts about the Blue Whale Challenge, an alleged game promoting suicide, over Twitter, YouTube, Reddit, Tumblr and other forums across 127 countries ( Sumner et al., 2019 ). These findings show that it is critical to monitor the actual content of social media posts, such as determining whether content is hostile or promotes harm to self or others. This is pertinent because existing research looking at duration of exposure cannot account for the impact of specific types of content on mental health and is insufficient to fully understand the effects of using these platforms on mental health.

Consequences for Daily Life

The ways in which individuals use social media can also impact their offline relationships and everyday activities. To date, reports have described risks of social media use pertaining to privacy, confidentiality, and unintended consequences of disclosing personal health information online ( Torous & Keshavan, 2016 ). Additionally, concerns have been raised about poor quality or misleading health information shared on social media, and that social media users may not be aware of misleading information or conflicts of interest especially when the platforms promote popular content regardless of whether it is from a trustworthy source ( Moorhead et al., 2013 ; Ventola, 2014 ). For persons living with mental illness there may be additional risks from using social media. A recent study that specifically explored the perspectives of social media users with serious mental illnesses, including participants with schizophrenia spectrum disorders, bipolar disorder, or major depression, found that over one third of participants expressed concerns about privacy when using social media ( Naslund & Aschbrenner, 2019 ). The reported risks of social media use were directly related to many aspects of everyday life, including concerns about threats to employment, fear of stigma and being judged, impact on personal relationships, and facing hostility or being hurt ( Naslund & Aschbrenner, 2019 ). While few studies have specifically explored the dangers of social media use from the perspectives of individuals living with mental illness, it is important to recognize that use of these platforms may contribute to risks that extend beyond worsening symptoms and that can affect different aspects of daily life.

In this commentary we considered ways in which social media may yield benefits for individuals living with mental illness, while contrasting these with the possible harms. Studies reporting on the threats of social media for individuals with mental illness are mostly cross-sectional, making it difficult to draw conclusions about direction of causation. However, the risks are potentially serious. These risks should be carefully considered in discussions pertaining to use of social media and the broader use of digital mental health technologies, as avenues for mental health promotion, or for supporting access to evidence-based programs or mental health services. At this point, it would be premature to view the benefits of social media as outweighing the possible harms, when it is clear from the studies summarized here that social media use can have negative effects on mental health symptoms, can potentially expose individuals to hurtful content and hostile interactions, and can result in serious consequences for daily life, including threats to employment and personal relationships. Despite these risks, it is also necessary to recognize that individuals with mental illness will continue to use social media given the ease of accessing these platforms and the immense popularity of online social networking. With this in mind, it may be ideal to raise awareness about these possible risks so that individuals can implement necessary safeguards, while also highlighting that there could also be benefits. For individuals with mental illness who use social media, being aware of the risks is an essential first step, and then highlighting ways that use of these popular platforms could also contribute to some benefits, ranging from finding meaningful interactions with others, engaging with peer support networks, and accessing information and services.

To capitalize on the widespread use of social media, and to achieve the promise that these platforms may hold for supporting the delivery of targeted mental health interventions, there is need for continued research to better understand how individuals living with mental illness use social media. Such efforts could inform safety measures and also encourage use of social media in ways that maximize potential benefits while minimizing risk of harm. It will be important to recognize how gender and race contribute to differences in use of social media for seeking mental health information or accessing interventions, as well as differences in how social media might impact mental wellbeing. For example, a national survey of 14- to 22-year olds in the United States found that female respondents were more likely to search online for information about depression or anxiety, and to try to connect with other people online who share similar mental health concerns, when compared to male respondents ( Rideout & Fox, 2018 ). In the same survey, there did not appear to be any differences between racial or ethnic groups in social media use for seeking mental health information ( Rideout & Fox, 2018 ). Social media use also appears to have a differential impact on mental health and emotional wellbeing between females and males ( Booker, Kelly, & Sacker, 2018 ), highlighting the need to explore unique experiences between gender groups to inform tailored programs and services. Research shows that lesbian, gay, bisexual or transgender individuals frequently use social media for searching for health information and may be more likely compared to heterosexual individuals to share their own personal health experiences with others online ( Rideout & Fox, 2018 ). Less is known about use of social media for seeking support for mental health concerns among gender minorities, though this is an important area for further investigation as these individuals are more likely to experience mental health problems and more likely to experience online victimization when compared to heterosexual individuals ( Mereish, Sheskier, Hawthorne, & Goldbach, 2019 ).

Similarly, efforts are needed to explore the relationship between social media use and mental health among ethnic and racial minorities. A recent study found that exposure to traumatic online content on social media showing violence or hateful posts directed at racial minorities contributed to increases in psychological distress, PTSD symptoms, and depression among African American and Latinx adolescents in the United States ( Tynes, Willis, Stewart, & Hamilton, 2019 ). These concerns are contrasted by growing interest in the potential for new technologies including social media to expand the reach of services to underrepresented minority groups ( Schueller, Hunter, Figueroa, & Aguilera, 2019 ). Therefore, greater attention is needed to understanding the perspectives of ethnic and racial minorities to inform effective and safe use of social media for mental health promotion efforts.

Research has found that individuals living with mental illness have expressed interest in accessing mental health services through social media platforms. A survey of social media users with mental illness found that most respondents were interested in accessing programs for mental health on social media targeting symptom management, health promotion, and support for communicating with health care providers and interacting with the health system ( Naslund et al., 2017 ). Importantly, individuals with serious mental illness have also emphasized that any mental health intervention on social media would need to be moderated by someone with adequate training and credentials, would need to have ground rules and ways to promote safety and minimize risks, and importantly, would need to be free and easy to access.

An important strength with this commentary is that it combines a range of studies broadly covering the topic of social media and mental health. We have provided a summary of recent evidence in a rapidly advancing field with the goal of presenting unique ways that social media could offer benefits for individuals with mental illness, while also acknowledging the potentially serious risks and the need for further investigation. There are also several limitations with this commentary that warrant consideration. Importantly, as we aimed to address this broad objective, we did not conduct a systematic review of the literature. Therefore, the studies reported here are not exhaustive, and there may be additional relevant studies that were not included. Additionally, we only summarized published studies, and as a result, any reports from the private sector or websites from different organizations using social media or other apps containing social media-like features would have been omitted. Though it is difficult to rigorously summarize work from the private sector, sometimes referred to as “gray literature”, because many of these projects are unpublished and are likely selective in their reporting of findings given the target audience may be shareholders or consumers.

Another notable limitation is that we did not assess risk of bias in the studies summarized in this commentary. We found many studies that highlighted risks associated with social media use for individuals living with mental illness; however, few studies of programs or interventions reported negative findings, suggesting the possibility that negative findings may go unpublished. This concern highlights the need for a future more rigorous review of the literature with careful consideration of bias and an accompanying quality assessment. Most of the studies that we described were from the United States, as well as from other higher income settings such as Australia or the United Kingdom. Despite the global reach of social media platforms, there is a dearth of research on the impact of these platforms on the mental health of individuals in diverse settings, as well as the ways in which social media could support mental health services in lower income countries where there is virtually no access to mental health providers. Future research is necessary to explore the opportunities and risks for social media to support mental health promotion in low-income and middle-income countries, especially as these countries face a disproportionate share of the global burden of mental disorders, yet account for the majority of social media users worldwide ( Naslund et al., 2019 ).

Future Directions for Social Media and Mental Health

As we consider future research directions, the near ubiquitous social media use also yields new opportunities to study the onset and manifestation of mental health symptoms and illness severity earlier than traditional clinical assessments. There is an emerging field of research referred to as ‘digital phenotyping’ aimed at capturing how individuals interact with their digital devices, including social media platforms, in order to study patterns of illness and identify optimal time points for intervention ( Jain, Powers, Hawkins, & Brownstein, 2015 ; Onnela & Rauch, 2016 ). Given that most people access social media via mobile devices, digital phenotyping and social media are closely related ( Torous et al., 2019 ). To date, the emergence of machine learning, a powerful computational method involving statistical and mathematical algorithms ( Shatte, Hutchinson, & Teague, 2019 ), has made it possible to study large quantities of data captured from popular social media platforms such as Twitter or Instagram to illuminate various features of mental health ( Manikonda & De Choudhury, 2017 ; Reece et al., 2017 ). Specifically, conversations on Twitter have been analyzed to characterize the onset of depression ( De Choudhury, Gamon, Counts, & Horvitz, 2013 ) as well as detecting users’ mood and affective states ( De Choudhury, Gamon, & Counts, 2012 ), while photos posted to Instagram can yield insights for predicting depression ( Reece & Danforth, 2017 ). The intersection of social media and digital phenotyping will likely add new levels of context to social media use in the near future.

Several studies have also demonstrated that when compared to a control group, Twitter users with a self-disclosed diagnosis of schizophrenia show unique online communication patterns ( Michael L Birnbaum, Ernala, Rizvi, De Choudhury, & Kane, 2017 ), including more frequent discussion of tobacco use ( Hswen et al., 2017 ), symptoms of depression and anxiety ( Hswen, Naslund, Brownstein, & Hawkins, 2018b ), and suicide ( Hswen, Naslund, Brownstein, & Hawkins, 2018a ). Another study found that online disclosures about mental illness appeared beneficial as reflected by fewer posts about symptoms following self-disclosure (Ernala, Rizvi, Birnbaum, Kane, & De Choudhury, 2017). Each of these examples offers early insights into the potential to leverage widely available online data for better understanding the onset and course of mental illness. It is possible that social media data could be used to supplement additional digital data, such as continuous monitoring using smartphone apps or smart watches, to generate a more comprehensive ‘digital phenotype’ to predict relapse and identify high-risk health behaviors among individuals living with mental illness ( Torous et al., 2019 ).

With research increasingly showing the valuable insights that social media data can yield about mental health states, greater attention to the ethical concerns with using individual data in this way is necessary ( Chancellor, Birnbaum, Caine, Silenzio, & De Choudhury, 2019 ). For instance, data is typically captured from social media platforms without the consent or awareness of users ( Bidargaddi et al., 2017 ), which is especially crucial when the data relates to a socially stigmatizing health condition such as mental illness ( Guntuku, Yaden, Kern, Ungar, & Eichstaedt, 2017 ). Precautions are needed to ensure that data is not made identifiable in ways that were not originally intended by the user who posted the content, as this could place an individual at risk of harm or divulge sensitive health information ( Webb et al., 2017 ; Williams, Burnap, & Sloan, 2017 ). Promising approaches for minimizing these risks include supporting the participation of individuals with expertise in privacy, clinicians, as well as the target individuals with mental illness throughout the collection of data, development of predictive algorithms, and interpretation of findings ( Chancellor et al., 2019 ).

In recognizing that many individuals living with mental illness use social media to search for information about their mental health, it is possible that they may also want to ask their clinicians about what they find online to check if the information is reliable and trustworthy. Alternatively, many individuals may feel embarrassed or reluctant to talk to their clinicians about using social media to find mental health information out of concerns of being judged or dismissed. Therefore, mental health clinicians may be ideally positioned to talk with their patients about using social media, and offer recommendations to promote safe use of these sites, while also respecting their patients’ autonomy and personal motivations for using these popular platforms. Given the gap in clinical knowledge about the impact of social media on mental health, clinicians should be aware of the many potential risks so that they can inform their patients, while remaining open to the possibility that their patients may also experience benefits through use of these platforms. As awareness of these risks grows, it may be possible that new protections will be put in place by industry or through new policies that will make the social media environment safer. It is hard to estimate a number needed to treat or harm today given the nascent state of research, which means the patient and clinician need to weigh the choice on a personal level. Thus offering education and information is an important first step in that process. As patients increasingly show interest in accessing mental health information or services through social media, it will be necessary for health systems to recognize social media as a potential avenue for reaching or offering support to patients. This aligns with growing emphasis on the need for greater integration of digital psychiatry, including apps, smartphones, or wearable devices, into patient care and clinical services through institution-wide initiatives and training clinical providers ( Hilty, Chan, Torous, Luo, & Boland, 2019 ). Within a learning healthcare environment where research and care are tightly intertwined and feedback between both is rapid, the integration of digital technologies into services may create new opportunities for advancing use of social media for mental health.

As highlighted in this commentary, social media has become an important part of the lives of many individuals living with mental disorders. Many of these individuals use social media to share their lived experiences with mental illness, to seek support from others, and to search for information about treatment recommendations, accessing mental health services, and coping with symptoms ( Bucci et al., 2019 ; Highton-Williamson et al., 2015 ; Naslund, Aschbrenner, et al., 2016b ). As the field of digital mental health advances, the wide reach, ease of access, and popularity of social media platforms could be used to allow individuals in need of mental health services or facing challenges of mental illness to access evidence-based treatment and support. To achieve this end and to explore whether social media platforms can advance efforts to close the gap in available mental health services in the United States and globally, it will be essential for researchers to work closely with clinicians and with those affected by mental illness to ensure that possible benefits of using social media are carefully weighed against anticipated risks.

Acknowledgements

Dr. Naslund is supported by a grant from the National Institute of Mental Health (U19MH113211). Dr. Aschbrenner is supported by a grant from the National Institute of Mental Health (1R01MH110965-01).

Publisher's Disclaimer: This Author Accepted Manuscript is a PDF file of a an unedited peer-reviewed manuscript that has been accepted for publication but has not been copyedited or corrected. The official version of record that is published in the journal is kept up to date and so may therefore differ from this version.

Conflict of Interest

The authors have nothing to disclose.

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Generative AI Can Harm Learning

59 Pages Posted: 18 Jul 2024

Hamsa Bastani

University of Pennsylvania - The Wharton School

Osbert Bastani

University of Pennsylvania - Department of Computer and Information Science

Özge Kabakcı

International Business School - Budapest (IBS)

Rei Mariman

Independent; Independent

Date Written: July 15, 2024

Generative artificial intelligence (AI) is poised to revolutionize how humans work, and has already demonstrated promise in significantly improving human productivity. However, a key remaining question is how generative AI affects learning , namely, how humans acquire new skills as they perform tasks. This kind of skill learning is critical to long-term productivity gains, especially in domains where generative AI is fallible and human experts must check its outputs. We study the impact of generative AI, specifically OpenAI's GPT-4, on human learning in the context of math classes at a high school. In a field experiment involving nearly a thousand students, we have deployed and evaluated two GPT based tutors, one that mimics a standard ChatGPT interface (called GPT Base) and one with prompts designed to safeguard learning (called GPT Tutor). These tutors comprise about 15% of the curriculum in each of three grades. Consistent with prior work, our results show that access to GPT-4 significantly improves performance (48% improvement for GPT Base and 127% for GPT Tutor). However, we additionally find that when access is subsequently taken away, students actually perform worse than those who never had access (17% reduction for GPT Base). That is, access to GPT-4 can harm educational outcomes. These negative learning effects are largely mitigated by the safeguards included in GPT Tutor. Our results suggest that students attempt to use GPT-4 as a "crutch" during practice problem sessions, and when successful, perform worse on their own. Thus, to maintain long-term productivity, we must be cautious when deploying generative AI to ensure humans continue to learn critical skills. * HB, OB, and AS contributed equally

Keywords: Generative AI, Human Capital Development, Education, Human-AI Collaboration, Large Language Models

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Sodhi M , Rezaeianzadeh R , Kezouh A , Etminan M. Risk of Gastrointestinal Adverse Events Associated With Glucagon-Like Peptide-1 Receptor Agonists for Weight Loss. JAMA. 2023;330(18):1795–1797. doi:10.1001/jama.2023.19574

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Risk of Gastrointestinal Adverse Events Associated With Glucagon-Like Peptide-1 Receptor Agonists for Weight Loss

• 1 Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
• 2 StatExpert Ltd, Laval, Quebec, Canada
• 3 Department of Ophthalmology and Visual Sciences and Medicine, University of British Columbia, Vancouver, Canada
• Medical News & Perspectives As Ozempic’s Popularity Soars, Here’s What to Know About Semaglutide and Weight Loss Melissa Suran, PhD, MSJ JAMA
• Special Communication Patents and Regulatory Exclusivities on GLP-1 Receptor Agonists Rasha Alhiary, PharmD; Aaron S. Kesselheim, MD, JD, MPH; Sarah Gabriele, LLM, MBE; Reed F. Beall, PhD; S. Sean Tu, JD, PhD; William B. Feldman, MD, DPhil, MPH JAMA
• Medical News & Perspectives What to Know About Wegovy’s Rare but Serious Adverse Effects Kate Ruder, MSJ JAMA
• Comment & Response GLP-1 Receptor Agonists and Gastrointestinal Adverse Events—Reply Ramin Rezaeianzadeh, BSc; Mohit Sodhi, MSc; Mahyar Etminan, PharmD, MSc JAMA
• Comment & Response GLP-1 Receptor Agonists and Gastrointestinal Adverse Events Karine Suissa, PhD; Sara J. Cromer, MD; Elisabetta Patorno, MD, DrPH JAMA
• Research Letter GLP-1 Receptor Agonist Use and Risk of Postoperative Complications Anjali A. Dixit, MD, MPH; Brian T. Bateman, MD, MS; Mary T. Hawn, MD, MPH; Michelle C. Odden, PhD; Eric C. Sun, MD, PhD JAMA
• Original Investigation Glucagon-Like Peptide-1 Receptor Agonist Use and Risk of Gallbladder and Biliary Diseases Liyun He, MM; Jialu Wang, MM; Fan Ping, MD; Na Yang, MM; Jingyue Huang, MM; Yuxiu Li, MD; Lingling Xu, MD; Wei Li, MD; Huabing Zhang, MD JAMA Internal Medicine
• Research Letter Cholecystitis Associated With the Use of Glucagon-Like Peptide-1 Receptor Agonists Daniel Woronow, MD; Christine Chamberlain, PharmD; Ali Niak, MD; Mark Avigan, MDCM; Monika Houstoun, PharmD, MPH; Cindy Kortepeter, PharmD JAMA Internal Medicine

Glucagon-like peptide 1 (GLP-1) agonists are medications approved for treatment of diabetes that recently have also been used off label for weight loss. 1 Studies have found increased risks of gastrointestinal adverse events (biliary disease, 2 pancreatitis, 3 bowel obstruction, 4 and gastroparesis 5 ) in patients with diabetes. 2 - 5 Because such patients have higher baseline risk for gastrointestinal adverse events, risk in patients taking these drugs for other indications may differ. Randomized trials examining efficacy of GLP-1 agonists for weight loss were not designed to capture these events 2 due to small sample sizes and short follow-up. We examined gastrointestinal adverse events associated with GLP-1 agonists used for weight loss in a clinical setting.

We used a random sample of 16 million patients (2006-2020) from the PharMetrics Plus for Academics database (IQVIA), a large health claims database that captures 93% of all outpatient prescriptions and physician diagnoses in the US through the International Classification of Diseases, Ninth Revision (ICD-9) or ICD-10. In our cohort study, we included new users of semaglutide or liraglutide, 2 main GLP-1 agonists, and the active comparator bupropion-naltrexone, a weight loss agent unrelated to GLP-1 agonists. Because semaglutide was marketed for weight loss after the study period (2021), we ensured all GLP-1 agonist and bupropion-naltrexone users had an obesity code in the 90 days prior or up to 30 days after cohort entry, excluding those with a diabetes or antidiabetic drug code.

Patients were observed from first prescription of a study drug to first mutually exclusive incidence (defined as first ICD-9 or ICD-10 code) of biliary disease (including cholecystitis, cholelithiasis, and choledocholithiasis), pancreatitis (including gallstone pancreatitis), bowel obstruction, or gastroparesis (defined as use of a code or a promotility agent). They were followed up to the end of the study period (June 2020) or censored during a switch. Hazard ratios (HRs) from a Cox model were adjusted for age, sex, alcohol use, smoking, hyperlipidemia, abdominal surgery in the previous 30 days, and geographic location, which were identified as common cause variables or risk factors. 6 Two sensitivity analyses were undertaken, one excluding hyperlipidemia (because more semaglutide users had hyperlipidemia) and another including patients without diabetes regardless of having an obesity code. Due to absence of data on body mass index (BMI), the E-value was used to examine how strong unmeasured confounding would need to be to negate observed results, with E-value HRs of at least 2 indicating BMI is unlikely to change study results. Statistical significance was defined as 2-sided 95% CI that did not cross 1. Analyses were performed using SAS version 9.4. Ethics approval was obtained by the University of British Columbia’s clinical research ethics board with a waiver of informed consent.

Our cohort included 4144 liraglutide, 613 semaglutide, and 654 bupropion-naltrexone users. Incidence rates for the 4 outcomes were elevated among GLP-1 agonists compared with bupropion-naltrexone users ( Table 1 ). For example, incidence of biliary disease (per 1000 person-years) was 11.7 for semaglutide, 18.6 for liraglutide, and 12.6 for bupropion-naltrexone and 4.6, 7.9, and 1.0, respectively, for pancreatitis.

Use of GLP-1 agonists compared with bupropion-naltrexone was associated with increased risk of pancreatitis (adjusted HR, 9.09 [95% CI, 1.25-66.00]), bowel obstruction (HR, 4.22 [95% CI, 1.02-17.40]), and gastroparesis (HR, 3.67 [95% CI, 1.15-11.90) but not biliary disease (HR, 1.50 [95% CI, 0.89-2.53]). Exclusion of hyperlipidemia from the analysis did not change the results ( Table 2 ). Inclusion of GLP-1 agonists regardless of history of obesity reduced HRs and narrowed CIs but did not change the significance of the results ( Table 2 ). E-value HRs did not suggest potential confounding by BMI.

This study found that use of GLP-1 agonists for weight loss compared with use of bupropion-naltrexone was associated with increased risk of pancreatitis, gastroparesis, and bowel obstruction but not biliary disease.

Given the wide use of these drugs, these adverse events, although rare, must be considered by patients who are contemplating using the drugs for weight loss because the risk-benefit calculus for this group might differ from that of those who use them for diabetes. Limitations include that although all GLP-1 agonist users had a record for obesity without diabetes, whether GLP-1 agonists were all used for weight loss is uncertain.

Accepted for Publication: September 11, 2023.

Published Online: October 5, 2023. doi:10.1001/jama.2023.19574

Correction: This article was corrected on December 21, 2023, to update the full name of the database used.

Corresponding Author: Mahyar Etminan, PharmD, MSc, Faculty of Medicine, Departments of Ophthalmology and Visual Sciences and Medicine, The Eye Care Center, University of British Columbia, 2550 Willow St, Room 323, Vancouver, BC V5Z 3N9, Canada ( [email protected] ).

Author Contributions: Dr Etminan had full access to all of the data in the study and takes responsibility for the integrity of the data and the accuracy of the data analysis.

Concept and design: Sodhi, Rezaeianzadeh, Etminan.

Acquisition, analysis, or interpretation of data: All authors.

Drafting of the manuscript: Sodhi, Rezaeianzadeh, Etminan.

Critical review of the manuscript for important intellectual content: All authors.

Statistical analysis: Kezouh.

Obtained funding: Etminan.

Administrative, technical, or material support: Sodhi.

Supervision: Etminan.

Conflict of Interest Disclosures: None reported.

Funding/Support: This study was funded by internal research funds from the Department of Ophthalmology and Visual Sciences, University of British Columbia.

Role of the Funder/Sponsor: The funder had no role in the design and conduct of the study; collection, management, analysis, and interpretation of the data; preparation, review, or approval of the manuscript; and decision to submit the manuscript for publication.

Data Sharing Statement: See Supplement .

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July 18, 2024

The Trump Assassination Attempt Caused Psychological Distress and Fueled Polarization

Political violence has a different effect on people today than it did in the past because of social media and extreme partisanship

By Tanya Lewis

The attempted assassination of former president Donald Trump during a Pennsylvania campaign rally may have produced a kind of collective trauma, as people attempted to make sense of the event through real-time media coverage and online images.

Jabin Botsford/The Washington Post via Getty Images

The attempted assassination of former president Donald Trump was a massive shock that has jarred society, regardless of where one falls on the political spectrum. The shooting at Trump’s Pennsylvania campaign rally appeared to have nicked the candidate’s ear and bloodied his face, killed one bystander and critically wounded two others. And it came amid profound and increasingly dangerous social divisions in the country. Experts have found that dramatic instances of political violence can have distressing psychological effects, not only on those who witness them in person but also on the millions of people exposed to such events through online images, videos and social media.

From the assassination of then president John F. Kennedy to the shooting of then U.S. representative Gabrielle Giffords of Arizona, violence toward a political leader or public figure often triggers not just an initial sense of shock but also a need to make sense of what has happened—and what it says about the society each us is part of. Yet unlike when these earlier tragedies occurred, people had to process graphic images and nonstop media coverage of the Trump shooting in close to real time.

“What’s different here, of course, is the growth of social media—the fact that we can see pictures and videos of the shooting or the shooting’s aftermath or former president Trump with blood streaming down his face instantaneously,”says Roxane Cohen Silver, a professor of psychological science, medicine and public health at the University of California, Irvine. Exposure to these images and the news coverage surrounding them can lead to a form of collective trauma , she says.

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Silver’s research focuses on how people cope with traumatic events, such as the September 11 attacks and the Boston Marathon bombings . When 9/11 happened, most people got their news from television coverage. Today many people get their news online, often via a smartphone they carry with them all the time. “The speed with which we can access graphic images, the speed in which we can transmit graphic images, the overwhelming number of images that can be distributed rapidly without context [are] unprecedented,”Silver says.

Her research on the Boston Marathon bombings found that exposure to bloody, graphic images had a serious effect on people’s psychological functioning. One study that she and her colleagues published found that being exposed to six or more daily hours of media related to the bombings in the week afterward was linked to higher levels of acute stress than direct, in-person exposure to the attacks themselves. While perhaps not quite as graphic, the images and video of the recent Trump shooting showed blood dripping down the side of a former president’s face, and there were videos of the shooter’s body on the roof of a nearby building after he was killed by the Secret Service.

Another key difference from some previous violent events is that the Trump shooting took place in an environment of extreme political polarization—which led individuals to interpret the same event very differently. While some people reacted to the attempted assassination with outrage or distress, others did so with apathy or sarcasm, even making jokes about how the bullet had missed its mark.

And this polarization itself can be severely stressful. Silver and her colleagues have been conducting a study of several thousand people they have been following since the early days of the COVID pandemic. The study has since focused on other events, such as mass shootings, climate disasters and the police murder of George Floyd . Some of the data are still under review for publication, but “we found that political polarization was... one of the most stressful experiences that people reported,” Silver says. Although she doesn’t yet have data on how the Trump shooting affected people’s views, her team plans to collect more survey information before the November 5 presidential election.

Silver also highlights the potential for misinformation and disinformation after events like the attempted Trump assassination. Indeed, conspiracy theories about the shooting arose immediately afterward at both ends of the political spectrum. At times like these, she says, it’s crucial to verify that information is coming from a reputable source.

When we experience a collective trauma like this, “we need to take a step back,” says Robin Gurwitch, a psychologist and a professor at Duke University Medical Center, who works with people who have been exposed to traumatic events such as mass shootings. “When these events happen, one of the things we have to do is take a breath and consider, ‘What do I really know, and how does this fit into my understanding of the world around me?’” Gurwitch says.

Not everyone reacts the same. “You may have some people who use this as a sign that we need to take a step back. We need to consider our actions and our words, how we treat each other and how we talk about each other,” Gurwitch says. “Others’ first response may be wanting to double down and come out louder and stronger.” But she cautions against meeting violence with violence. “Before taking any action, we should decide ‘what is our overall goal, and what will be the most productive and effective way to accomplish this goal?’” she says.

After these kinds of events, experts recommend that people limit their media consumption as needed to protect their mental health. “ We do advocate that people monitor their media exposure to graphic images,” Silver says. “There’s likely to be no psychological benefit to seeing graphic images over and over again.” Journalists, in particular, are often exposed to traumatic images or topics through their reporting, and there are resources to help cope with that.

It’s also important for parents to talk to their children about what has happened, Gurwitch says. “First and foremost, you need to make sure, as the adult, that you’ve thought through your emotions, thoughts, ideas, beliefs and values. What’s the message you want to communicate?” she says. If you seem stressed or scared, she adds, your children are going to pick up on that, so you want to be open about discussing it.“When these kinds of events happen, this is also an opportunity for us to communicate to our children: ‘How do we think about it? What are our values about handling disagreements?’” Gurwitch says. It’s not necessary to expose your children to gruesome details, she says, but you should explain the news in a manner that’s appropriate for their age and level of understanding. The National Child Traumatic Stress Network is one organization that offers resources to help parents talk to their children about mass violence.

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• Published: 12 July 2024

The nature of the last universal common ancestor and its impact on the early Earth system

• Edmund R. R. Moody   ORCID: orcid.org/0000-0002-8785-5006 1 ,
• Sandra Álvarez-Carretero   ORCID: orcid.org/0000-0002-9508-6286 1 ,
• Tara A. Mahendrarajah   ORCID: orcid.org/0000-0001-7032-6581 2 ,
• James W. Clark 3 ,
• Holly C. Betts 1 ,
• Nina Dombrowski   ORCID: orcid.org/0000-0003-1917-2577 2 ,
• Lénárd L. Szánthó   ORCID: orcid.org/0000-0003-3363-2488 4 , 5 , 6 ,
• Richard A. Boyle 7 ,
• Stuart Daines 7 ,
• Xi Chen   ORCID: orcid.org/0000-0001-7098-607X 8 ,
• Nick Lane   ORCID: orcid.org/0000-0002-5433-3973 9 ,
• Ziheng Yang   ORCID: orcid.org/0000-0003-3351-7981 9 ,
• Graham A. Shields   ORCID: orcid.org/0000-0002-7828-3966 8 ,
• Gergely J. Szöllősi 5 , 6 , 10 ,
• Anja Spang   ORCID: orcid.org/0000-0002-6518-8556 2 , 11 ,
• Davide Pisani   ORCID: orcid.org/0000-0003-0949-6682 1 , 12 ,
• Tom A. Williams   ORCID: orcid.org/0000-0003-1072-0223 12 ,
• Timothy M. Lenton   ORCID: orcid.org/0000-0002-6725-7498 7 &
• Philip C. J. Donoghue   ORCID: orcid.org/0000-0003-3116-7463 1  

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• Microbial genetics
• Molecular evolution
• Phylogenetics

The nature of the last universal common ancestor (LUCA), its age and its impact on the Earth system have been the subject of vigorous debate across diverse disciplines, often based on disparate data and methods. Age estimates for LUCA are usually based on the fossil record, varying with every reinterpretation. The nature of LUCA’s metabolism has proven equally contentious, with some attributing all core metabolisms to LUCA, whereas others reconstruct a simpler life form dependent on geochemistry. Here we infer that LUCA lived ~4.2 Ga (4.09–4.33 Ga) through divergence time analysis of pre-LUCA gene duplicates, calibrated using microbial fossils and isotope records under a new cross-bracing implementation. Phylogenetic reconciliation suggests that LUCA had a genome of at least 2.5 Mb (2.49–2.99 Mb), encoding around 2,600 proteins, comparable to modern prokaryotes. Our results suggest LUCA was a prokaryote-grade anaerobic acetogen that possessed an early immune system. Although LUCA is sometimes perceived as living in isolation, we infer LUCA to have been part of an established ecological system. The metabolism of LUCA would have provided a niche for other microbial community members and hydrogen recycling by atmospheric photochemistry could have supported a modestly productive early ecosystem.

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The common ancestry of all extant cellular life is evidenced by the universal genetic code, machinery for protein synthesis, shared chirality of the almost-universal set of 20 amino acids and use of ATP as a common energy currency 1 . The last universal common ancestor (LUCA) is the node on the tree of life from which the fundamental prokaryotic domains (Archaea and Bacteria) diverge. As such, our understanding of LUCA impacts our understanding of the early evolution of life on Earth. Was LUCA a simple or complex organism? What kind of environment did it inhabit and when? Previous estimates of LUCA are in conflict either due to conceptual disagreement about what LUCA is 2 or as a result of different methodological approaches and data 3 , 4 , 5 , 6 , 7 , 8 , 9 . Published analyses differ in their inferences of LUCA’s genome, from conservative estimates of 80 orthologous proteins 10 up to 1,529 different potential gene families 4 . Interpretations range from little beyond an information-processing and metabolic core 6 through to a prokaryote-grade organism with much of the gene repertoire of modern Archaea and Bacteria 8 , recently reviewed in ref. 7 . Here we use molecular clock methodology, horizontal gene-transfer-aware phylogenetic reconciliation and existing biogeochemical models to address questions about LUCA’s age, gene content, metabolism and impact on the early Earth system.

Estimating the age of LUCA

Life’s evolutionary timescale is typically calibrated to the oldest fossil occurrences. However, the veracity of fossil discoveries from the early Archaean period has been contested 11 , 12 . Relaxed Bayesian node-calibrated molecular clock approaches provide a means of integrating the sparse fossil and geochemical record of early life with the information provided by molecular data; however, constraining LUCA’s age is challenging due to limited prokaryote fossil calibrations and the uncertainty in their placement on the phylogeny. Molecular clock estimates of LUCA 13 , 14 , 15 have relied on conserved universal single-copy marker genes within phylogenies for which LUCA represented the root. Dating the root of a tree is difficult because errors propagate from the tips to the root of the dated phylogeny and information is not available to estimate the rate of evolution for the branch incident on the root node. Therefore, we analysed genes that duplicated before LUCA with two (or more) copies in LUCA’s genome 16 . The root in these gene trees represents this duplication preceding LUCA, whereas LUCA is represented by two descendant nodes. Use of these universal paralogues also has the advantage that the same calibrations can be applied at least twice. After duplication, the same species divergences are represented on both sides of the gene tree 17 , 18 and thus can be assumed to have the same age. This considerably reduces the uncertainty when genetic distance (branch length) is resolved into absolute time and rate. When a shared node is assigned a fossil calibration, such cross-bracing also serves to double the number of calibrations on the phylogeny, improving divergence time estimates. We calibrated our molecular clock analyses using 13 calibrations (see ‘Fossil calibrations’ in Supplementary Information ). The calibration on the root of the tree of life is of particular importance. Some previous studies have placed a younger maximum constraint on the age of LUCA based on the assumption that life could not have survived Late Heavy Bombardment (LHB) (~3.7–3.9 billion years ago (Ga)) 19 . However, the LHB hypothesis is extrapolated and scaled from the Moon’s impact record, the interpretation of which has been questioned in terms of the intensity, duration and even the veracity of an LHB episode 20 , 21 , 22 , 23 . Thus, the LHB hypothesis should not be considered a credible maximum constraint on the age of LUCA. We used soft-uniform bounds, with the maximum-age bound based on the time of the Moon-forming impact (4,510 million years ago (Ma) ± 10 Myr), which would have effectively sterilized Earth’s precursors, Tellus and Theia 13 . Our minimum bound on the age of LUCA is based on low δ 98 Mo isotope values indicative of Mn oxidation compatible with oxygenic photosynthesis and, therefore, total-group Oxyphotobacteria in the Mozaan Group, Pongola Supergroup, South Africa 24 , 25 , dated minimally to 2,954 Ma ± 9 Myr (ref. 26 ).

Our estimates for the age of LUCA are inferred with a concatenated and a partitioned dataset, both consisting of five pre-LUCA paralogues: catalytic and non-catalytic subunits from ATP synthases, elongation factor Tu and G, signal recognition protein and signal recognition particle receptor, tyrosyl-tRNA and tryptophanyl-tRNA synthetases, and leucyl- and valyl-tRNA synthetases 27 . Marginal densities (commonly referred to as effective priors) fall within calibration densities (that is, user-specified priors) when topologically adjacent calibrations do not overlap temporally, but may differ when they overlap, to ensure the relative age relationships between ancestor-descendant nodes. We consider the marginal densities a reasonable interpretation of the calibration evidence given the phylogeny; we are not attempting to test the hypothesis that the fossil record is an accurate temporal archive of evolutionary history because it is not 28 . The duplicated LUCA node age estimates we obtained under the autocorrelated rates (geometric Brownian motion (GBM)) 29 , 30 and independent-rates log-normal (ILN) 31 , 32 relaxed-clock models with our partitioned dataset (GBM, 4.18–4.33 Ga; ILN, 4.09–4.32 Ga; Fig. 1 ) fall within our composite age estimate for LUCA ranging from 3.94 Ga to 4.52 Ga, comparable to previous studies 13 , 18 , 33 . Dating analyses based on single genes, or concatenations that excluded each gene in turn, returned compatible timescales (Extended Data Figs. 1 and 2 and ‘Additional methods’ in Methods ).

Our results suggest that LUCA lived around 4.2 Ga, with a 95% confidence interval spanning 4.09–4.33 Ga under the ILN relaxed-clock model (orange) and 4.18–4.33 Ga under the GBM relaxed-clock model (teal). Under a cross-bracing approach, nodes corresponding to the same species divergences (that is, mirrored nodes) have the same posterior time densities. This figure shows the corresponding posterior time densities of the mirrored nodes for the last universal, archaeal, bacterial and eukaryotic common ancestors (LUCA, LACA, LBCA and LECA, respectively); the last common ancestor of the mitochondrial lineage (Mito-LECA); and the last plastid-bearing common ancestor (LPCA). Purple stars indicate nodes calibrated with fossils. Arc, Archaea; Bac, Bacteria; Euk, Eukarya.

LUCA’s physiology

To estimate the physiology of LUCA, we first inferred an updated microbial phylogeny from 57 phylogenetic marker genes (see ‘Universal marker genes’ in Methods ) on 700 genomes, comprising 350 Archaea and 350 Bacteria 15 . This tree was in good agreement with recent phylogenies of the archaeal and bacterial domains of life 34 , 35 . For example, the TACK 36 and Asgard clades of Archaea 37 , 38 , 39 and Gracilicutes within Bacteria 40 , 41 were recovered as monophyletic. However, the analysis was equivocal as to the phylogenetic placement of the Patescibacteria (CPR) 42 and DPANN 43 , which are two small-genome lineages that have been difficult to place in trees. Approximately unbiased 44 tests could not distinguish the placement of these clades, neither at the root of their respective domains nor in derived positions, with CPR sister to Chloroflexota (as reported recently in refs. 35 , 41 , 45 ) and DPANN sister to Euryarchaeota. To account for this phylogenetic uncertainty, we performed LUCA reconstructions on two trees: our maximum likelihood (ML) tree (topology 1; Extended Data Fig. 3 ) and a tree in which CPR were placed as the sister of Chloroflexota, with DPANN sister to all other Archaea (topology 2; Extended Data Fig. 4 ). In both cases, the gene families mapped to LUCA were very similar (correlation of LUCA presence probabilities (PP), r  = 0.6720275, P  < 2.2 × 10 − 16 ). We discuss the results on the tree with topology 2 and discuss the residual differences in Supplementary Information , ‘Topology 1’ (Supplementary Data 1 ).

We used the probabilistic gene- and species-tree reconciliation algorithm ALE 46 to infer the evolution of gene family trees for each sampled entry in the KEGG Orthology (KO) database 47 on our species tree. ALE infers the history of gene duplications, transfers and losses based on a comparison between a distribution of bootstrapped gene trees and the reference species tree, allowing us to estimate the probability that the gene family was present at a node in the tree 35 , 48 , 49 . This reconciliation approach has several advantages for drawing inferences about LUCA. Most gene families have experienced gene transfer since the time of LUCA 50 , 51 and so explicitly modelling transfers enables us to include many more gene families in the analysis than has been possible using previous approaches. As the analysis is probabilistic, we can also account for uncertainty in gene family origins and evolutionary history by averaging over different scenarios using the reconciliation model. Using this approach, we estimated the probability that each KEGG gene family (KO) was present in LUCA and then used the resulting probabilities to construct a hypothetical model of LUCA’s gene content, metabolic potential (Fig. 2 ) and environmental context (Fig. 3 ). Using the KEGG annotation is beneficial because it allows us to connect our inferences to curated functional annotations; however, it has the drawback that some widespread gene families that were likely present in LUCA are divided into multiple KO families that individually appear to be restricted to particular taxonomic groups and inferred to have arisen later. To account for this limitation, we also performed an analysis of COG (Clusters of Orthologous Genes) 52 gene families, which correspond to more coarse-grained functional annotations (Supplementary Data 2 ).

In black: enzymes and metabolic pathways inferred to be present in LUCA with at least PP = 0.75, with sampling in both prokaryotic domains. In grey: those inferred in our least-stringent threshold of PP = 0.50. The analysis supports the presence of a complete WLP and an almost complete TCA cycle across multiple confidence thresholds. Metabolic maps derived from KEGG 47 database through iPath 109 . GPI, glycosylphosphatidylinositol; DDT, 1,1,1-trichloro-2,2-bis(p-chlorophenyl)ethane.

a , A representation of LUCA based on our ancestral gene content reconstruction. Gene names in black have been inferred to be present in LUCA under the most-stringent threshold (PP = 0.75, sampled in both domains); those in grey are present at the least-stringent threshold (PP = 0.50, without a requirement for presence in both domains). b , LUCA in the context of the tree of life. Branches on the tree of life that have left sampled descendants today are coloured black, those that have left no sampled descendants are in grey. As the common ancestor of extant cellular life, LUCA is the oldest node that can be reconstructed using phylogenetic methods. It would have shared the early Earth with other lineages (highlighted in teal) that have left no descendants among sampled cellular life today. However, these lineages may have left a trace in modern organisms by transferring genes into the sampled tree of life (red lines) before their extinction. c , LUCA’s chemoautotrophic metabolism probably relied on gas exchange with the immediate environment to achieve organic carbon (C org ) fixation via acetogenesis and it may also have run the metabolism in reverse. d , LUCA within the context of an early ecosystem. The CO 2 and H 2 that fuelled LUCA’s plausibly acetogenic metabolism could have come from both geochemical and biotic inputs. The organic matter and acetate that LUCA produced could have created a niche for other metabolisms, including ones that recycled CO 2 and H 2 (as in modern sediments). e , LUCA in an Earth system context. Acetogenic LUCA could have been a key part of both surface and deep (chemo)autotrophic ecosystems, powered by H 2 . If methanogens were also present, hydrogen would be released as CH 4 to the atmosphere, converted to H 2 by photochemistry and thus recycled back to the surface ecosystem, boosting its productivity. Ferm., fermentation.

Genome size and cellular features

By using modern prokaryotic genomes as training data, we used a predictive model to estimate the genome size and the number of protein families encoded by LUCA based on the relationship between the number of KEGG gene families and the total number of proteins encoded by modern prokaryote genomes (Extended Data Figs. 5 and 6 ). On the basis of the PPs for KEGG KO gene families, we identified a conservative subset of 399 KOs that were likely to be present in LUCA, with PPs ≥0.75, and found in both Archaea and Bacteria (Supplementary Data 1 ); these families form the basis of our metabolic reconstruction. However, by integrating over the inferred PPs of all KO gene families, including those with low probabilities, we also estimate LUCA’s genome size. Our predictive model estimates a genome size of 2.75 Mb (2.49–2.99 Mb) encoding 2,657 (2,451–2,855) proteins ( Methods ). Although we can estimate the number of genes in LUCA’s genome, it is more difficult to identify the specific gene families that might have already been present in LUCA based on the genomes of modern Archaea and Bacteria. It is likely that the modern version of the pathways would be considered incomplete based on LUCA’s gene content through subsequent evolutionary changes. We should therefore expect reconstructions of metabolic pathways to be incomplete due to this phylogenetic noise and other limitations of the analysis pipeline. For example, when looking at genes and pathways that can uncontroversially be mapped to LUCA, such as the ribosome and aminoacyl-tRNA synthetases for implementing the genetic code, we find that we map many (but not all) of the key components to LUCA (see ‘Notes’ in Supplementary Information ). We interpret this to mean that our reconstruction is probably incomplete but our interpretation of LUCA’s metabolism relies on our inference of pathways, not individual genes.

The inferred gene content of LUCA suggests it was an anaerobe as we do not find support for the presence of terminal oxidases (Supplementary Data 1 ). Instead we identified almost all genes encoding proteins of the archaeal (and most of the bacterial) versions of the Wood–Ljungdahl pathway (WLP) (PP > 0.7), indicating that LUCA had the potential for acetogenic growth and/or carbon fixation 53 , 54 , 55 (Supplementary Data 3 ). LUCA encoded some NiFe hydrogenase subunits ( K06281 , PP = 0.90; K14126 , PP = 0.92), which may have enabled growth on hydrogen (see ‘Notes’ in Supplementary Information ). Complexes involved in methanogenesis such as methyl-coenzyme M reductase and tetrahydromethanopterin S-methyltransferase were inferred to be absent, suggesting that LUCA was unlikely to function as a modern methanogen. We found strong support for some components of the TCA cycle (including subunits of oxoglutarate/2-oxoacid ferredoxin oxidoreductase ( K00175 and K00176 ), succinate dehydrogenase ( K00239 ) and homocitrate synthase ( K02594 )), although some steps are missing. LUCA was probably capable of gluconeogenesis/glycolysis in that we find support for most subunits of enzymes involved in these pathways (Supplementary Data 1 and 3 ). Considering the presence of the WLP, this may indicate that LUCA had the ability to grow organoheterotrophically and potentially also autotrophically. Gluconeogenesis would have been important in linking carbon fixation to nucleotide biosynthesis via the pentose phosphate pathway, most enzymes of which seem to be present in LUCA (see ‘Notes’ in Supplementary Information ). We found no evidence that LUCA was photosynthetic, with low PPs for almost all components of oxygenic and anoxygenic photosystems (Supplementary Data 3 ).

We find strong support for the presence of ATP synthase, specifically, the A ( K02117 , PP = 0.98) and B ( K02118 , PP = 0.94) subunit components of the hydrophilic V/A1 subunit, and the I (subunit a, K02123 , PP = 0.99) and K (subunit c, K02124 , PP = 0.82) subunits of the transmembrane V/A0 subunit. In addition, if we relax the sampling threshold, we also infer the presence of the F1-type β-subunit ( K02112 , PP = 0.94). This is consistent with many previous studies that have mapped ATP synthase subunits to LUCA 6 , 17 , 18 , 56 , 57 .

We obtain moderate support for the presence of pathways for assimilatory nitrate (ferredoxin-nitrate reductase, K00367 , PP = 0.69; ferredoxin-nitrite reductase, K00367 , PP = 0.53) and sulfate reduction (sulfate adenylyltransferase, K00957 , PP = 0.80, and K00958 , PP = 0.73; sulfite reductase, K00392 , PP = 0.82; phosphoadenosine phosphosulfate reductase, K00390 , PP = 0.56), probably to fuel amino acid biosynthesis, for which we inferred the presence of 37 partially complete pathways.

We found support for the presence of 19 class 1 CRISPR–Cas effector protein families in the genome of LUCA, including types I and III (cas3, K07012 , PP = 0.80, and K07475 , PP = 0.74; cas10, K07016 , PP = 0.96, and K19076 , PP = 0.67; and cas7, K07061 , PP = 0.90, K09002 , PP = 0.84, K19075 , PP = 0.97, K19115 , PP = 0.98, and K19140 , PP = 0.80). The absence of Cas1 and Cas2 may suggest LUCA encoded an early Cas system with the means to deliver an RNA-based immune response by cutting (Cas6/Cas3) and binding (CSM/Cas10) RNA, but lacking the full immune-system-site CRISPR. This supports the idea that the effector stage of CRISPR–Cas immunity evolved from RNA sensing for signal transduction, based on the similarities in RNA binding modules of the proteins 58 . This is consistent with the idea that cellular life was already involved in an arms race with viruses at the time of LUCA 59 , 60 . Our results indicate that an early Cas system was an ancestral immune system of extant cellular life.

Altogether, our metabolic reconstructions suggest that LUCA was a relatively complex organism, similar to extant Archaea and Bacteria 6 , 7 . On the basis of ancient duplications of the Sec and ATP synthase genes before LUCA, along with high PPs for key components of those systems, membrane-bound ATP synthase subunits, genes involved in peptidoglycan synthesis ( mraY , K01000 ; murC , K01924 ) and the cytoskeletal actin-like protein, MreB ( K03569 ) (Supplementary Data 3 ), it is highly likely that LUCA possessed the core cellular apparatus of modern prokaryotic life. This might include the basic constituents of a phospholipid membrane, although our analysis did not conclusively establish its composition. In particular, we recovered the following enzymes involved in the synthesis of ether and ester lipids, (alkyldihydroxyacetonephosphate synthase, glycerol 3-phosphate and glycerol 1-phosphate) and components of the mevalonate pathway (mevalonate 5-phosphate dehydratase (PP = 0.84), hydroxymethylglutaryl-CoA reductase (PP = 0.52), mevalonate kinase (PP = 0.51) and hydroxymethylglutaryl-CoA synthase (PP = 0.51)).

Compared with previous estimates of LUCA’s gene content, we find 81 overlapping COG gene families with the consensus dataset of ref. 7 and 69 overlapping KOs with the dataset of ref. 6 . Key points of agreement between previous studies include the presence of signal recognition particle protein, ffh (COG0541, K03106 ) 7 used in the targeting and delivery of proteins for the plasma membrane, a high number of aminoacyl-tRNA synthetases for amino acid synthesis and glycolysis/gluconeogenesis enzymes.

Ref. 6 inferred LUCA to be a thermophilic anaerobic autotroph using the WLP for carbon fixation based on the presence of a single enzyme (CODH), and similarly suggested that LUCA was capable of nitrogen fixation using a nitrogenase. Our reconstruction agrees with ref. 6 that LUCA was an anaerobic autotroph using the WLP for carbon fixation, but we infer the presence of a much more complete WLP than that previously obtained. We did not find strong evidence for nitrogenase or nitrogen fixation, and the reconstruction was not definitive with respect to the optimal growth environment of LUCA.

We used a probabilistic approach to reconstruct LUCA—that is, we estimated the probability with which each gene family was present in LUCA based on a model of how gene families evolve along an overarching species tree. This approach differs from analyses of phylogenetic presence–absence profiles 3 , 4 , 9 or those that used filtering criteria (such as broadly distributed or highly vertically evolving families) to define a high-confidence subset of modern genes that might have been present in LUCA. Our reconstruction maps many more genes to LUCA—albeit each with lower probability—than previous analyses 8 and yields an estimate of LUCA’s genome size that is within the range of modern prokaryotes. The result is an incomplete picture of a cellular organism that was prokaryote grade rather than progenotic 2 and that, similarly to prokaryotes today, probably existed as part of an ecosystem. As the common ancestor of sampled, extant prokaryotic life, LUCA is the oldest node on the species tree that we can reconstruct via phylogenomics but, as Fig. 3 illustrates, it was already the product of a highly innovative period in evolutionary history during which most of the core components of cells were established. By definition, we cannot reconstruct LUCA’s contemporaries using phylogenomics but we can propose hypotheses about their physiologies based on the reconstructed LUCA whose features immediately suggest the potential for interactions with other prokaryotic metabolisms.

LUCA’s environment, ecosystem and Earth system context

The inference that LUCA used the WLP helps constrain the environment and ecology in which it could have lived. Modern acetogens can grow autotrophically on H 2 (and CO 2 ) or heterotrophically on a wide range of alternative electron donors including alcohols, sugars and carboxylic acids 55 . This metabolic flexibility is key to their modern ecological success. Acetogenesis, whether autotrophic or heterotrophic, has a low energy yield and growth efficiency (although use of the reductive acetyl-CoA pathway for both energy production and biosynthesis reduces the energy cost of biosynthesis). This would be consistent with an energy-limited early biosphere 61 .

If LUCA functioned as an organoheterotrophic acetogen, it was necessarily part of an ecosystem containing autotrophs providing a source of organic compounds (because the abiotic source flux of organic molecules was minimal on the early Earth). Alternatively, if LUCA functioned as a chemoautotrophic acetogen it could (in principle) have lived independently off an abiotic source of H 2 (and CO 2 ). However, it is implausible that LUCA would have existed in isolation as the by-products of its chemoautotrophic metabolism would have created a niche for a consortium of other metabolisms (as in modern sediments) (Fig. 3d ). This would include the potential for LUCA itself to grow as an organoheterotroph.

A chemoautotrophic acetogenic LUCA could have occupied two major potential habitats (Fig. 3e ): the first is the deep ocean where hydrothermal vents and serpentinization of sea-floor provided a source of H 2 (ref. 62 ). Consistent with this, we find support for the presence of reverse gyrase (PP = 0.97), a hallmark enzyme of hyperthermophilic prokaryotes 6 , 63 , 64 , 65 , which would not be expected if early life existed at the ocean surface (although the evolution of reverse gyrase is complex 63 ; see ‘Reverse gyrase’ in Supplementary Information ). The second habitat is the ocean surface where the atmosphere would have provided a source of H 2 derived from volcanoes and metamorphism. Indeed, we detected the presence of spore photoproduct lyase (COG1533, K03716 , PP = 0.88) that in extant organisms repairs methylene-bridged thymine dimers occurring in spore DNA as a result of damage induced through ultraviolet (UV) radiation 66 , 67 . However, this gene family also occurs in modern taxa that neither form endospores nor dwell in environments where they are likely to accrue UV damage to their DNA and so is not an exclusive hallmark of environments exposed to UV. Previous studies often favoured a deep-ocean environment for LUCA as early life would have been better protected there from an episode of LHB. However, if the LHB was less intense than initially proposed 20 , 22 , or just a sampling artefact 21 , these arguments weaken. Another possibility may be that LUCA inhabited a shallow hydrothermal vent or a hot spring.

Hydrogen fluxes in these ecosystems could have been several times higher on the early Earth (with its greater internal heat source) than today. Volcanism today produces ~1 × 10 12  mol H 2  yr −1 and serpentinization produces ~0.4 × 10 12  mol H 2  yr − 1 . With the present H 2 flux and the known scaling of the H 2 escape rate to space, an abiotic atmospheric concentration of H 2 of ~150 ppmv is predicted 68 . Chemoautotrophic acetogens would have locally drawn down the concentration of H 2 (in either surface or deep niche) but their low growth efficiency would ensure H 2 (and CO 2 ) remained available. This and the organic matter and acetate produced would have created niches for other metabolisms, including methanogenesis (Fig. 3d ).

On the basis of thermodynamic considerations, CH 4 and CO 2 are expected to be the eventual metabolic end products of the resulting ecosystem, with a small fraction of the initial hydrogen consumption buried as organic matter. The resulting flux of CH 4 to the atmosphere would fuel photochemical H 2 regeneration and associated productivity in the surface ocean (Fig. 3e ). Existing models suggest the resulting global H 2 recycling system is highly effective, such that the supply flux of H 2 to the surface could have exceeded the volcanic input of H 2 to the atmosphere by at least an order of magnitude, in turn implying that the productivity of such a biosphere was boosted by a comparable factor 69 . Photochemical recycling to CO would also have supported a surface niche for organisms consuming CO (ref. 69 ).

In deep-ocean habitats, there could be some localized recycling of electrons (Fig. 3d ) but a quantitative loss of highly insoluble H 2 and CH 4 to the atmosphere and minimal return after photochemical conversion of CH 4 to H 2 means global recycling to depth would be minimal (Fig. 3e ). Hence the surface environment for LUCA could have become dominant (albeit recycling of the resulting organic matter could be spread through ocean depth; ‘Deep heterotrophic ecosystem’ in Fig. 3e ). The global net primary productivity of an early chemoautotrophic biosphere including acetogenic LUCA and methanogens could have been of order ~1 × 10 12 to 7 × 10 12  mol C yr − 1 (~3 orders of magnitude less than today) 69 .

The nutrient supply (for example, N) required to support such a biosphere would need to balance that lost in the burial flux of organic matter. Earth surface redox balance dictates that hydrogen loss to space and burial of electrons/hydrogen must together balance input of electrons/hydrogen. Considering contemporary H 2 inputs, and the above estimate of net primary productivity, this suggests a maximum burial flux in the order of ~10 12  mol C yr − 1 , which, with contemporary stoichiometry (C:N ratio of ~7) could demand >10 11  mol N yr − 1 . Lightning would have provided a source of nitrite and nitrate 70 , consistent with LUCA’s inferred pathways of nitrite and (possibly) nitrate reduction. However, it would only have been of the order 3 × 10 9  mol N yr − 1 (ref. 71 ). Instead, in a global hydrogen-recycling system, HCN from photochemistry higher in the atmosphere, deposited and hydrolysed to ammonia in water, would have increased available nitrogen supply by orders of magnitude toward ~3 × 10 12  mol N yr − 1 (refs. 71 , 72 ). This HCN pathway is consistent with the anomalously light nitrogen isotopic composition of the earliest plausible biogenic matter of 3.8–3.7 Ga (ref. 73 ), although that considerably postdates our inferred age of LUCA. These considerations suggest that the proposed LUCA biosphere (Fig. 3e ) would have been energy or hydrogen limited not nitrogen limited.

Conclusions

By treating gene presence probabilistically, our reconstruction maps many more genes (2,657) to LUCA than previous analyses and results in an estimate of LUCA’s genome size (2.75 Mb) that is within the range of modern prokaryotes. The result is a picture of a cellular organism that was prokaryote grade rather than progenotic 2 and that probably existed as a component of an ecosystem, using the WLP for acetogenic growth and carbon fixation. We cannot use phylogenetics to reconstruct other members of this early ecosystem but we can infer their physiologies based on the metabolic inputs and outputs of LUCA. How evolution proceeded from the origin of life to early communities at the time of LUCA remains an open question, but the inferred age of LUCA (~4.2 Ga) compared with the origin of the Earth and Moon suggests that the process required a surprisingly short interval of geologic time.

Universal marker genes

A list of 298 markers were identified by creating a non-redundant list of markers used in previous studies on archaeal and bacterial phylogenies 10 , 35 , 38 , 74 , 75 , 76 , 77 , 78 , 79 . These markers were mapped to the corresponding COG, arCOG and TIGRFAM profile to identify which profile is best suited to extract proteins from taxa of interest. To evaluate whether the markers cover all archaeal and bacterial diversity, proteins from a set of 574 archaeal and 3,020 bacterial genomes were searched against the COG, arCOG and TIGRFAM databases using hmmsearch (v.3.1b2; settings, hmmsearch–tblout output–domtblout–notextw) 52 , 80 , 81 , 82 . Only hits with an e-value less than or equal to 1 × 10 −5 were investigated further and for each protein the best hit was determined based on the e-value (expect value) and bit-score. Results from all database searches were merged based on the protein identifiers and the table was subsetted to only include hits against the 298 markers of interest. On the basis of this table we calculated whether the markers occurred in Archaea, Bacteria or both Archaea and Bacteria. Markers were only included if they were present in at least 50% of taxa and contained less than 10% of duplications, leaving a set of 265 markers. Sequences for each marker were aligned using MAFFT L-INS-i v.7.407 (ref. 83 ) for markers with less than 1,000 sequences or MAFFT 84 for those with more than 1,000 sequences (setting, –reorder) 84 and sequences were trimmed using BMGE 85 , set for amino acids, a BLOcks SUbstitution Matrix 30 similarity matrix, with a entropy score of 0.5 (v.1.12; settings, -t AA -m BLOSUM30 -h 0.5). Single gene trees were generated with IQ-TREE 2 (ref. 86 ), using the LG substitution matrix, with ten-profile mixture models, four CPUs, with 1,000 ultrafast bootstraps optimized by nearest neighbour interchange written to a file retaining branch lengths (v.2.1.2; settings, -m LG + C10 + F + R -nt 4 -wbtl -bb 1,000 -bnni). These single gene trees were investigated for archaeal and bacterial monophyly and the presence of paralogues. Markers that failed these tests were not included in further analyses, leaving a set of 59 markers (3 arCOGs, 46 COGs and 10 TIGRFAMs) suited for phylogenies containing both Archaea and Bacteria (Supplementary Data 4 ).

Marker gene sequence selection

To limit selecting distant paralogues and false positives, we used a bidirectional or reciprocal approach to identify the sequences corresponding to the 59 single-copy markers. In the first inspection (query 1), the 350 archaeal and 350 bacterial reference genomes were queried against all arCOG HMM (hidden Markov model) profiles (All_Arcogs_2018.hmm), all COG HMM profiles (NCBI_COGs_Oct2020.hmm) and all TIGRFAM HMM profiles (TIGRFAMs_15.0_HMM.LIB) using a custom script built on hmmsearch: hmmsearchTable <genomes.faa> <database.hmm> -E 1 × 10 −5 >HMMscan_Output_e5 (HMMER v.3.3.2) 87 . HMM profiles corresponding to the 59 single-copy marker genes (Supplementary Data 4 ) were extracted from each query and the best-hit sequences were identified based on the e-value and bit-score. We used the same custom hmmsearchTable script and conditions (see above) in the second inspection (query 2) to query the best-hit sequences identified above against the full COG HMM database (NCBI_COGs_Oct2020.hmm). Results were parsed and the COG family assigned in query 2 was compared with the COG family assigned to sequences based on the marker gene identity (Supplementary Data 4 ). Sequence hits were validated using the matching COG identifier, resulting in 353 mismatches (that is, COG family in query 1 does not match COG family in query 2) that were removed from the working set of marker gene sequences. These sequences were aligned using MAFFT L-INS-i 83 and then trimmed using BMGE 85 with a BLOSUM30 matrix. Individual gene trees were inferred under ML using IQ-TREE 2 (ref. 86 ) with model fitting, including both the default homologous substitution models and the following complex heterogeneous substitution models (LG substitution matrices with 10–60-profile mixture models, with empirical base frequencies and a discrete gamma model with four categories accounting for rate heterogeneity across sites): LG + C60 + F + G, LG + C50 + F + G, LG + C40 + F + G, LG + C30 + F + G, LG + C20 + F + G and LG + C10 + F + G, with 10,000 ultrafast bootstraps and 10 independent runs to avoid local optima. These 59 gene trees were manually inspected and curated over multiple rounds. Any horizontal gene transfer events, paralogous genes or sequences that violated domain monophyly were removed and two genes (arCOG01561, tuf ; COG0442, ProS ) were dropped at this stage due to the high number of transfer events, resulting in 57 single-copy orthologues for further tree inference.

Species-tree inference

These 57 orthologous sequences were concatenated and ML trees were inferred after three independent runs with IQ-TREE 2 (ref. 86 ) using the same model fitting and bootstrap settings as described above. The tree with the highest log-likelihood of the three runs was chosen as the ML species tree (topology 1). To test the effect of removing the CPR bacteria, we removed all CPR bacteria from the alignment before inferring a species tree (same parameters as above). We also performed approximately unbiased 44 tree topology tests (with IQ-TREE 2 (ref. 86 ), using LG + C20 + F + G) when testing the significance of constraining the species-tree topology (ML tree; Supplementary Fig. 1 ) to have a DPANN clade as sister to all other Archaea (same parameters as above but with a minimally constrained topology with monophyletic Archaea and DPANN sister to other Archaea present in a polytomy (Supplementary Fig. 2 )) and testing a constraint of CPR to be sister to Chloroflexi (Supplementary Fig. 3 ), and a combination of both the DPANN and CPR constraints (topology 2); these were tested against the ML topology, both using the normal 20 amino acid alignments and also with Susko–Roger recoding 88 .

Gene families

For the 700 representative species 15 , gene family clustering was performed using EGGNOGMAPPER v.2 (ref. 89 ), with the following parameters: using the DIAMOND 90 search, a query cover of 50% and an e-value threshold of 0.0000001. Gene families were collated using their KEGG 47 identifier, resulting in 9,365 gene families. These gene families were then aligned using MAFFT 84 v.7.5 with default settings and trimmed using BMGE 85 (with the same settings as above). Five independent sets of ML trees were then inferred using IQ-TREE 2 (ref. 86 ), using LG + F + G, with 1,000 ultrafast bootstrap replicates. We also performed a COG-based clustering analysis in which COGs were assigned based on the modal COG identifier annotated for each KEGG gene family based on the results from EGGNOGMAPPER v.2 (ref. 89 ). These gene families were aligned, trimmed and one set of gene trees (with 1,000 ultrafast bootstrap replicates) was inferred using the same parameters as described above for the KEGG gene families.

Reconciliations

The five sets of bootstrap distributions were converted into ALE files, using ALEobserve, and reconciled against topology 1 and topology 2 using ALEml_undated 91 with the fraction missing for each genome included (where available). Gene family root origination rates were optimized for each COG functional category as previously described 35 and families were categorized into four different groups based on the probability of being present in the LUCA node in the tree. The most-stringent category was that with sampling above 1% in both domains and a PP ≥ 0.75, another category was with PP ≥ 0.75 with no sampling requirement, another with PP ≥ 0.5 with the sampling requirement; the least stringent was PP ≥ 0.5 with no sampling requirement. We used the median probability at the root from across the five runs to avoid potential biases from failed runs in the mean and to account for variation across bootstrap distributions (see Supplementary Fig. 4 for distributions of the inferred ratio of duplications, transfers and losses for all gene families across all tips in the species tree; see Supplementary Data 5 for the inferred duplications, transfers and losses ratios for LUCA, the last bacterial common ancestor and the last archaeal common ancestor).

Metabolic pathway analysis

Metabolic pathways for gene families mapped to the LUCA node were inferred using the KEGG 47 website GUI and metabolic completeness for individual modules was estimated with Anvi’o 92 (anvi-estimate-metabolism), with pathwise completeness.

Additional testing

We tested for the effects of model complexity on reconciliation by using posterior mean site frequency LG + C20 + F + G across three independent runs in comparison with 3 LG + F + G independent runs. We also performed a 10% subsampling of the species trees and gene family alignments across two independent runs for two different subsamples, one with and one without the presence of Asgard archaea. We also tested the likelihood of the gene families under a bacterial root (between Terrabacteria and Gracilicutes) using reconciliations of the gene families under a species-tree topology rooted as such.

Fossil calibrations

On the basis of well-established geological events and the fossil record, we modelled 13 uniform densities to constrain the maximum and minimum ages of various nodes in our phylogeny. We constrained the bounds of the uniform densities to be either hard (no tail probability is allowed after the age constraint) or soft (a 2.5% tail probability is allowed after the age constraint) depending on the interpretation of the fossil record ( Supplementary Information ). Nodes that refer to the same duplication event are identified by MCMCtree as cross-braced (that is, one is chosen as the ‘driver’ node, the rest are ‘mirrored’ nodes). In other words, the sampling during the Markov chain Monte Carlo (MCMC) for cross-braced nodes is not independent: the same posterior time density is inferred for matching mirror–driver nodes (see ‘Additional methods’ for details on our cross-bracing approach).

Timetree inference analyses

Timetree inference with the program MCMCtree (PAML v.4.10.7 (ref. 93 )) proceeded under both the GBM and ILN relaxed-clock models. We specified a vague rate prior with the shape parameter equal to 2 and the scale parameter equal to 2.5: Γ(2, 2.5). This gamma distribution is meant to account for the uncertainty on our estimate for the mean evolutionary rate, ~0.81 substitutions per site per time unit, which we calculated by dividing the tree height of our best-scoring ML tree ( Supplementary Information ) into the estimated mean root age of our phylogeny (that is, 4.520 Ga, time unit = 10 9 years; see ‘Fossil calibrations’ in Supplementary Information for justifications on used calibrations). Given that we are estimating very deep divergences, the molecular clock may be seriously violated. Therefore, we applied a very diffuse gamma prior on the rate variation parameter ( σ 2 ), Γ(1, 10), so that it is centred around σ 2  = 0.1. To incorporate our uncertainty regarding the tree shape, we specified a uniform kernel density for the birth–death sampling process by setting the birth and death processes to 1, λ  (per-lineage birth rate) =  μ  (per-lineage death rate) = 1, and the sampling frequency to ρ  (sampling fraction) = 0.1. Our main analysis consisted of inferring the timetree for the partitioned dataset under both the GBM and the ILN relaxed-clock models in which nodes that correspond to the same divergences are cross-braced (that is, hereby referred to as cross-bracing A). In addition, we ran 10 additional inference analyses to benchmark the effect that partitioning, cross-bracing and relaxed-clock models can have on species divergence time estimation: (1) GBM + concatenated alignment + cross-bracing A, (2) GBM + concatenated alignment + cross-bracing B (only nodes that correspond to the same divergences for which there are fossil constraints are cross-braced), (3) GBM + concatenated alignment + without cross-bracing, (4) GBM + partitioned alignment + cross-bracing B, (5) GBM + partitioned alignment + without cross-bracing, (6) ILN + concatenated alignment + cross-bracing A, (7) ILN + concatenated alignment + cross-bracing B, (8) ILN + concatenated alignment + without cross-bracing, (9) ILN + partitioned alignment + cross-bracing B, and (10) ILN + partitioned alignment + without cross-bracing. Lastly, we used (1) individual gene alignments, (2) a leave-one-out strategy (rate prior changed for alignments without ATP and Leu , Γ(2, 2.2), and without Tyr , Γ(2, 2.3), but was Γ(2, 2.5) for the rest; see ‘Additional methods’), and (3) a more complex substitution model 94 to assess their impact on timetree inference. Refer to ‘Additional methods’ for details on how we parsed the dataset we used for timetree inference analyses, ran PAML programs CODEML and MCMCtree to approximate the likelihood calculation 95 , and carried out the MCMC diagnostics for the results obtained under each of the previously mentioned scenarios.

We simulated 100 samples of ‘KEGG genomes’ based on the probabilities of each of the (7,467) gene families being present in LUCA using the random.rand function in numpy 96 . The mean number of KEGG gene families was 1,298.25, the 95% HPD (highest posterior density) minimum was 1,255 and the maximum was 1,340. To infer the relationship between the number of KEGG KO gene families encoded by a genome, the number of proteins and the genome size, we used LOESS (locally estimated scatter-plot smoothing) regression to estimate the relationship between the number of KOs and (1) the number of protein-coding genes and (2) the genome size for the 700 prokaryotic genomes used in the LUCA reconstruction. To ensure that our inference of genome size is robust to uncertainty in the number of paralogues that can be expected to have been present in LUCA, we used the presence of probability for each of these KEGG KO gene families rather than the estimated copy number. We used the predict function to estimate the protein-coding genes and genome size of LUCA using these models and the simulated gene contents encoded with 95% confidence intervals.

Additional methods

Cross-bracing approach implemented in mcmctree.

The PAML program MCMCtree was implemented to allow for the analysis of duplicated genes or proteins so that some nodes in the tree corresponding to the same speciation events in different paralogues share the same age. We used the tree topology depicted in Supplementary Fig. 5 to explain how users can label driver or mirror nodes (more on these terms below) so that the program identifies them as sharing the same speciation events. The tree topology shown in Supplementary Fig. 5 can be written in Newick format as:

(((A1,A2),A3),((B1,B2),B3));

In this example, A and B are paralogues and the corresponding tips labelled as A1–A3 and B1–B3 represent different species. Node r represents a duplication event, whereas other nodes are speciation events. If we want to constrain the same speciation events to have the same age (that is, Supplementary Fig. 5 , see labels a and b (that is, A1–A2 ancestor and B1–B2 ancestor, respectively) and labels v and b (that is, A1–A2–A3 ancestor and B1–B2–B3 ancestor, respectively), we use node labels in the format #1, #2, and so on to identify such nodes:

(((A1, A2) #1, A3) #2, ((B1, B2) [#1 B{0.2, 0.4}], B3) #2) 'B(0.9,1.1)';

Node a and node b are assigned the same label (#1) and so they share the same age ( t ): t a  =  t b . Similarly, node u and node v have the same age: t u  =  t v . The former nodes are further constrained by a soft-bound calibration based on the fossil record or geological evidence: 0.2 <  t a  =  t b  < 0.4. The latter, however, does not have fossil constraints and thus the only restriction imposed is that both t u and t v are equal. Finally, there is another soft-bound calibration on the root age: 0.9 <  t r  < 1.1.

Among the nodes on the tree with the same label (for example, those nodes labelled with #1 and those with #2 in our example), one is chosen as the driver node, whereas the others are mirror nodes. If calibration information is provided on one of the shared nodes (for example, nodes a and b in Supplementary Fig. 5 ), the same information therefore applies to all shared nodes. If calibration information is provided on multiple shared nodes, that information has to be the same (for example, you could not constrain node a with a different calibration used to constrain node b in Supplementary Fig. 5 ). The time prior (or the prior on all node ages on the tree) is constructed by using a density at the root of the tree, which is specified by the user (for example, 'B(0.9,1.1)' in our example, which has a minimum of 0.9 and a maximum of 1.1). The ages of all non-calibrated nodes are given by the uniform density. This time prior is similar to that used by ref. 29 . The parameters in the birth–death sampling process ( λ , μ , ρ ; specified using the option BDparas in the control file that executes MCMCtree) are ignored. It is noteworthy that more than two nodes can have the same label but one node cannot have two or more labels. In addition, the prior on rates does not distinguish between speciation and duplication events. The implemented cross-bracing approach can only be enabled if option duplication = 1 is included in the control file. By default, this option is set to 0 and users are not required to include it in the control file (that is, the default option is duplication = 0 ).

Timetree inference

Data parsing.

Eight paralogues were initially selected based on previous work showing a likely duplication event before LUCA: the amino- and carboxy-terminal regions from carbamoyl phosphate synthetase, aspartate and ornithine transcarbamoylases, histidine biosynthesis genes A and F , catalytic and non-catalytic subunits from ATP synthase ( ATP ), elongation factor Tu and G ( EF ), signal recognition protein and signal recognition particle receptor ( SRP ), tyrosyl-tRNA and tryptophanyl-tRNA synthetases ( Tyr ), and leucyl- and valyl-tRNA synthetases ( Leu ) 27 . Gene families were identified using BLASTp 97 . Sequences were downloaded from NCBI 98 , aligned with MUSCLE 99 and trimmed with TrimAl 100 (-strict). Individual gene trees were inferred under the LG + C20 + F + G substitution model implemented in IQ-TREE 2 (ref. 86 ). These trees were manually inspected and curated to remove non-homologous sequences, horizontal gene transfers, exceptionally short or long sequences and extremely long branches. Recent paralogues or taxa of inconsistent and/or uncertain placement inferred with RogueNaRok 101 were also removed. Independent verification of an archaeal or bacterial deep split was achieved using minimal ancestor deviation 102 . This filtering process resulted in the five pairs of paralogous gene families 27 ( ATP , EF , SRP , Tyr and Leu ) that we used to estimate the origination time of LUCA. The alignment used for timetree inference consisted of 246 species, with the majority of taxa having at least two copies (for some eukaryotes, they may be represented by plastid, mitochondrial and nuclear sequences).

To assess the impact that partitioning can have on divergence time estimates, we ran our inference analyses with both a concatenated and a partitioned alignment (that is, gene partitioning scheme). We used PAML v.4.10.7 (programs CODEML and MCMCtree) for all divergence time estimation analyses. Given that a fixed tree topology is required for timetree inference with MCMCtree, we inferred the best-scoring ML tree with IQ-TREE 2 under the LG + C20 + F + G4 (ref. 103 ) model following our previous phylogenetic analyses. We then modified the resulting inferred tree topology following consensus views of species-level relationships 34 , 35 , 104 , which we calibrated with the available fossil calibrations (see below). In addition, we ran three sensitivity tests: timetree inference (1) with each gene alignment separately, (2) under a leave-one-out strategy in which each gene alignment was iteratively removed from the concatenated dataset (for example, remove gene ATP but keep genes EF , Leu , SRP and Tyr concatenated in a unique alignment block; apply the same procedure for each gene family), and (3) using the vector of branch lengths, the gradient vector and the Hessian matrix estimated under a complex substitution model (bsinBV method described in ref. 94 ) with the concatenated dataset used for our core analyses. Four of the gene alignments generated for the leave-one-out strategy had gap-only sequences, these were removed when re-inferring the branch lengths under the LG + C20 + F + G4 model (that is, without ATP , 241 species; without EF , 236 species; without Leu , 243 species; without Tyr , 244 species). We used these trees to set the rate prior used for timetree inference for those alignments not including ATP , EF , Leu or Tyr , respectively. The β value (scale parameter) for the rate prior used when analysing alignments without ATP , Leu and Tyr changed minimally but we updated the corresponding rate priors accordingly (see above). When not including SRP , the alignment did not have any sequences removed (that is, 246 species). All alignments were analysed with the same rate prior, Γ(2, 2.5), except for the three previously mentioned alignments.

Approximating the likelihood calculation during timetree inference using PAML programs

Before timetree inference, we ran the CODEML program to infer the branch lengths of the fixed tree topology, the gradient (first derivative of the likelihood function) and the Hessian matrix (second derivative of the likelihood function); the vectors and matrix are required to approximate the likelihood function in the dating program MCMCtree 95 , an approach that substantially reduces computational time 105 . Given that CODEML does not implement the CAT (Bayesian mixture model for across-site heterogeneity) model, we ran our analyses under the closest available substitution model: LG + F + G4 (model = 3). We calculated the aforementioned vectors and matrix for each of the five gene alignments (that is, required for the partitioned alignment), for the concatenated alignment and for the concatenated alignments used for the leave-one-out strategy; the resulting values are written out in an output file called rst2. We appended the rst2 files generated for each of the five individual alignments in the same order the alignment blocks appear in the partitioned alignment file (for example, the first alignment block corresponds to the ATP gene alignment, and thus the first rst2 block will be the one generated when analysing the ATP gene alignment with CODEML). We named this file in_5parts.BV. There is only one rst2 output file for the concatenated alignments, which we renamed in.BV (main concatenated alignment and concatenated alignments under leave-one-out strategy). When analysing each gene alignment separately, we renamed the rst2 files generated for each gene alignment as in.BV.

MCMC diagnostics

All the chains that we ran with MCMCtree for each type of analysis underwent a protocol of MCMC diagnostics consisting of the following steps: (1) flagging and removal of problematic chains; (2) generating convergence plots before and after chain filtering; (3) using the samples collected by those chains that passed the filters (that is, assumed to have converged to the same target distribution) to summarize the results; (4) assessing chain efficiency and convergence by calculating statistics such as R-hat, tail-ESS and bulk-ESS (in-house wrapper function calling Rstan functions, Rstan v.2.21.7; https://mc-stan.org/rstan/ ); and (5) generating the timetrees for each type of analysis with confidence intervals and high-posterior densities to show the uncertainty surrounding the estimated divergence times. Tail-ESS is a diagnostic tool that we used to assess the sampling efficiency in the tails of the posterior distributions of all estimated divergence times, which corresponds to the minimum of the effective sample sizes for quantiles 2.5% and 97.5%. To assess the sampling efficiency in the bulk of the posterior distributions of all estimated divergence, we used bulk-ESS, which uses rank-normalized draws. Note that if tail-ESS and bulk-ESS values are larger than 100, the chains are assumed to have been efficient and reliable parameter estimates (that is, divergence times in our case). R-hat is a convergence diagnostic measure that we used to compare between- and within-chain divergence time estimates to assess chain mixing. If R-hat values are larger than 1.05, between- and within-chain estimates do not agree and thus mixing has been poor. Lastly, we assessed the impact that truncation may have on the estimated divergence times by running MCMCtree when sampling from the prior (that is, the same settings specified above but without using sequence data, which set the prior distribution to be the target distribution during the MCMC). To summarize the samples collected during this analysis, we carried out the same MCMC diagnostics procedure previously mentioned. Supplementary Fig. 6 shows our calibration densities (commonly referred to as user-specified priors, see justifications for used calibrations above) versus the marginal densities (also known as effective priors) that MCMCtree infers when building the joint prior (that is, a prior built without sequence data that considers age constraints specified by the user, the birth–death with sampling process to infer the time densities for the uncalibrated nodes, the rate priors, and so on). We provide all our results for these quality-control checks in our GitHub repository ( https://github.com/sabifo4/LUCA-divtimes ) and in Extended Data Fig. 1 , Supplementary Figs. 7 – 10 and Supplementary Data 6 . Data, figures and tables used and/or generated following a step-by-step tutorial are detailed in the GitHub repository for each inference analysis.

Additional sensitivity analyses

We compared the divergence times we estimated with the concatenated dataset under the calibration strategy cross-bracing A with those inferred (1) for each gene, (2) for gene alignments analysed under a leave-one-out strategy, and (3) for the main concatenated dataset but when using the vector of branch lengths, the gradient vector and the Hessian matrix estimated under a more complex substitution model 94 . The results are summarized in Extended Data Fig. 2 and Supplementary Data 7 and 8 . The same pattern regarding the calibration densities and marginal densities when the tree topology was pruned (that is, see above for details on the leave-one-out strategy) was observed, and thus no additional figures have been generated. As for our main analyses, the results for these additional sensitivity analyses can be found on our GitHub repository ( https://github.com/sabifo4/LUCA-divtimes ).

Reporting summary

Further information on research design is available in the Nature Portfolio Reporting Summary linked to this article.

Data availability

All data required to interpret, verify and extend the research in this article can be found at our figshare repository at https://doi.org/10.6084/m9.figshare.24428659 (ref. 106 ) for the reconciliation and phylogenomic analyses and GitHub at https://github.com/sabifo4/LUCA-divtimes (ref. 107 ) for the molecular clock analyses. Additional data are available at the University of Bristol data repository, data.bris, at https://doi.org/10.5523/bris.405xnm7ei36d2cj65nrirg3ip (ref. 108 ).

Code availability

All code relating to the dating analysis can be found on GitHub at https://github.com/sabifo4/LUCA-divtimes (ref. 107 ), and other custom scripts can be found in our figshare repository at https://doi.org/10.6084/m9.figshare.24428659 (ref. 106 ).

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Acknowledgements

Our research is funded by the John Templeton Foundation (62220 to P.C.J.D., N.L., T.M.L., D.P., G.A.S., T.A.W. and Z.Y.; the opinions expressed in this publication are those of the authors and do not necessarily reflect the views of the John Templeton Foundation), Biotechnology and Biological Sciences Research Council (BB/T012773/1 to P.C.J.D. and Z.Y.; BB/T012951/1 to Z.Y.), by the European Research Council under the European Union’s Horizon 2020 research and innovation programme (947317 ASymbEL to A.S.; 714774, GENECLOCKS to G.J.S.), Leverhulme Trust (RF-2022-167 to P.C.J.D.), Gordon and Betty Moore Foundation (GBMF9741 to T.A.W., D.P., P.C.J.D., A.S. and G.J.S.; GBMF9346 to A.S.), Royal Society (University Research Fellowship (URF) to T.A.W.), the Simons Foundation (735929LPI to A.S.) and the University of Bristol (University Research Fellowship (URF) to D.P.).

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Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK

Edmund R. R. Moody, Sandra Álvarez-Carretero, Holly C. Betts, Davide Pisani & Philip C. J. Donoghue

Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, Den Burg, The Netherlands

Tara A. Mahendrarajah, Nina Dombrowski & Anja Spang

Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath, UK

James W. Clark

Department of Biological Physics, Eötvös University, Budapest, Hungary

Lénárd L. Szánthó

MTA-ELTE ‘Lendulet’ Evolutionary Genomics Research Group, Budapest, Hungary

Lénárd L. Szánthó & Gergely J. Szöllősi

Institute of Evolution, HUN-REN Center for Ecological Research, Budapest, Hungary

Global Systems Institute, University of Exeter, Exeter, UK

Richard A. Boyle, Stuart Daines & Timothy M. Lenton

Department of Earth Sciences, University College London, London, UK

Xi Chen & Graham A. Shields

Department of Genetics, Evolution and Environment, University College London, London, UK

Nick Lane & Ziheng Yang

Model-Based Evolutionary Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan

Gergely J. Szöllősi

Department of Evolutionary & Population Biology, Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands

Bristol Palaeobiology Group, School of Biological Sciences, University of Bristol, Bristol, UK

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Contributions

The project was conceived and designed by P.C.J.D., T.M.L., D.P., G.J.S., A.S. and T.A.W. Dating analyses were performed by H.C.B., J.W.C., S.Á.-C., P.J.C.D. and E.R.R.M. T.A.M., N.D. and E.R.R.M. performed single-copy orthologue analysis for species-tree inference. L.L.S., G.J.S., T.A.W. and E.R.R.M. performed reconciliation analysis. E.R.R.M. performed homologous gene family annotation, sequence, alignment, gene tree inference and sensitivity tests. E.R.R.M., A.S. and T.A.W. performed metabolic analysis and interpretation. T.M.L., S.D. and R.A.B. provided biogeochemical interpretation. E.R.R.M., T.M.L., A.S., T.A.W., D.P. and P.J.C.D. drafted the article to which all authors (including X.C., N.L., Z.Y. and G.A.S.) contributed.

Corresponding authors

Correspondence to Edmund R. R. Moody , Davide Pisani , Tom A. Williams , Timothy M. Lenton or Philip C. J. Donoghue .

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Nature Ecology & Evolution thanks Aaron Goldman and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Peer reviewer reports are available.

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Extended data

Extended data fig. 1 comparison of the mean divergence times and confidence intervals estimated for the two duplicates of luca under each timetree inference analysis..

Black dots refer to estimated mean divergence times for analyses without cross-bracing, stars are used to identify those under cross-bracing and triangles for estimated upper and lower confidence intervals. Straight lines are used to link mean divergence time estimates across the various inference analyses we carried out, while dashed lines are used to link the estimated confidence intervals. The node label for the driver node is “248”, while it is “368” for the mirror node, as shown in the title of each graph. Coloured stars and triangles are used to identify which LUCA time estimates were inferred under the same cross-braced analysis for the driver-mirror nodes (that is, equal time and CI estimates). Black dots and triangles are used to identify those inferred when cross-bracing was not enabled (that is, different time and CI estimates). -Abbreviations. “GBM”: Geometric Brownian motion relaxed-clock model; “ILN”: Independent-rate log-normal relaxed-clock model; “conc, cb” dots/triangles: results under cross-bracing A when the concatenated dataset was analysed under GBM (red) and ILN (blue); “conc, fosscb”: results under cross-bracing B when the concatenated dataset was analysed under GBM (orange) and ILN (cyan); “part, cb” dots/triangles: results under cross-bracing A when the partitioned dataset was analysed under GBM (pink) and ILN (purple); “part, fosscb”: results under cross-bracing B when the concatenated dataset was analysed under GBM (light green) and ILN (grey); black dots and triangles: results when cross-bracing was not enabled for both concatenated and partitioned datasets.

Extended Data Fig. 2 Comparison of the posterior time estimates and confidence intervals for the two duplicates of LUCA inferred under the main calibration strategy cross-bracing A with the concatenated dataset and with the datasets for the three additional sensitivity analyses.

Dots refer to estimated mean divergence times and triangles to estimated 2.5% and 97.5% quantiles. Straight lines are used to link the mean divergence times estimated in the same analysis under the two different relaxed-clock models (GBM and ILN). Labels in the x axis are informative about the clock model under which the analysis ran and the type of analysis we carried (see abbreviations below). Coloured dots are used to identify which time estimates were inferred when using the same dataset and strategy under GBM and ILN, while triangles refer to the corresponding upper and lower quantiles for the 95% confidence interval. -Abbreviations. “GBM”: Geometric Brownian motion relaxed-clock model; “ILN”: Independent-rate log-normal relaxed-clock model; “main-conc”: results obtained with the concatenated dataset analysed in our main analyses under cross-bracing A; “ATP/EF/Leu/SRP/Tyr”: results obtained when using each gene alignment separately; “noATP/noEF/noLeu/noSRP/noTyr”: results obtained when using concatenated alignments without the gene alignment mentioned in the label as per the “leave-one-out” strategy; “main-bsinbv”: results obtained with the concatenated dataset analysed in our main analyses when using branch lengths, Hessian, and gradient calculated under a more complex substitution model to infer divergence times.

Extended Data Fig. 3 Maximum Likelihood species tree.

The Maximum Likelihood tree inferred across three independent runs, under the best fitting model (according to BIC: LG + F + G + C60) from a concatenation of 57 orthologous proteins, support values are from 10,000 ultrafast bootstraps. Referred to as topology I in the main text. Tips coloured according to taxonomy: Euryarchaeota (teal), DPANN (purple), Asgardarchaeota (cyan), TACK (blue), Gracilicutes (orange), Terrabacteria (red), DST (brown), CPR (green).

Extended Data Fig. 4 Maximum Likelihood tree for focal reconciliation analysis.

Maximum Likelihood tree (topology II in the main text), where DPANN is constrained to be sister to all other Archaea, and CPR is sister to Chloroflexi. Tips coloured according to taxonomy: Euryarchaeota (teal), DPANN (purple), Asgardarchaeota (cyan), TACK (blue), Gracilicutes (orange), Terrabacteria (red), DST (brown), CPR (green). AU topology test, P = 0.517, this is a one-sided statistical test.

Extended Data Fig. 5 The relationship between the number of KO gene families encoded on a genome and its size.

LOESS regression of the number of KOs per sampled genome against the genome size in megabases. We used the inferred relationship for modern prokaryotes to estimate LUCA’s genome size based on reconstructed KO gene family content, as described in the main text. Shaded area represents the 95% confidence interval.

Extended Data Fig. 6 The relationship between the number of KO gene families encoded on a genome and the total number of protein-coding genes.

LOESS regression of the number of KOs per sampled genome against the number of proteins encoded for per sampled genome. We used the inferred relationship for modern prokaryotes to estimate the total number of protein-coding genes encoded by LUCA based on reconstructed KO gene family content, as described in the main text. Shaded area represents the 95% confidence interval.

Supplementary information

Supplementary information.

Supplementary Notes and Figs. 1–10.

Reporting Summary

Peer review file, supplementary data 1.

This table contains the results of the reconciliations for each gene family. KEGG_ko is the KEGG orthology ID; arc_domain_prop is the proportion of the sampled Archaea; bac_domain_prop is the proportion of the sampled bacteria; gene refers to gene name, description and enzyme code; map refers to the different KEGG maps of which this KEGG gene family is a component; pathway is a text description of the metabolic pathways of which these genes are a component; alignment_length refers to the length of the alignment in amino acids; highest_COG_cat refers to the number of sequences placed in the most frequent COG category; difference_1st_and_2nd is the difference between the most frequent COG category and the second most frequent COG category; categories is the number of different COG categories assigned to this KEGG gene family; COG_freq is the proportion of the sequences placed in the most frequent COG category; COG_cat is the most frequent COG functional category; Archaea is the number of archaeal sequences sampled in the gene family; Bacteria is the number of bacterial sequences sampled in the gene family; alternative_COGs is the number of alternative COG gene families assigned across this KEGG orthologous gene family; COG_perc is the proportion of the most frequent COG ID assigned to this KEGG gene family; COG is the COG ID of the most frequenty COG assigned to this gene family; COG_NAME is the description of the most frequent COG ID assigned to this gene family; COG_TAG is the symbol associated with the most frequent COG gene familiy; sequences is the total number of sequences assigned to this gene family; Arc_prop is the proportion of Archaea that make up this gene family; Bac_prop is the proportion of Bacteria that make up this gene family; constrained_median is the median probability (PP) that this gene was present in LUCA from our reconciliation under the focal constrained tree search across the 5 independent bootstrap distribution reconciliations; ML_median is the median PP of the gene family being present in LUCA with gene tree bootstrap distributions against the ML species-tree topology across the 15 independent bootstrap distribution reconciliations; MEAN_OF_MEDIANS is the mean value across the constrained and ML PP results; RANGE_OF_MEDIANS is the range of the PPs for the constrained and ML topology PPs for LUCA; Probable_and_sampling_threshold_met is our most stringent category of gene families inferred in LUCA with 0.75 + PP and a sampling requirement of 1% met in both Archaea and Bacteria; Possible_and_sampling_threshold_met is a threshold of 0.50 + PP and sampling both domains; probable is simply 0.75 + PP; and possible is 0.50 + PP.

Supplementary Data 2

PP for COGs. This table contains the results for the reconciliations of COG-based gene family clustering against the constrained focal species-tree topology. Columns are named similarly to Supplementary Data 1 but each row is a different COG family. The column Modal_KEGG_ko refers to the most frequent KEGG gene family in which a given COG is found; sequences_in_modal_KEGG refers to the number of sequences in the most frequent KEGG gene family.

Supplementary Data 3

Module completeness. Estimated pathway completeness for KEGG metabolic modules (with a completeness greater than zero in at least one confidence threshold) using Anvi’o’s stepwise pathway completeness 48 . Module_name is the name of the module; module_category is the broader category into which the module falls; module_subcategory is a more specific category; possible_anvio includes the gene families with a median PP ≥ 0.50; probable_anvio related to gene families PP ≥ 0.75; and _ws refers to the sampling requirement being met (presence in at least 1% of the sampled Archaea and Bacteria).

Supplementary Data 4

Marker gene metadata for all markers checked during marker gene curation, including the initial 59 single-copy marker genes used in species-tree inference (see Methods ). Data include marker gene set provenance, marker gene name, marker gene description, presence in different marker gene sets 49 , 50 , 51 , 52 , 53 , 54 , 55 , 56 , 57 , 58 , and presence in Archaea and Bacteria. When available, marker genes are matched with their arCOG, TIGR, and COG ID and their respective occurrence across different taxonomic sets is quantified.

Supplementary Data 5

The ratio of duplications, transfers and losses in relation to the total number of copies for the deep ancestral nodes: the LUCA, archaeal (LACA) and bacterial (LBCA) common ancestors, and the average (mean) and 95th percentile.

Supplementary Data 6

Spreadsheet containing a list of the estimated divergence times for all timetree inferences carried out and the corresponding results of the MCMC diagnostics. Tabs Divtimes_GBM-allnodes and Divtimes_ILN-allnodes represent a list of the estimated divergence times (Ma) for all nodes under the 12 inference analyses we ran under GBM and ILN, respectively. Tabs Divtimes_GBM-highlighted and Divtimes_ILN-highlighted represent a list of the estimated divergence times (Ma) for selected nodes ordered according to their mirrored nodes under the 12 inference analyses we ran under GBM and ILN, respectively. Each of the tabs MCMCdiagn_prior, MCMCdiagn_postGBM and MCMCdiagn_postILN contains the statistical results of the MCMC diagnostics we ran for each inference analysis. Note that, despite the analyses carried out when sampling from the prior could have only been done three times (that is, data are not used, and thus only once under each calibration strategy was enough), we repeated them with each dataset regardless. In other words, results for (1) ‘concatenated + cross-bracing A’ and ‘partitioned + cross-bracing A’; (2) ‘concatenated + without cross-bracing’ and ‘partitioned + without cross-bracing’; and (3) ‘concatenated + cross-bracing B’ and ‘partitioned + cross-bracing B’ would be equivalent, respectively. For tabs 1–4, part represents partitioned dataset; conc, concatenated dataset; cb, cross-bracing A; notcb, without cross-bracing; fosscb, cross-bracing B; mean_t, mean posterior time estimate; 2.5%q, 2.5% quantile of the posterior time density for a given node; and 97.5%q, 97.5% quantile of the posterior time density for a given node. For tabs 5–7, med. num. samples collected per chain represents median of the total amount of samples collected per chain; min. num. samples collected per chain, minimum number of samples collected per chain; max. num. samples collected per chain, minimum number of samples collected per chain; num. samples used to calculate stats, number of samples collected by all chains that passed the filters that were used to calculate the tail-ESS, bulk-ESS and R-hat values. For tail-ESS, we report the median, minimum, and maximum tail-ESS values; all larger than 100 as required for assuming reliable parameter estimates. For bulk-ESS, we report the median, minimum and maximum bulk-ESS values; all larger than 100 as required for assuming reliable parameter estimates. For R-hat, minimum and maximum values reported, all smaller than 1.05 as required to assume good mixing.

Supplementary Data 7

Spreadsheet containing a list of the posterior time estimates for LUCA obtained under the main calibration strategy cross-bracing A with the concatenated dataset and with the datasets for the three additional sensitivity analyses. The first column ‘label’ contains the node number for both the driver and mirror nodes for LUCA (the latter includes the term -dup in the label). Columns mean_t, 2.5%q, and 97.5%q refer to the estimated mean divergence times, and the 2.5%/97.5% quantiles of the posterior time density for the corresponding node. Main-conc, refers to results obtained with the concatenated dataset analysed in our main analyses under cross-bracing A; ATP/EF/Leu/SRP/Tyr, results obtained when using each gene alignment separately; noATP/noEF/noLeu/noSRP/noTyr, results obtained when using concatenated alignments without the gene alignment mentioned in the label as per the leave-one-out strategy; main-bsinbv, results obtained with the concatenated dataset analysed in our main analyses when using branch lengths, Hessian and gradient calculated under a more complex substitution model to infer divergence times.

Supplementary Data 8

Spreadsheet containing a list of the estimated divergence times for all timetree inferences carried out for the sensitivity analyses and the corresponding results for the MCMC diagnostics. Tabs Divtimes_GBM-allnodes and Divtimes_ILN-allnodes represent a list of the estimated divergence times (Ma) for all nodes under the 11 inference analyses we ran under GBM and ILN when testing the impact on divergence times estimation when (1) analysing each gene alignment individually, (2) following a leave-one-out strategy, and (3) using the branch lengths, Hessian and gradient estimated under a more complex model for timetree inference (bsinBV approach). Tabs Divtimes_GBM-highlighted and Divtimes_ILN-highlighted represent a list of the estimated divergence times (Ma) for selected nodes ordered according to their mirrored nodes we ran under GBM and ILN for the sensitivity analyses (we also included the results with the main concatenated dataset for reference). Each of tabs MCMCdiagn_prior, MCMCdiagn_postGBM and MCMCdiagn_postILN contains the statistical results of the MCMC diagnostics we ran for the sensitivity analyses. Note that, despite the analyses carried out when sampling from the prior could have only been done once for each different tree topology (that is, data are not used, only topological changes may affect the resulting marginal densities), we ran them with each dataset regardless as part of our pipeline. For tabs 1–4, main-conc represents results obtained with the concatenated dataset analysed in our main analyses under cross-bracing A; ATP/EF/Leu/SRP/Tyr, results obtained when using each gene alignment separately; noATP/noEF/noLeu/noSRP/noTyr, results obtained when using concatenated alignments without the gene alignment mentioned in the label as per the leave-one-out strategy; main-bsinbv, results obtained with the concatenated dataset analysed in our main analyses when using branch lengths, Hessian and gradient calculated under a more complex substitution model to infer divergence times; mean_t, mean posterior time estimate; 2.5%q, 2.5% quantile of the posterior time density for a given node; and 97.5%q, 97.5% quantile of the posterior time density for a given node. For tabs 5–7, med. num. samples collected per chain represents the median of the total amount of samples collected per chain; min. num. samples collected per chain, minimum number of samples collected per chain; max. num. samples collected per chain, minimum number of samples collected per chain; num. samples used to calculate stats, number of samples collected by all chains that passed the filters that were used to calculate the tail-ESS, bulk-ESS and R-hat values. For tail-ESS, we report the median, minimum and maximum tail-ESS values; all larger than 100 as required for assuming reliable parameter estimates. For bulk-ESS, we report the median, minimum and maximum bulk-ESS values; all larger than 100 as required for assuming reliable parameter estimates. For R-hat, minimum and maximum values are reported, all smaller than 1.05 as required to assume good mixing.

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Moody, E.R.R., Álvarez-Carretero, S., Mahendrarajah, T.A. et al. The nature of the last universal common ancestor and its impact on the early Earth system. Nat Ecol Evol (2024). https://doi.org/10.1038/s41559-024-02461-1

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DOI : https://doi.org/10.1038/s41559-024-02461-1

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