1
|
Kawakatsu M, Kessinger TA, Plotkin JB. A mechanistic model of gossip, reputations, and cooperation. Proc Natl Acad Sci U S A 2024; 121:e2400689121. [PMID: 38717858 PMCID: PMC11098103 DOI: 10.1073/pnas.2400689121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 04/12/2024] [Indexed: 05/18/2024] Open
Abstract
Social reputations facilitate cooperation: those who help others gain a good reputation, making them more likely to receive help themselves. But when people hold private views of one another, this cycle of indirect reciprocity breaks down, as disagreements lead to the perception of unjustified behavior that ultimately undermines cooperation. Theoretical studies often assume population-wide agreement about reputations, invoking rapid gossip as an endogenous mechanism for reaching consensus. However, the theory of indirect reciprocity lacks a mechanistic description of how gossip actually generates consensus. Here, we develop a mechanistic model of gossip-based indirect reciprocity that incorporates two alternative forms of gossip: exchanging information with randomly selected peers or consulting a single gossip source. We show that these two forms of gossip are mathematically equivalent under an appropriate transformation of parameters. We derive an analytical expression for the minimum amount of gossip required to reach sufficient consensus and stabilize cooperation. We analyze how the amount of gossip necessary for cooperation depends on the benefits and costs of cooperation, the assessment rule (social norm), and errors in reputation assessment, strategy execution, and gossip transmission. Finally, we show that biased gossip can either facilitate or hinder cooperation, depending on the direction and magnitude of the bias. Our results contribute to the growing literature on cooperation facilitated by communication, and they highlight the need to study strategic interactions coupled with the spread of social information.
Collapse
Affiliation(s)
- Mari Kawakatsu
- Department of Biology, University of Pennsylvania, Philadelphia, PA19104
- Center for Mathematical Biology, University of Pennsylvania, Philadelphia, PA19104
| | | | - Joshua B. Plotkin
- Department of Biology, University of Pennsylvania, Philadelphia, PA19104
- Center for Mathematical Biology, University of Pennsylvania, Philadelphia, PA19104
| |
Collapse
|
2
|
Meyer DH, Schumacher B. Aging clocks based on accumulating stochastic variation. Nat Aging 2024:10.1038/s43587-024-00619-x. [PMID: 38724736 DOI: 10.1038/s43587-024-00619-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 03/28/2024] [Indexed: 05/15/2024]
Abstract
Aging clocks have provided one of the most important recent breakthroughs in the biology of aging, and may provide indicators for the effectiveness of interventions in the aging process and preventive treatments for age-related diseases. The reproducibility of accurate aging clocks has reinvigorated the debate on whether a programmed process underlies aging. Here we show that accumulating stochastic variation in purely simulated data is sufficient to build aging clocks, and that first-generation and second-generation aging clocks are compatible with the accumulation of stochastic variation in DNA methylation or transcriptomic data. We find that accumulating stochastic variation is sufficient to predict chronological and biological age, indicated by significant prediction differences in smoking, calorie restriction, heterochronic parabiosis and partial reprogramming. Although our simulations may not explicitly rule out a programmed aging process, our results suggest that stochastically accumulating changes in any set of data that have a ground state at age zero are sufficient for generating aging clocks.
Collapse
Affiliation(s)
- David H Meyer
- Institute for Genome Stability in Aging and Disease, University Hospital and University of Cologne, Cologne, Germany.
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.
| | - Björn Schumacher
- Institute for Genome Stability in Aging and Disease, University Hospital and University of Cologne, Cologne, Germany.
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.
| |
Collapse
|
3
|
Heins C, Millidge B, Da Costa L, Mann RP, Friston KJ, Couzin ID. Collective behavior from surprise minimization. Proc Natl Acad Sci U S A 2024; 121:e2320239121. [PMID: 38630721 PMCID: PMC11046639 DOI: 10.1073/pnas.2320239121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 03/08/2024] [Indexed: 04/19/2024] Open
Abstract
Collective motion is ubiquitous in nature; groups of animals, such as fish, birds, and ungulates appear to move as a whole, exhibiting a rich behavioral repertoire that ranges from directed movement to milling to disordered swarming. Typically, such macroscopic patterns arise from decentralized, local interactions among constituent components (e.g., individual fish in a school). Preeminent models of this process describe individuals as self-propelled particles, subject to self-generated motion and "social forces" such as short-range repulsion and long-range attraction or alignment. However, organisms are not particles; they are probabilistic decision-makers. Here, we introduce an approach to modeling collective behavior based on active inference. This cognitive framework casts behavior as the consequence of a single imperative: to minimize surprise. We demonstrate that many empirically observed collective phenomena, including cohesion, milling, and directed motion, emerge naturally when considering behavior as driven by active Bayesian inference-without explicitly building behavioral rules or goals into individual agents. Furthermore, we show that active inference can recover and generalize the classical notion of social forces as agents attempt to suppress prediction errors that conflict with their expectations. By exploring the parameter space of the belief-based model, we reveal nontrivial relationships between the individual beliefs and group properties like polarization and the tendency to visit different collective states. We also explore how individual beliefs about uncertainty determine collective decision-making accuracy. Finally, we show how agents can update their generative model over time, resulting in groups that are collectively more sensitive to external fluctuations and encode information more robustly.
Collapse
Affiliation(s)
- Conor Heins
- Department of Collective Behaviour, Max Planck Institute of Animal Behavior, KonstanzD-78457, Germany
- Centre for the Advanced Study of Collective Behaviour, University of Konstanz, KonstanzD-78457, Germany
- Department of Biology, University of Konstanz, KonstanzD-78457, Germany
- VERSES Research Lab, Los Angeles, CA90016
| | - Beren Millidge
- Medical Research Council Brain Networks Dynamics Unit, University of Oxford, OxfordOX1 3TH, United Kingdom
| | - Lancelot Da Costa
- VERSES Research Lab, Los Angeles, CA90016
- Department of Mathematics, Imperial College London, LondonSW7 2AZ, United Kingdom
- Wellcome Centre for Human Neuroimaging, University College London, LondonWC1N 3AR, United Kingdom
| | - Richard P. Mann
- Department of Statistics, School of Mathematics, University of Leeds, LeedsLS2 9JT, United Kingdom
| | - Karl J. Friston
- VERSES Research Lab, Los Angeles, CA90016
- Wellcome Centre for Human Neuroimaging, University College London, LondonWC1N 3AR, United Kingdom
| | - Iain D. Couzin
- Department of Collective Behaviour, Max Planck Institute of Animal Behavior, KonstanzD-78457, Germany
- Centre for the Advanced Study of Collective Behaviour, University of Konstanz, KonstanzD-78457, Germany
- Department of Biology, University of Konstanz, KonstanzD-78457, Germany
| |
Collapse
|
4
|
Milocco L, Uller T. Utilizing developmental dynamics for evolutionary prediction and control. Proc Natl Acad Sci U S A 2024; 121:e2320413121. [PMID: 38530898 PMCID: PMC10998628 DOI: 10.1073/pnas.2320413121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 02/20/2024] [Indexed: 03/28/2024] Open
Abstract
Understanding, predicting, and controlling the phenotypic consequences of genetic and environmental change is essential to many areas of fundamental and applied biology. In evolutionary biology, the generative process of development is a major source of organismal evolvability that constrains or facilitates adaptive change by shaping the distribution of phenotypic variation that selection can act upon. While the complex interactions between genetic and environmental factors during development may appear to make it impossible to infer the consequences of perturbations, the persistent observation that many perturbations result in similar phenotypes indicates that there is a logic to what variation is generated. Here, we show that a general representation of development as a dynamical system can reveal this logic. We build a framework that allows predicting the phenotypic effects of perturbations, and conditions for when the effects of perturbations of different origins are concordant. We find that this concordance is explained by two generic features of development, namely the dynamical dependence of the phenotype on itself and the fact that all perturbations must affect the developmental process to have an effect on the phenotype. We apply our theoretical framework to classical models of development and show that it can be used to predict the evolutionary response to selection using information of plasticity and to accelerate evolution in a desired direction. The framework we introduce provides a way to quantitatively interchange perturbations, opening an avenue of perturbation design to control the generation of variation.
Collapse
Affiliation(s)
| | - Tobias Uller
- Department of Biology, Lund University, 223 62Lund, Sweden
| |
Collapse
|
5
|
Sheng A, Su Q, Wang L, Plotkin JB. Strategy evolution on higher-order networks. Nat Comput Sci 2024; 4:274-284. [PMID: 38622347 DOI: 10.1038/s43588-024-00621-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 03/12/2024] [Indexed: 04/17/2024]
Abstract
Cooperation is key to prosperity in human societies. Population structure is well understood as a catalyst for cooperation, where research has focused on pairwise interactions. But cooperative behaviors are not simply dyadic, and they often involve coordinated behavior in larger groups. Here we develop a framework to study the evolution of behavioral strategies in higher-order population structures, which include pairwise and multi-way interactions. We provide an analytical treatment of when cooperation will be favored by higher-order interactions, accounting for arbitrary spatial heterogeneity and nonlinear rewards for cooperation in larger groups. Our results indicate that higher-order interactions can act to promote the evolution of cooperation across a broad range of networks, in public goods games. Higher-order interactions consistently provide an advantage for cooperation when interaction hyper-networks feature multiple conjoined communities. Our analysis provides a systematic account of how higher-order interactions modulate the evolution of prosocial traits.
Collapse
Affiliation(s)
- Anzhi Sheng
- Center for Systems and Control, College of Engineering, Peking University, Beijing, China
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Qi Su
- Department of Automation, Shanghai Jiao Tong University, Shanghai, China.
- Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai, China.
- Shanghai Engineering Research Center of Intelligent Control and Management, Shanghai, China.
| | - Long Wang
- Center for Systems and Control, College of Engineering, Peking University, Beijing, China.
- Center for Multi-Agent Research, Institute for Artificial Intelligence, Peking University, Beijing, China.
| | - Joshua B Plotkin
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA.
- Center for Mathematical Biology, University of Pennsylvania, Philadelphia, PA, USA.
| |
Collapse
|
6
|
Paczkó M, Vörös D, Szabó P, Jékely G, Szathmáry E, Szilágyi A. A neural network-based model framework for cell-fate decisions and development. Commun Biol 2024; 7:323. [PMID: 38486083 PMCID: PMC10940658 DOI: 10.1038/s42003-024-05985-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 02/28/2024] [Indexed: 03/18/2024] Open
Abstract
Gene regulatory networks (GRNs) fulfill the essential function of maintaining the stability of cellular differentiation states by sustaining lineage-specific gene expression, while driving the progression of development. However, accounting for the relative stability of intermediate differentiation stages and their divergent trajectories remains a major challenge for models of developmental biology. Here, we develop an empirical data-based associative GRN model (AGRN) in which regulatory networks store multilineage stage-specific gene expression profiles as associative memory patterns. These networks are capable of responding to multiple instructive signals and, depending on signal timing and identity, can dynamically drive the differentiation of multipotent cells toward different cell state attractors. The AGRN dynamics can thus generate diverse lineage-committed cell populations in a robust yet flexible manner, providing an attractor-based explanation for signal-driven cell fate decisions during differentiation and offering a readily generalizable modelling tool that can be applied to a wide variety of cell specification systems.
Collapse
Affiliation(s)
- Mátyás Paczkó
- Institute of Evolution, HUN-REN Centre for Ecological Research, Konkoly-Thege M. út 29-33, 1121, Budapest, Hungary
- Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117, Budapest, Hungary
| | - Dániel Vörös
- Institute of Evolution, HUN-REN Centre for Ecological Research, Konkoly-Thege M. út 29-33, 1121, Budapest, Hungary
- Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117, Budapest, Hungary
| | - Péter Szabó
- Institute of Evolution, HUN-REN Centre for Ecological Research, Konkoly-Thege M. út 29-33, 1121, Budapest, Hungary
| | - Gáspár Jékely
- Living Systems Institute, University of Exeter, Stocker Road 4QD, EX4, Exeter, UK
| | - Eörs Szathmáry
- Institute of Evolution, HUN-REN Centre for Ecological Research, Konkoly-Thege M. út 29-33, 1121, Budapest, Hungary.
- Center for the Conceptual Foundations of Science, Parmenides Foundation, Hindenburgstr. 15, 82343, Pöcking, Germany.
- Department of Plant Systematics, Ecology and Theoretical Biology, Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117, Budapest, Hungary.
| | - András Szilágyi
- Institute of Evolution, HUN-REN Centre for Ecological Research, Konkoly-Thege M. út 29-33, 1121, Budapest, Hungary
| |
Collapse
|
7
|
Twomey CR, Brainard DH, Plotkin JB. History constrains the evolution of efficient color naming, enabling historical inference. Proc Natl Acad Sci U S A 2024; 121:e2313603121. [PMID: 38416682 DOI: 10.1073/pnas.2313603121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 12/16/2023] [Indexed: 03/01/2024] Open
Abstract
Color naming in natural languages is not arbitrary: It reflects efficient partitions of perceptual color space [T. Regier, P. Kay, N. Khetarpal, Proc. Natl. Acad. Sci. U.S.A. 104, 1436-1441 (2007)] modulated by the relative needs to communicate about different colors [C. Twomey, G. Roberts, D. Brainard, J. Plotkin, Proc. Natl. Acad. Sci. U.S.A. 118, e2109237118 (2021)]. These psychophysical and communicative constraints help explain why languages around the world have remarkably similar, but not identical, mappings of colors to color terms. Languages converge on a small set of efficient representations.But languages also evolve, and the number of terms in a color vocabulary may change over time. Here we show that history, i.e. the existence of an antecedent color vocabulary, acts as a nonadaptive constraint that biases the choice of efficient solution as a language transitions from a vocabulary of size [Formula: see text] to [Formula: see text] terms. Moreover, as efficient vocabularies evolve to include more terms they explore a smaller fraction of all possible efficient vocabularies compared to equally sized vocabularies constructed de novo. This path dependence of the cultural evolution of color naming presents an opportunity. Historical constraints can be used to reconstruct ancestral color vocabularies, allowing us to answer long-standing questions about the evolutionary sequences of color words, and enabling us to draw inferences from phylogenetic patterns of language change.
Collapse
Affiliation(s)
- Colin R Twomey
- Data Driven Discovery Initiative, University of Pennsylvania, Philadelphia, PA 19104
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104
| | - David H Brainard
- Department of Psychology, University of Pennsylvania, Philadelphia, PA 19104
| | - Joshua B Plotkin
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104
| |
Collapse
|
8
|
Stewart AJ, Arechar AA, Rand DG, Plotkin JB. The distorting effects of producer strategies: Why engagement does not reveal consumer preferences for misinformation. Proc Natl Acad Sci U S A 2024; 121:e2315195121. [PMID: 38412133 DOI: 10.1073/pnas.2315195121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 01/17/2024] [Indexed: 02/29/2024] Open
Abstract
A great deal of empirical research has examined who falls for misinformation and why. Here, we introduce a formal game-theoretic model of engagement with news stories that captures the strategic interplay between (mis)information consumers and producers. A key insight from the model is that observed patterns of engagement do not necessarily reflect the preferences of consumers. This is because producers seeking to promote misinformation can use strategies that lead moderately inattentive readers to engage more with false stories than true ones-even when readers prefer more accurate over less accurate information. We then empirically test people's preferences for accuracy in the news. In three studies, we find that people strongly prefer to click and share news they perceive as more accurate-both in a general population sample, and in a sample of users recruited through Twitter who had actually shared links to misinformation sites online. Despite this preference for accurate news-and consistent with the predictions of our model-we find markedly different engagement patterns for articles from misinformation versus mainstream news sites. Using 1,000 headlines from 20 misinformation and 20 mainstream news sites, we compare Facebook engagement data with 20,000 accuracy ratings collected in a survey experiment. Engagement with a headline is negatively correlated with perceived accuracy for misinformation sites, but positively correlated with perceived accuracy for mainstream sites. Taken together, these theoretical and empirical results suggest that consumer preferences cannot be straightforwardly inferred from empirical patterns of engagement.
Collapse
Affiliation(s)
- Alexander J Stewart
- School of Mathematics and Statistics, University of St Andrews, St Andrews KY16 9SS, United Kingdom
| | - Antonio A Arechar
- División de Economía, Center for Research and Teaching in Economics, Centro de Investigación y Docencia Económicas, Aguascalientes, MX 20314
- Sloan School of Management, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - David G Rand
- Sloan School of Management, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Joshua B Plotkin
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104
| |
Collapse
|
9
|
McGrath KM, Russell SJ, Fer E, Garmendia E, Hosgel A, Baltrus DA, Kaçar B. Fitness benefits of a synonymous substitution in an ancient EF-Tu gene depend on the genetic background. J Bacteriol 2024; 206:e0032923. [PMID: 38289064 PMCID: PMC10882980 DOI: 10.1128/jb.00329-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 01/05/2024] [Indexed: 02/13/2024] Open
Abstract
Synonymous mutations are changes to DNA sequence, which occur within translated genes but which do not affect the protein sequence. Although often referred to as silent mutations, evidence suggests that synonymous mutations can affect gene expression, mRNA stability, and even translation efficiency. A collection of both experimental and bioinformatic data has shown that synonymous mutations can impact cell phenotype, yet less is known about the molecular mechanisms and potential of beneficial or adaptive effects of such changes within evolved populations. Here, we report a beneficial synonymous mutation acquired via experimental evolution in an essential gene variant encoding the translation elongation factor protein EF-Tu. We demonstrate that this particular synonymous mutation increases EF-Tu mRNA and protein levels as well as global polysome abundance on RNA transcripts. Although presence of the synonymous mutation is clearly causative of such changes, we also demonstrate that fitness benefits are highly contingent on other potentiating mutations present within the genetic background in which the mutation arose. Our results underscore the importance of beneficial synonymous mutations, especially those that affect levels of proteins that are key for cellular processes.IMPORTANCEThis study explores the degree to which synonymous mutations in essential genes can influence adaptation in bacteria. An experimental system whereby an Escherichia coli strain harboring an engineered translation protein elongation factor-Tu (EF-Tu) was subjected to laboratory evolution. We find that a synonymous mutation acquired on the gene encoding for EF-Tu is conditionally beneficial for bacterial fitness. Our findings provide insight into the importance of the genetic background when a synonymous substitution is favored by natural selection and how such changes have the potential to impact evolution when critical cellular processes are involved.
Collapse
Affiliation(s)
- Kaitlyn M. McGrath
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, USA
- School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Steven J. Russell
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Evrim Fer
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Microbial Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Eva Garmendia
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Ali Hosgel
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - David A. Baltrus
- School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Betül Kaçar
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| |
Collapse
|
10
|
Mallick S, Micco A, Mah M, Ringbauer H, Lazaridis I, Olalde I, Patterson N, Reich D. The Allen Ancient DNA Resource (AADR) a curated compendium of ancient human genomes. Sci Data 2024; 11:182. [PMID: 38341426 PMCID: PMC10858950 DOI: 10.1038/s41597-024-03031-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 01/31/2024] [Indexed: 02/12/2024] Open
Abstract
More than two hundred papers have reported genome-wide data from ancient humans. While the raw data for the vast majority are fully publicly available testifying to the commitment of the paleogenomics community to open data, formats for both raw data and meta-data differ. There is thus a need for uniform curation and a centralized, version-controlled compendium that researchers can download, analyze, and reference. Since 2019, we have been maintaining the Allen Ancient DNA Resource (AADR), which aims to provide an up-to-date, curated version of the world's published ancient human DNA data, represented at more than a million single nucleotide polymorphisms (SNPs) at which almost all ancient individuals have been assayed. The AADR has gone through six public releases at the time of writing and review of this manuscript, and crossed the threshold of >10,000 individuals with published genome-wide ancient DNA data at the end of 2022. This note is intended as a citable descriptor of the AADR.
Collapse
Affiliation(s)
- Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Howard Hughes Medical Institute, Boston, MA, 02115, USA.
| | - Adam Micco
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Boston, MA, 02115, USA
| | - Matthew Mah
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Boston, MA, 02115, USA
| | - Harald Ringbauer
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
- Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany
| | - Iosif Lazaridis
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Iñigo Olalde
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- BIOMICs Research Group, University of the Basque Country, 01006, Vitoria-Gasteiz, Spain
| | - Nick Patterson
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Howard Hughes Medical Institute, Boston, MA, 02115, USA.
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA.
| |
Collapse
|
11
|
Ringbauer H, Huang Y, Akbari A, Mallick S, Olalde I, Patterson N, Reich D. Accurate detection of identity-by-descent segments in human ancient DNA. Nat Genet 2024; 56:143-151. [PMID: 38123640 PMCID: PMC10786714 DOI: 10.1038/s41588-023-01582-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 10/20/2023] [Indexed: 12/23/2023]
Abstract
Long DNA segments shared between two individuals, known as identity-by-descent (IBD), reveal recent genealogical connections. Here we introduce ancIBD, a method for identifying IBD segments in ancient human DNA (aDNA) using a hidden Markov model and imputed genotype probabilities. We demonstrate that ancIBD accurately identifies IBD segments >8 cM for aDNA data with an average depth of >0.25× for whole-genome sequencing or >1× for 1240k single nucleotide polymorphism capture data. Applying ancIBD to 4,248 ancient Eurasian individuals, we identify relatives up to the sixth degree and genealogical connections between archaeological groups. Notably, we reveal long IBD sharing between Corded Ware and Yamnaya groups, indicating that the Yamnaya herders of the Pontic-Caspian Steppe and the Steppe-related ancestry in various European Corded Ware groups share substantial co-ancestry within only a few hundred years. These results show that detecting IBD segments can generate powerful insights into the growing aDNA record, both on a small scale relevant to life stories and on a large scale relevant to major cultural-historical events.
Collapse
Affiliation(s)
- Harald Ringbauer
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA.
| | - Yilei Huang
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Bioinformatics Group, Institute of Computer Science, Universität Leipzig, Leipzig, Germany
| | - Ali Akbari
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Iñigo Olalde
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- BIOMICs Research Group, University of the Basque Country, Vitoria-Gasteiz, Spain
- Ikerbasque-Basque Foundation of Science, Bilbao, Spain
| | - Nick Patterson
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - David Reich
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA.
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
12
|
Higgins WC, Savalei V, Polito V, Ross RM. Validation of the reading the mind in the eyes test requires an interpretable factor model. Proc Natl Acad Sci U S A 2023; 120:e2303706120. [PMID: 38109524 PMCID: PMC10756292 DOI: 10.1073/pnas.2303706120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2023] Open
Affiliation(s)
- Wendy C. Higgins
- School of Psychological Sciences, Macquarie University, North Ryde, NSW2109, Australia
| | - Victoria Savalei
- Department of Psychology, University of British Colombia, Vancouver, BC V6T 1Z4, Canada
| | - Vince Polito
- School of Psychological Sciences, Macquarie University, North Ryde, NSW2109, Australia
| | - Robert M. Ross
- Department of Philosophy, Macquarie University, North Ryde, NSW2109, Australia
| |
Collapse
|
13
|
Bustamante LA, Oshinowo T, Lee JR, Tong E, Burton AR, Shenhav A, Cohen JD, Daw ND. Effort Foraging Task reveals positive correlation between individual differences in the cost of cognitive and physical effort in humans. Proc Natl Acad Sci U S A 2023; 120:e2221510120. [PMID: 38064507 PMCID: PMC10723129 DOI: 10.1073/pnas.2221510120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 10/26/2023] [Indexed: 12/17/2023] Open
Abstract
Effort-based decisions, in which people weigh potential future rewards against effort costs required to achieve those rewards involve both cognitive and physical effort, though the mechanistic relationship between them is not yet understood. Here, we use an individual differences approach to isolate and measure the computational processes underlying effort-based decisions and test the association between cognitive and physical domains. Patch foraging is an ecologically valid reward rate maximization problem with well-developed theoretical tools. We developed the Effort Foraging Task, which embedded cognitive or physical effort into patch foraging, to quantify the cost of both cognitive and physical effort indirectly, by their effects on foraging choices. Participants chose between harvesting a depleting patch, or traveling to a new patch that was costly in time and effort. Participants' exit thresholds (reflecting the reward they expected to receive by harvesting when they chose to travel to a new patch) were sensitive to cognitive and physical effort demands, allowing us to quantify the perceived effort cost in monetary terms. The indirect sequential choice style revealed effort-seeking behavior in a minority of participants (preferring high over low effort) that has apparently been missed by many previous approaches. Individual differences in cognitive and physical effort costs were positively correlated, suggesting that these are perceived and processed in common. We used canonical correlation analysis to probe the relationship of task measures to self-reported affect and motivation, and found correlations of cognitive effort with anxiety, cognitive function, behavioral activation, and self-efficacy, but no similar correlations with physical effort.
Collapse
Affiliation(s)
- Laura A. Bustamante
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ08544
- Department of Psychological and Brain Sciences, Washington University in Saint Louis, Saint Louis, MO63130
| | - Temitope Oshinowo
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ08544
| | - Jeremy R. Lee
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ08544
| | - Elizabeth Tong
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ08544
| | - Allison R. Burton
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ08544
| | - Amitai Shenhav
- Department of Cognitive, Linguistic, and Psychological Sciences, Brown University, Providence, RI02912
- Carney Institute for Brain Science, Brown University, Providence, RI02906
| | - Jonathan D. Cohen
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ08544
| | - Nathaniel D. Daw
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ08544
| |
Collapse
|
14
|
Ke Q, Gates AJ, Barabási AL. A network-based normalized impact measure reveals successful periods of scientific discovery across discipline. Proc Natl Acad Sci U S A 2023; 120:e2309378120. [PMID: 37983494 PMCID: PMC10691329 DOI: 10.1073/pnas.2309378120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 10/19/2023] [Indexed: 11/22/2023] Open
Abstract
The impact of a scientific publication is often measured by the number of citations it receives from the scientific community. However, citation count is susceptible to well-documented variations in citation practices across time and discipline, limiting our ability to compare different scientific achievements. Previous efforts to account for citation variations often rely on a priori discipline labels of papers, assuming that all papers in a discipline are identical in their subject matter. Here, we propose a network-based methodology to quantify the impact of an article by comparing it with locally comparable research, thereby eliminating the discipline label requirement. We show that the developed measure is not susceptible to discipline bias and follows a universal distribution for all articles published in different years, offering an unbiased indicator for impact across time and discipline. We then use the indicator to identify science-wide high impact research in the past half century and quantify its temporal production dynamics across disciplines, helping us identifying breakthroughs from diverse, smaller disciplines, such as geosciences, radiology, and optics, as opposed to citation-rich biomedical sciences. Our work provides insights into the evolution of science and paves a way for fair comparisons of the impact of diverse contributions across many fields.
Collapse
Affiliation(s)
- Qing Ke
- School of Data Science, City University of Hong Kong, Hong Kong, China
| | - Alexander J. Gates
- School of Data Science, University of Virginia, Charlottesville, VA22904
| | - Albert-László Barabási
- Network Science Institute, Northeastern University, Boston, MA02115
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA02115
- Department of Network and Data Science, Central European University, Budapest1051, Hungary
| |
Collapse
|
15
|
Nelson JO, Kumon T, Yamashita YM. rDNA magnification is a unique feature of germline stem cells. Proc Natl Acad Sci U S A 2023; 120:e2314440120. [PMID: 37967216 PMCID: PMC10666004 DOI: 10.1073/pnas.2314440120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 10/16/2023] [Indexed: 11/17/2023] Open
Abstract
Ribosomal DNA (rDNA) encodes ribosomal RNA and exists as tandem repeats of hundreds of copies in the eukaryotic genome to meet the high demand of ribosome biogenesis. Tandemly repeated DNA elements are inherently unstable; thus, mechanisms must exist to maintain rDNA copy number (CN), in particular in the germline that continues through generations. A phenomenon called rDNA magnification was discovered over 50 y ago in Drosophila as a process that recovers the rDNA CN on chromosomes that harbor minimal CN. Our recent studies indicated that rDNA magnification is the mechanism to maintain rDNA CN under physiological conditions to counteract spontaneous CN loss that occurs during aging. Our previous studies that explored the mechanism of rDNA magnification implied that asymmetric division of germline stem cells (GSCs) may be particularly suited to achieve rDNA magnification. However, it remains elusive whether GSCs are the unique cell type that undergoes rDNA magnification or differentiating germ cells are also capable of magnification. In this study, we provide empirical evidence that suggests that rDNA magnification operates uniquely in GSCs, but not in differentiating germ cells. We further provide computer simulation that suggests that rDNA magnification is only achievable through asymmetric GSC divisions. We propose that despite known plasticity and transcriptomic similarity between GSCs and differentiating germ cells, GSCs' unique ability to divide asymmetrically serves a critical role of maintaining rDNA CN through generations, supporting germline immortality.
Collapse
Affiliation(s)
- Jonathan O Nelson
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142
- HHMI, Chevy Chase, MD 20815
| | - Tomohiro Kumon
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142
- HHMI, Chevy Chase, MD 20815
| | - Yukiko M Yamashita
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142
- HHMI, Chevy Chase, MD 20815
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142
| |
Collapse
|
16
|
Mahendrarajah TA, Moody ERR, Schrempf D, Szánthó LL, Dombrowski N, Davín AA, Pisani D, Donoghue PCJ, Szöllősi GJ, Williams TA, Spang A. ATP synthase evolution on a cross-braced dated tree of life. Nat Commun 2023; 14:7456. [PMID: 37978174 PMCID: PMC10656485 DOI: 10.1038/s41467-023-42924-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 10/25/2023] [Indexed: 11/19/2023] Open
Abstract
The timing of early cellular evolution, from the divergence of Archaea and Bacteria to the origin of eukaryotes, is poorly constrained. The ATP synthase complex is thought to have originated prior to the Last Universal Common Ancestor (LUCA) and analyses of ATP synthase genes, together with ribosomes, have played a key role in inferring and rooting the tree of life. We reconstruct the evolutionary history of ATP synthases using an expanded taxon sampling set and develop a phylogenetic cross-bracing approach, constraining equivalent speciation nodes to be contemporaneous, based on the phylogenetic imprint of endosymbioses and ancient gene duplications. This approach results in a highly resolved, dated species tree and establishes an absolute timeline for ATP synthase evolution. Our analyses show that the divergence of ATP synthase into F- and A/V-type lineages was a very early event in cellular evolution dating back to more than 4 Ga, potentially predating the diversification of Archaea and Bacteria. Our cross-braced, dated tree of life also provides insight into more recent evolutionary transitions including eukaryogenesis, showing that the eukaryotic nuclear and mitochondrial lineages diverged from their closest archaeal (2.67-2.19 Ga) and bacterial (2.58-2.12 Ga) relatives at approximately the same time, with a slightly longer nuclear stem-lineage.
Collapse
Affiliation(s)
- Tara A Mahendrarajah
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, AB Den Burg, The Netherlands
| | - Edmund R R Moody
- Bristol Palaeobiology Group, School of Biological Sciences, University of Bristol, BS8 1TQ, Bristol, UK
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, BS8 1TQ, Bristol, UK
| | - Dominik Schrempf
- Department Biological Physics, Eötvös University, Pázmány P. stny. 1A., H-1117, Budapest, Hungary
- MTA-ELTE "Lendulet" Evolutionary Genomics Research Group, Pázmány P. stny. 1A., H-1117, Budapest, Hungary
| | - Lénárd L Szánthó
- Department Biological Physics, Eötvös University, Pázmány P. stny. 1A., H-1117, Budapest, Hungary
- MTA-ELTE "Lendulet" Evolutionary Genomics Research Group, Pázmány P. stny. 1A., H-1117, Budapest, Hungary
- Institute of Evolution, Centre for Ecological Research, Karolina ut 29, H-1113, Budapest, Hungary
| | - Nina Dombrowski
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, AB Den Burg, The Netherlands
| | - Adrián A Davín
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Davide Pisani
- Bristol Palaeobiology Group, School of Biological Sciences, University of Bristol, BS8 1TQ, Bristol, UK
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, BS8 1TQ, Bristol, UK
| | - Philip C J Donoghue
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, BS8 1TQ, Bristol, UK
| | - Gergely J Szöllősi
- Department Biological Physics, Eötvös University, Pázmány P. stny. 1A., H-1117, Budapest, Hungary
- MTA-ELTE "Lendulet" Evolutionary Genomics Research Group, Pázmány P. stny. 1A., H-1117, Budapest, Hungary
- Model-Based Evolutionary Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Tom A Williams
- Bristol Palaeobiology Group, School of Biological Sciences, University of Bristol, BS8 1TQ, Bristol, UK.
| | - Anja Spang
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, AB Den Burg, The Netherlands.
- Department of Evolutionary & Population Biology, Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands.
| |
Collapse
|
17
|
Zheng J, Mallon J, Lammers A, Rados T, Litschel T, Moody ERR, Ramirez-Diaz DA, Schmid A, Williams TA, Bisson-Filho AW, Garner E. Salactin, a dynamically unstable actin homolog in Haloarchaea. mBio 2023; 14:e0227223. [PMID: 37966230 PMCID: PMC10746226 DOI: 10.1128/mbio.02272-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 10/05/2023] [Indexed: 11/16/2023] Open
Abstract
IMPORTANCE Protein filaments play important roles in many biological processes. We discovered an actin homolog in halophilic archaea, which we call Salactin. Just like the filaments that segregate DNA in eukaryotes, Salactin grows out of the cell poles towards the middle, and then quickly depolymerizes, a behavior known as dynamic instability. Furthermore, we see that Salactin affects the distribution of DNA in daughter cells when cells are grown in low-phosphate media, suggesting Salactin filaments might be involved in segregating DNA when the cell has only a few copies of the chromosome.
Collapse
Affiliation(s)
- Jenny Zheng
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA
| | - John Mallon
- Department of Biology, Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, Massachusetts, USA
| | - Alex Lammers
- Physiology Course, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
- Department of Biomedical Engineering, The Biological Design Center, Boston University, Boston, Massachusetts, USA
- The Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
| | - Theopi Rados
- Department of Biology, Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, Massachusetts, USA
| | - Thomas Litschel
- Physiology Course, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, USA
| | - Edmund R. R. Moody
- School of Earth Sciences, University of Bristol, Bristol, United Kingdom
| | - Diego A. Ramirez-Diaz
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Amy Schmid
- Department of Biology, Duke University, Durham, North Carolina, USA
- Center for Genomics and Computational Biology, Duke University, Durham, North Carolina, USA
| | - Tom A. Williams
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Alexandre W. Bisson-Filho
- Department of Biology, Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, Massachusetts, USA
| | - Ethan Garner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA
| |
Collapse
|
18
|
Cuevas-Zuviría B, Fer E, Adam ZR, Kaçar B. The modular biochemical reaction network structure of cellular translation. NPJ Syst Biol Appl 2023; 9:52. [PMID: 37884541 PMCID: PMC10603163 DOI: 10.1038/s41540-023-00315-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 10/12/2023] [Indexed: 10/28/2023] Open
Abstract
Translation is an essential attribute of all living cells. At the heart of cellular operation, it is a chemical information decoding process that begins with an input string of nucleotides and ends with the synthesis of a specific output string of peptides. The translation process is interconnected with gene expression, physiological regulation, transcription, and responses to signaling molecules, among other cellular functions. Foundational efforts have uncovered a wealth of knowledge about the mechanistic functions of the components of translation and their many interactions between them, but the broader biochemical connections between translation, metabolism and polymer biosynthesis that enable translation to occur have not been comprehensively mapped. Here we present a multilayer graph of biochemical reactions describing the translation, polymer biosynthesis and metabolism networks of an Escherichia coli cell. Intriguingly, the compounds that compose these three layers are distinctly aggregated into three modes regardless of their layer categorization. Multimodal mass distributions are well-known in ecosystems, but this is the first such distribution reported at the biochemical level. The degree distributions of the translation and metabolic networks are each likely to be heavy-tailed, but the polymer biosynthesis network is not. A multimodal mass-degree distribution indicates that the translation and metabolism networks are each distinct, adaptive biochemical modules, and that the gaps between the modes reflect evolved responses to the functional use of metabolite, polypeptide and polynucleotide compounds. The chemical reaction network of cellular translation opens new avenues for exploring complex adaptive phenomena such as percolation and phase changes in biochemical contexts.
Collapse
Affiliation(s)
- Bruno Cuevas-Zuviría
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
| | - Evrim Fer
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Zachary R Adam
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
- Department of Geosciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Betül Kaçar
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA.
| |
Collapse
|
19
|
Wong ML, Cleland CE, Arend D, Bartlett S, Cleaves HJ, Demarest H, Prabhu A, Lunine JI, Hazen RM. On the roles of function and selection in evolving systems. Proc Natl Acad Sci U S A 2023; 120:e2310223120. [PMID: 37844243 PMCID: PMC10614609 DOI: 10.1073/pnas.2310223120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 09/10/2023] [Indexed: 10/18/2023] Open
Abstract
Physical laws-such as the laws of motion, gravity, electromagnetism, and thermodynamics-codify the general behavior of varied macroscopic natural systems across space and time. We propose that an additional, hitherto-unarticulated law is required to characterize familiar macroscopic phenomena of our complex, evolving universe. An important feature of the classical laws of physics is the conceptual equivalence of specific characteristics shared by an extensive, seemingly diverse body of natural phenomena. Identifying potential equivalencies among disparate phenomena-for example, falling apples and orbiting moons or hot objects and compressed springs-has been instrumental in advancing the scientific understanding of our world through the articulation of laws of nature. A pervasive wonder of the natural world is the evolution of varied systems, including stars, minerals, atmospheres, and life. These evolving systems appear to be conceptually equivalent in that they display three notable attributes: 1) They form from numerous components that have the potential to adopt combinatorially vast numbers of different configurations; 2) processes exist that generate numerous different configurations; and 3) configurations are preferentially selected based on function. We identify universal concepts of selection-static persistence, dynamic persistence, and novelty generation-that underpin function and drive systems to evolve through the exchange of information between the environment and the system. Accordingly, we propose a "law of increasing functional information": The functional information of a system will increase (i.e., the system will evolve) if many different configurations of the system undergo selection for one or more functions.
Collapse
Affiliation(s)
- Michael L. Wong
- Earth and Planets Laboratory, Carnegie Institution for Science, Washington, DC20015
- Sagan Fellow, NASA Hubble Fellowship Program, Space Telescope Science Institute, Baltimore, MD21218
| | - Carol E. Cleland
- Department of Philosophy, University of Colorado, Boulder, CO80309
| | - Daniel Arend
- Department of Philosophy, University of Colorado, Boulder, CO80309
| | - Stuart Bartlett
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA91125
| | - H. James Cleaves
- Earth and Planets Laboratory, Carnegie Institution for Science, Washington, DC20015
- Earth Life Science Institute, Tokyo Institute of Technology, Tokyo152-8550, Japan
- Blue Marble Space Institute for Science, Seattle, WA98104
| | - Heather Demarest
- Department of Philosophy, University of Colorado, Boulder, CO80309
| | - Anirudh Prabhu
- Earth and Planets Laboratory, Carnegie Institution for Science, Washington, DC20015
| | | | - Robert M. Hazen
- Earth and Planets Laboratory, Carnegie Institution for Science, Washington, DC20015
| |
Collapse
|
20
|
Lundin NB, Brown JW, Johns BT, Jones MN, Purcell JR, Hetrick WP, O’Donnell BF, Todd PM. Neural evidence of switch processes during semantic and phonetic foraging in human memory. Proc Natl Acad Sci U S A 2023; 120:e2312462120. [PMID: 37824523 PMCID: PMC10589708 DOI: 10.1073/pnas.2312462120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 09/06/2023] [Indexed: 10/14/2023] Open
Abstract
Humans may retrieve words from memory by exploring and exploiting in "semantic space" similar to how nonhuman animals forage for resources in physical space. This has been studied using the verbal fluency test (VFT), in which participants generate words belonging to a semantic or phonetic category in a limited time. People produce bursts of related items during VFT, referred to as "clustering" and "switching." The strategic foraging model posits that cognitive search behavior is guided by a monitoring process which detects relevant declines in performance and then triggers the searcher to seek a new patch or cluster in memory after the current patch has been depleted. An alternative body of research proposes that this behavior can be explained by an undirected rather than strategic search process, such as random walks with or without random jumps to new parts of semantic space. This study contributes to this theoretical debate by testing for neural evidence of strategically timed switches during memory search. Thirty participants performed category and letter VFT during functional MRI. Responses were classified as cluster or switch events based on computational metrics of similarity and participant evaluations. Results showed greater hippocampal and posterior cerebellar activation during switching than clustering, even while controlling for interresponse times and linguistic distance. Furthermore, these regions exhibited ramping activity which increased during within-patch search leading up to switches. Findings support the strategic foraging model, clarifying how neural switch processes may guide memory search in a manner akin to foraging in patchy spatial environments.
Collapse
Affiliation(s)
- Nancy B. Lundin
- Department of Psychological and Brain Sciences, Indiana University, Bloomington, IN47405
- Program in Neuroscience, Indiana University, Bloomington, IN47405
- Department of Psychiatry and Behavioral Health, The Ohio State University, Columbus, OH43210
| | - Joshua W. Brown
- Department of Psychological and Brain Sciences, Indiana University, Bloomington, IN47405
- Program in Neuroscience, Indiana University, Bloomington, IN47405
- Cognitive Science Program, Indiana University, Bloomington, IN47405
| | - Brendan T. Johns
- Department of Psychology, McGill University, Montréal, QCH3A 1G1, Canada
| | - Michael N. Jones
- Department of Psychological and Brain Sciences, Indiana University, Bloomington, IN47405
- Cognitive Science Program, Indiana University, Bloomington, IN47405
| | - John R. Purcell
- Department of Psychological and Brain Sciences, Indiana University, Bloomington, IN47405
- Program in Neuroscience, Indiana University, Bloomington, IN47405
- Department of Psychiatry, Brain Health Institute, Rutgers University, Piscataway, NJ08854
| | - William P. Hetrick
- Department of Psychological and Brain Sciences, Indiana University, Bloomington, IN47405
- Program in Neuroscience, Indiana University, Bloomington, IN47405
- Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN46202
| | - Brian F. O’Donnell
- Department of Psychological and Brain Sciences, Indiana University, Bloomington, IN47405
- Program in Neuroscience, Indiana University, Bloomington, IN47405
- Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN46202
| | - Peter M. Todd
- Department of Psychological and Brain Sciences, Indiana University, Bloomington, IN47405
- Cognitive Science Program, Indiana University, Bloomington, IN47405
| |
Collapse
|
21
|
Cleaves HJ, Hystad G, Prabhu A, Wong ML, Cody GD, Economon S, Hazen RM. A robust, agnostic molecular biosignature based on machine learning. Proc Natl Acad Sci U S A 2023; 120:e2307149120. [PMID: 37748080 PMCID: PMC10576141 DOI: 10.1073/pnas.2307149120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 07/17/2023] [Indexed: 09/27/2023] Open
Abstract
The search for definitive biosignatures-unambiguous markers of past or present life-is a central goal of paleobiology and astrobiology. We used pyrolysis-gas chromatography coupled to mass spectrometry to analyze chemically disparate samples, including living cells, geologically processed fossil organic material, carbon-rich meteorites, and laboratory-synthesized organic compounds and mixtures. Data from each sample were employed as training and test subsets for machine-learning methods, which resulted in a model that can identify the biogenicity of both contemporary and ancient geologically processed samples with ~90% accuracy. These machine-learning methods do not rely on precise compound identification: Rather, the relational aspects of chromatographic and mass peaks provide the needed information, which underscores this method's utility for detecting alien biology.
Collapse
Affiliation(s)
- H. James Cleaves
- Earth and Planets Laboratory, Carnegie Institution for Science, Washington, DC20015
- Earth Life Science Institute, Tokyo Institute of Technology, Tokyo152-8550, Japan
- Blue Marble Space Institute for Science, Seattle, WA98104
| | - Grethe Hystad
- Department of Mathematics and Statistics, Purdue University Northwest, Hammond, IN46323
| | - Anirudh Prabhu
- Earth and Planets Laboratory, Carnegie Institution for Science, Washington, DC20015
| | - Michael L. Wong
- Earth and Planets Laboratory, Carnegie Institution for Science, Washington, DC20015
- Sagan Fellow, NASA Hubble Fellowship Program, Space Telescope Science Institute, Baltimore, MD21218
| | - George D. Cody
- Earth and Planets Laboratory, Carnegie Institution for Science, Washington, DC20015
| | - Sophia Economon
- Department of Earth and Planetary Sciences, Johns Hopkins University, Baltimore, MD21218
| | - Robert M. Hazen
- Earth and Planets Laboratory, Carnegie Institution for Science, Washington, DC20015
| |
Collapse
|
22
|
Clark JW, Hetherington AJ, Morris JL, Pressel S, Duckett JG, Puttick MN, Schneider H, Kenrick P, Wellman CH, Donoghue PCJ. Evolution of phenotypic disparity in the plant kingdom. Nat Plants 2023; 9:1618-1626. [PMID: 37666963 PMCID: PMC10581900 DOI: 10.1038/s41477-023-01513-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 08/07/2023] [Indexed: 09/06/2023]
Abstract
The plant kingdom exhibits diverse bodyplans, from single-celled algae to complex multicellular land plants, but it is unclear how this phenotypic disparity was achieved. Here we show that the living divisions comprise discrete clusters within morphospace, separated largely by reproductive innovations, the extinction of evolutionary intermediates and lineage-specific evolution. Phenotypic complexity correlates not with disparity but with ploidy history, reflecting the role of genome duplication in plant macroevolution. Overall, the plant kingdom exhibits a pattern of episodically increasing disparity throughout its evolutionary history that mirrors the evolutionary floras and reflects ecological expansion facilitated by reproductive innovations. This pattern also parallels that seen in the animal and fungal kingdoms, suggesting a general pattern for the evolution of multicellular bodyplans.
Collapse
Affiliation(s)
- James W Clark
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK.
- School of Biological Sciences, University of Bristol, Bristol, UK.
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath, UK.
| | - Alexander J Hetherington
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK.
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.
| | - Jennifer L Morris
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK
| | | | | | - Mark N Puttick
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath, UK
| | - Harald Schneider
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK
- The Natural History Museum, London, UK
- Center of Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, China
| | | | | | - Philip C J Donoghue
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK.
| |
Collapse
|
23
|
Brinkworth A, Green E, Li Y, Oyston J, Ruta M, Wills MA. Bird clades with less complex appendicular skeletons tend to have higher species richness. Nat Commun 2023; 14:5817. [PMID: 37726273 PMCID: PMC10509246 DOI: 10.1038/s41467-023-41415-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 08/30/2023] [Indexed: 09/21/2023] Open
Abstract
Species richness is strikingly uneven across taxonomic groups at all hierarchical levels, but the reasons for this heterogeneity are poorly understood. It is well established that morphological diversity (disparity) is decoupled from taxonomic diversity, both between clades and across geological time. Morphological complexity has been much less studied, but there is theory linking complexity with differential diversity across groups. Here we devise an index of complexity from the differentiation of the fore and hind limb pairs for a sample of 983 species of extant birds. We test the null hypothesis that this index of morphological complexity is uncorrelated with clade diversity, revealing a significant and negative correlation between the species richness of clades and the mean morphological complexity of those clades. Further, we find that more complex clades tend to occupy a smaller number of dietary and habitat niches, and that this proxy for greater ecological specialisation correlates with lower species richness. Greater morphological complexity in the appendicular skeleton therefore appears to hinder the generation and maintenance of species diversity. This may result from entrenchment into morphologies and ecologies that are less capable of yielding further diversity.
Collapse
Affiliation(s)
- Andrew Brinkworth
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath, BA2 7AZ, UK.
| | - Emily Green
- Joseph Banks Laboratories, Department of Life Sciences, University of Lincoln, Green Lane, Lincoln, LN6 7DL, UK
| | - Yimeng Li
- Nanjing Institute of Geology and Paleontology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Jack Oyston
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath, BA2 7AZ, UK
- Centre for Integrative Anatomy, Department of Cell and Developmental Biology, University College London, London, WC1E 6BT, UK
| | - Marcello Ruta
- Joseph Banks Laboratories, Department of Life Sciences, University of Lincoln, Green Lane, Lincoln, LN6 7DL, UK
| | - Matthew A Wills
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath, BA2 7AZ, UK
| |
Collapse
|
24
|
van der Lugt T, Barrett J, Chiribella G. Device-independent certification of indefinite causal order in the quantum switch. Nat Commun 2023; 14:5811. [PMID: 37726274 PMCID: PMC10509257 DOI: 10.1038/s41467-023-40162-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 07/14/2023] [Indexed: 09/21/2023] Open
Abstract
Quantum theory is compatible with scenarios in which the order of operations is indefinite. Experimental investigations of such scenarios, all of which have been based on a process known as the quantum switch, have provided demonstrations of indefinite causal order conditioned on assumptions on the devices used in the laboratory. But is a device-independent certification possible, similar to the certification of Bell nonlocality through the violation of Bell inequalities? Previous results have shown that the answer is negative if the switch is considered in isolation. Here, however, we present an inequality that can be used to device-independently certify indefinite causal order in the quantum switch in the presence of an additional spacelike-separated observer under an assumption asserting the impossibility of superluminal and retrocausal influences.
Collapse
Affiliation(s)
- Tein van der Lugt
- Department of Computer Science, University of Oxford, Wolfson Building, Parks Road, Oxford, OX1 3QD, United Kingdom.
| | - Jonathan Barrett
- Department of Computer Science, University of Oxford, Wolfson Building, Parks Road, Oxford, OX1 3QD, United Kingdom
- Perimeter Institute for Theoretical Physics, Waterloo, ON, N2L 2Y5, Canada
| | - Giulio Chiribella
- Department of Computer Science, University of Oxford, Wolfson Building, Parks Road, Oxford, OX1 3QD, United Kingdom.
- Perimeter Institute for Theoretical Physics, Waterloo, ON, N2L 2Y5, Canada.
- QICI Quantum Information and Computation Initiative, Department of Computer Science, The University of Hong Kong, Pokfulam Road, Hong Kong, Hong Kong.
| |
Collapse
|
25
|
Krause AJ, Sluijs A, van der Ploeg R, Lenton TM, Pogge von Strandmann PAE. Erratum: Publisher Correction: Enhanced clay formation key in sustaining the Middle Eocene Climatic Optimum. Nat Geosci 2023; 17:104. [PMID: 38223495 PMCID: PMC10783542 DOI: 10.1038/s41561-023-01280-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
[This corrects the article DOI: 10.1038/s41561-023-01234-y.].
Collapse
Affiliation(s)
| | - Appy Sluijs
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, The Netherlands
| | - Robin van der Ploeg
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, The Netherlands
- Shell Global Solutions International B.V., Amsterdam, The Netherlands
| | | | | |
Collapse
|
26
|
Koban L, Andrews-Hanna JR, Ives L, Wager TD, Arch JJ. Brain mediators of biased social learning of self-perception in social anxiety disorder. Transl Psychiatry 2023; 13:292. [PMID: 37660045 PMCID: PMC10475036 DOI: 10.1038/s41398-023-02587-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 08/12/2023] [Accepted: 08/15/2023] [Indexed: 09/04/2023] Open
Abstract
Social anxiety disorder (SAD) is characterized by an excessive fear of social evaluation and a persistently negative view of the self. Here we test the hypothesis that negative biases in brain responses and in social learning of self-related information contribute to the negative self-image and low self-esteem characteristic of SAD. Adult participants diagnosed with social anxiety (N = 21) and matched controls (N = 23) rated their performance and received social feedback following a stressful public speaking task. We investigated how positive versus negative social feedback altered self-evaluation and state self-esteem and used functional Magnetic Resonance Imaging (fMRI) to characterize brain responses to positive versus negative feedback. Compared to controls, participants with SAD updated their self-evaluation and state self-esteem significantly more based on negative compared to positive social feedback. Responses in the frontoparietal network correlated with and mirrored these behavioral effects, with greater responses to positive than negative feedback in non-anxious controls but not in participants with SAD. Responses to social feedback in the anterior insula and other areas mediated the effects of negative versus positive feedback on changes in self-evaluation. In non-anxious participants, frontoparietal brain areas may contribute to a positive social learning bias. In SAD, frontoparietal areas are less recruited overall and less attuned to positive feedback, possibly reflecting differences in attention allocation and cognitive regulation. More negatively biased brain responses and social learning could contribute to maintaining a negative self-image in SAD and other internalizing disorders, thereby offering important new targets for interventions.
Collapse
Affiliation(s)
- Leonie Koban
- Lyon Neuroscience Research Center (CRNL), CNRS, INSERM, Université Claude Bernard Lyon 1, Bron, France.
| | | | - Lindsay Ives
- Department of Psychology and Neuroscience, University of Colorado, Boulder, CO, USA
| | - Tor D Wager
- Department of Cognitive and Brain Sciences, Dartmouth College, Hanover, NH, USA
| | - Joanna J Arch
- Department of Psychology and Neuroscience, University of Colorado, Boulder, CO, USA
| |
Collapse
|
27
|
Pawar H, Rymbekova A, Cuadros-Espinoza S, Huang X, de Manuel M, van der Valk T, Lobon I, Alvarez-Estape M, Haber M, Dolgova O, Han S, Esteller-Cucala P, Juan D, Ayub Q, Bautista R, Kelley JL, Cornejo OE, Lao O, Andrés AM, Guschanski K, Ssebide B, Cranfield M, Tyler-Smith C, Xue Y, Prado-Martinez J, Marques-Bonet T, Kuhlwilm M. Ghost admixture in eastern gorillas. Nat Ecol Evol 2023; 7:1503-1514. [PMID: 37500909 PMCID: PMC10482688 DOI: 10.1038/s41559-023-02145-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 06/30/2023] [Indexed: 07/29/2023]
Abstract
Archaic admixture has had a substantial impact on human evolution with multiple events across different clades, including from extinct hominins such as Neanderthals and Denisovans into modern humans. In great apes, archaic admixture has been identified in chimpanzees and bonobos but the possibility of such events has not been explored in other species. Here, we address this question using high-coverage whole-genome sequences from all four extant gorilla subspecies, including six newly sequenced eastern gorillas from previously unsampled geographic regions. Using approximate Bayesian computation with neural networks to model the demographic history of gorillas, we find a signature of admixture from an archaic 'ghost' lineage into the common ancestor of eastern gorillas but not western gorillas. We infer that up to 3% of the genome of these individuals is introgressed from an archaic lineage that diverged more than 3 million years ago from the common ancestor of all extant gorillas. This introgression event took place before the split of mountain and eastern lowland gorillas, probably more than 40 thousand years ago and may have influenced perception of bitter taste in eastern gorillas. When comparing the introgression landscapes of gorillas, humans and bonobos, we find a consistent depletion of introgressed fragments on the X chromosome across these species. However, depletion in protein-coding content is not detectable in eastern gorillas, possibly as a consequence of stronger genetic drift in this species.
Collapse
Affiliation(s)
- Harvinder Pawar
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, Spain
| | - Aigerim Rymbekova
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Wien, Austria
| | | | - Xin Huang
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Wien, Austria
| | - Marc de Manuel
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, Spain
| | - Tom van der Valk
- Department of Bioinformatics and Genetics, Scilifelab, Swedish Museum of Natural History, Stockholm, Sweden
- Centre for Palaeogenetics, Stockholm, Sweden
| | - Irene Lobon
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, Spain
| | | | - Marc Haber
- Institute of Cancer and Genomic Sciences, University of Birmingham, Dubai, United Arab Emirates
| | - Olga Dolgova
- Integrative Genomics Lab, CIC bioGUNE-Centro de Investigación Cooperativa en Biociencias, Parque Científico Tecnológico de Bizkaia building 801A, Derio, Spain
| | - Sojung Han
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, Spain
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Wien, Austria
| | | | - David Juan
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, Spain
| | - Qasim Ayub
- Wellcome Sanger Institute, Hinxton, UK
- Monash University Malaysia Genomics Facility, School of Science, Monash University Malaysia, Selangor Darul Ehsan, Malaysia
| | | | - Joanna L Kelley
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, USA
| | - Omar E Cornejo
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, USA
| | - Oscar Lao
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, Spain
| | - Aida M Andrés
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Katerina Guschanski
- Animal Ecology, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
- Science for Life Laboratory, Uppsala, Sweden
| | | | - Mike Cranfield
- Gorilla Doctors, Karen C. Drayer Wildlife Health Center, One Health Institute, University of California Davis, School of Veterinary Medicine, Davis, CA, USA
| | | | - Yali Xue
- Wellcome Sanger Institute, Hinxton, UK
| | - Javier Prado-Martinez
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, Spain
- Wellcome Sanger Institute, Hinxton, UK
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, Spain.
- Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, Barcelona, Spain.
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, Barcelona, Spain.
| | - Martin Kuhlwilm
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, Spain.
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Wien, Austria.
| |
Collapse
|
28
|
de la Hamette AC, Kabel V, Castro-Ruiz E, Brukner Č. Quantum reference frames for an indefinite metric. Commun Phys 2023; 6:231. [PMID: 38665408 PMCID: PMC11041732 DOI: 10.1038/s42005-023-01344-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 08/10/2023] [Indexed: 04/28/2024]
Abstract
The current theories of quantum physics and general relativity on their own do not allow us to study situations in which the gravitational source is quantum. Here, we propose a strategy to determine the dynamics of objects in the presence of mass configurations in superposition, and hence an indefinite spacetime metric, using quantum reference frame (QRF) transformations. Specifically, we show that, as long as the mass configurations in the different branches are related via relative-distance-preserving transformations, one can use an extension of the current framework of QRFs to change to a frame in which the mass configuration becomes definite. Assuming covariance of dynamical laws under quantum coordinate transformations, this allows to use known physics to determine the dynamics. We apply this procedure to find the motion of a probe particle and the behavior of clocks near the mass configuration, and thus find the time dilation caused by a gravitating object in superposition. Comparison with other models shows that semi-classical gravity and gravitational collapse models do not obey the covariance of dynamical laws under quantum coordinate transformations.
Collapse
Affiliation(s)
- Anne-Catherine de la Hamette
- Vienna Center for Quantum Science and Technology (VCQ), Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria
- Institute for Quantum Optics and Quantum Information (IQOQI), Austrian Academy of Sciences, Boltzmanngasse 3, A-1090 Vienna, Austria
| | - Viktoria Kabel
- Vienna Center for Quantum Science and Technology (VCQ), Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria
- Institute for Quantum Optics and Quantum Information (IQOQI), Austrian Academy of Sciences, Boltzmanngasse 3, A-1090 Vienna, Austria
| | - Esteban Castro-Ruiz
- Institute for Theoretical Physics, ETH Zurich, Zurich, Switzerland
- Université Paris-Saclay, Inria, CNRS, LMF, 91190 Gif-sur-Yvette, France
| | - Časlav Brukner
- Vienna Center for Quantum Science and Technology (VCQ), Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria
- Institute for Quantum Optics and Quantum Information (IQOQI), Austrian Academy of Sciences, Boltzmanngasse 3, A-1090 Vienna, Austria
| |
Collapse
|
29
|
Zheng X, Dolde J, Cambria MC, Lim HM, Kolkowitz S. A lab-based test of the gravitational redshift with a miniature clock network. Nat Commun 2023; 14:4886. [PMID: 37573452 PMCID: PMC10423269 DOI: 10.1038/s41467-023-40629-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 08/03/2023] [Indexed: 08/14/2023] Open
Abstract
Einstein's theory of general relativity predicts that a clock at a higher gravitational potential will tick faster than an otherwise identical clock at a lower potential, an effect known as the gravitational redshift. Here we perform a laboratory-based, blinded test of the gravitational redshift using differential clock comparisons within an evenly spaced array of 5 atomic ensembles spanning a height difference of 1 cm. We measure a fractional frequency gradient of [ - 12.4 ± 0. 7(stat) ± 2. 5(sys)] × 10-19/cm, consistent with the expected redshift gradient of - 10.9 × 10-19/cm. Our results can also be viewed as relativistic gravitational potential difference measurements with sensitivity to mm scale changes in height on the surface of the Earth. These results highlight the potential of local-oscillator-independent differential clock comparisons for emerging applications of optical atomic clocks including geodesy, searches for new physics, gravitational wave detection, and explorations of the interplay between quantum mechanics and gravity.
Collapse
Affiliation(s)
- Xin Zheng
- Department of Physics, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Jonathan Dolde
- Department of Physics, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Matthew C Cambria
- Department of Physics, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Hong Ming Lim
- Department of Physics, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Shimon Kolkowitz
- Department of Physics, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- Department of Physics, University of California, Berkeley, CA, 94720, USA.
| |
Collapse
|
30
|
Krause AJ, Sluijs A, van der Ploeg R, Lenton TM, Pogge von Strandmann PAE. Enhanced clay formation key in sustaining the Middle Eocene Climatic Optimum. Nat Geosci 2023; 16:730-738. [PMID: 37564379 PMCID: PMC10409649 DOI: 10.1038/s41561-023-01234-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 06/26/2023] [Indexed: 08/12/2023]
Abstract
The Middle Eocene Climatic Optimum (around 40 million years ago) was a roughly 400,000-year-long global warming phase associated with an increase in atmospheric CO2 concentrations and deep-ocean acidification that interrupted the Eocene's long-term cooling trend. The unusually long duration, compared with early Eocene global warming phases, is puzzling as temperature-dependent silicate weathering should have provided a negative feedback, drawing down CO2 over this timescale. Here we investigate silicate weathering during this climate warming event by measuring lithium isotope ratios (reported as δ7Li), which are a tracer for silicate weathering processes, from a suite of open-ocean carbonate-rich sediments. We find a positive δ7Li excursion-the only one identified for a warming event so far -of ~3‰. Box model simulations support this signal to reflect a global shift from congruent weathering, with secondary mineral dissolution, to incongruent weathering, with secondary mineral formation. We surmise that, before the climatic optimum, there was considerable soil shielding of the continents. An increase in continental volcanism initiated the warming event, but it was sustained by an increase in clay formation, which sequestered carbonate-forming cations, short-circuiting the carbonate-silicate cycle. Clay mineral dynamics may play an important role in the carbon cycle for climatic events occurring over intermediate (i.e., 100,000 year) timeframes.
Collapse
Affiliation(s)
| | - Appy Sluijs
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, The Netherlands
| | - Robin van der Ploeg
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, The Netherlands
- Shell Global Solutions International B.V., Amsterdam, The Netherlands
| | | | | |
Collapse
|
31
|
Bittleston LS, Wolock CJ, Maeda J, Infante V, Ané JM, Pierce NE, Pringle A. Carnivorous Nepenthes Pitchers with Less Acidic Fluid House Nitrogen-Fixing Bacteria. Appl Environ Microbiol 2023; 89:e0081223. [PMID: 37338413 PMCID: PMC10370301 DOI: 10.1128/aem.00812-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 05/24/2023] [Indexed: 06/21/2023] Open
Abstract
Carnivorous pitcher plants are uniquely adapted to nitrogen limitation, using pitfall traps to acquire nutrients from insect prey. Pitcher plants in the genus Sarracenia may also use nitrogen fixed by bacteria inhabiting the aquatic microcosms of their pitchers. Here, we investigated whether species of a convergently evolved pitcher plant genus, Nepenthes, might also use bacterial nitrogen fixation as an alternative strategy for nitrogen capture. First, we constructed predicted metagenomes of pitcher organisms from three species of Singaporean Nepenthes using 16S rRNA sequence data and correlated predicted nifH abundances with metadata. Second, we used gene-specific primers to amplify and quantify the presence or absence of nifH directly from 102 environmental samples and identified potential diazotrophs with significant differential abundance in samples that also had positive nifH PCR tests. Third, we analyzed nifH in eight shotgun metagenomes from four additional Bornean Nepenthes species. Finally, we conducted an acetylene reduction assay using greenhouse-grown Nepenthes pitcher fluids to confirm nitrogen fixation is indeed possible within the pitcher habitat. Results show active acetylene reduction can occur in Nepenthes pitcher fluid. Variation in nifH from wild samples correlates with Nepenthes host species identity and pitcher fluid acidity. Nitrogen-fixing bacteria are associated with more neutral fluid pH, while endogenous Nepenthes digestive enzymes are most active at low fluid pH. We hypothesize Nepenthes species experience a trade-off in nitrogen acquisition; when fluids are acidic, nitrogen is primarily acquired via plant enzymatic degradation of insects, but when fluids are neutral, Nepenthes plants take up more nitrogen via bacterial nitrogen fixation. IMPORTANCE Plants use different strategies to obtain the nutrients that they need to grow. Some plants access their nitrogen directly from the soil, while others rely on microbes to access the nitrogen for them. Carnivorous pitcher plants generally trap and digest insect prey, using plant-derived enzymes to break down insect proteins and generate a large portion of the nitrogen that they subsequently absorb. In this study, we present results suggesting that bacteria living in the fluids formed by Nepenthes pitcher plants can fix nitrogen directly from the atmosphere, providing an alternative pathway for plants to access nitrogen. These nitrogen-fixing bacteria are only likely to be present when pitcher plant fluids are not strongly acidic. Interestingly, the plant's enzymes are known to be more active under strongly acidic conditions. We propose a potential trade-off where pitcher plants sometimes access nitrogen using their own enzymes to digest prey and at other times take advantage of bacterial nitrogen fixation.
Collapse
Affiliation(s)
- Leonora S. Bittleston
- Department of Biological Sciences, Boise State University, Boise, Idaho, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Charles J. Wolock
- Department of Biostatistics, University of Washington, Seattle, Washington, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Junko Maeda
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Valentina Infante
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Jean-Michel Ané
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Agronomy, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Naomi E. Pierce
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
- Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts, USA
| | - Anne Pringle
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Botany, University of Wisconsin—Madison, Madison, Wisconsin, USA
| |
Collapse
|
32
|
Dulberg Z, Dubey R, Berwian IM, Cohen JD. Having multiple selves helps learning agents explore and adapt in complex changing worlds. Proc Natl Acad Sci U S A 2023; 120:e2221180120. [PMID: 37399387 PMCID: PMC10334746 DOI: 10.1073/pnas.2221180120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 05/09/2023] [Indexed: 07/05/2023] Open
Abstract
Satisfying a variety of conflicting needs in a changing environment is a fundamental challenge for any adaptive agent. Here, we show that designing an agent in a modular fashion as a collection of subagents, each dedicated to a separate need, powerfully enhanced the agent's capacity to satisfy its overall needs. We used the formalism of deep reinforcement learning to investigate a biologically relevant multiobjective task: continually maintaining homeostasis of a set of physiologic variables. We then conducted simulations in a variety of environments and compared how modular agents performed relative to standard monolithic agents (i.e., agents that aimed to satisfy all needs in an integrated manner using a single aggregate measure of success). Simulations revealed that modular agents a) exhibited a form of exploration that was intrinsic and emergent rather than extrinsically imposed; b) were robust to changes in nonstationary environments, and c) scaled gracefully in their ability to maintain homeostasis as the number of conflicting objectives increased. Supporting analysis suggested that the robustness to changing environments and increasing numbers of needs were due to intrinsic exploration and efficiency of representation afforded by the modular architecture. These results suggest that the normative principles by which agents have adapted to complex changing environments may also explain why humans have long been described as consisting of "multiple selves."
Collapse
Affiliation(s)
- Zack Dulberg
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ08544
| | - Rachit Dubey
- Department of Computer Science, Princeton University, Princeton, NJ08544
| | - Isabel M. Berwian
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ08544
| | - Jonathan D. Cohen
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ08544
| |
Collapse
|
33
|
Clark SA, Vazquez A, Furiya K, Splattstoesser MK, Bashmail AK, Schwartz H, Russell M, Bhark SJ, Moreno OK, McGovern M, Owsley ER, Nelson TA, Sanchez EL, Delgado T. Rewiring of the Host Cell Metabolome and Lipidome during Lytic Gammaherpesvirus Infection Is Essential for Infectious-Virus Production. J Virol 2023; 97:e0050623. [PMID: 37191529 PMCID: PMC10308918 DOI: 10.1128/jvi.00506-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 04/20/2023] [Indexed: 05/17/2023] Open
Abstract
Oncogenic virus infections are estimated to cause ~15% of all cancers. Two prevalent human oncogenic viruses are members of the gammaherpesvirus family: Epstein-Barr virus (EBV) and Kaposi's sarcoma herpesvirus (KSHV). We use murine herpesvirus 68 (MHV-68), which shares significant homology with KSHV and EBV, as a model system to study gammaherpesvirus lytic replication. Viruses implement distinct metabolic programs to support their life cycle, such as increasing the supply of lipids, amino acids, and nucleotide materials necessary to replicate. Our data define the global changes in the host cell metabolome and lipidome during gammaherpesvirus lytic replication. Our metabolomics analysis found that MHV-68 lytic infection induces glycolysis, glutaminolysis, lipid metabolism, and nucleotide metabolism. We additionally observed an increase in glutamine consumption and glutamine dehydrogenase protein expression. While both glucose and glutamine starvation of host cells decreased viral titers, glutamine starvation led to a greater loss in virion production. Our lipidomics analysis revealed a peak in triacylglycerides early during infection and an increase in free fatty acids and diacylglyceride later in the viral life cycle. Furthermore, we observed an increase in the protein expression of multiple lipogenic enzymes during infection. Interestingly, pharmacological inhibitors of glycolysis or lipogenesis resulted in decreased infectious virus production. Taken together, these results illustrate the global alterations in host cell metabolism during lytic gammaherpesvirus infection, establish essential pathways for viral production, and recommend targeted mechanisms to block viral spread and treat viral induced tumors. IMPORTANCE Viruses are intracellular parasites which lack their own metabolism, so they must hijack host cell metabolic machinery in order to increase the production of energy, proteins, fats, and genetic material necessary to replicate. Using murine herpesvirus 68 (MHV-68) as a model system to understand how similar human gammaherpesviruses cause cancer, we profiled the metabolic changes that occur during lytic MHV-68 infection and replication. We found that MHV-68 infection of host cells increases glucose, glutamine, lipid, and nucleotide metabolic pathways. We also showed inhibition or starvation of glucose, glutamine, or lipid metabolic pathways results in an inhibition of virus production. Ultimately, targeting changes in host cell metabolism due to viral infection can be used to treat gammaherpesvirus-induced cancers and infections in humans.
Collapse
Affiliation(s)
- Sarah A. Clark
- Northwest University, Department of Biology, Kirkland, Washington, USA
| | - Angie Vazquez
- Seattle Pacific University, Department of Biology, Seattle, Washington, USA
| | - Kelsey Furiya
- Seattle Pacific University, Department of Biology, Seattle, Washington, USA
| | | | | | - Haleigh Schwartz
- Northwest University, Department of Biology, Kirkland, Washington, USA
| | - Makaiya Russell
- Seattle Pacific University, Department of Biology, Seattle, Washington, USA
| | - Shun-Je Bhark
- Seattle Pacific University, Department of Biology, Seattle, Washington, USA
| | - Osvaldo K. Moreno
- San Francisco State University, Department of Biology, San Francisco, California, USA
| | - Morgan McGovern
- Seattle Pacific University, Department of Biology, Seattle, Washington, USA
| | - Eric R. Owsley
- Seattle Pacific University, Department of Biology, Seattle, Washington, USA
| | - Timothy A. Nelson
- Seattle Pacific University, Department of Biology, Seattle, Washington, USA
| | - Erica L. Sanchez
- San Francisco State University, Department of Biology, San Francisco, California, USA
- University of Texas at Dallas, Department of Biological Sciences, Richardson, Texas, USA
| | - Tracie Delgado
- Seattle Pacific University, Department of Biology, Seattle, Washington, USA
- Northwest University, Department of Biology, Kirkland, Washington, USA
| |
Collapse
|
34
|
Abstract
Reputations provide a powerful mechanism to sustain cooperation, as individuals cooperate with those of good social standing. But how should someone's reputation be updated as we observe their social behavior, and when will a population converge on a shared norm for judging behavior? Here, we develop a mathematical model of cooperation conditioned on reputations, for a population that is stratified into groups. Each group may subscribe to a different social norm for assessing reputations and so norms compete as individuals choose to move from one group to another. We show that a group initially comprising a minority of the population may nonetheless overtake the entire population-especially if it adopts the Stern Judging norm, which assigns a bad reputation to individuals who cooperate with those of bad standing. When individuals do not change group membership, stratifying reputation information into groups tends to destabilize cooperation, unless individuals are strongly insular and favor in-group social interactions. We discuss the implications of our results for the structure of information flow in a population and for the evolution of social norms of judgment.
Collapse
Affiliation(s)
| | - Corina E. Tarnita
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ08544
| | - Joshua B. Plotkin
- Department of Biology, University of Pennsylvania, Philadelphia, PA19104
- Center for Mathematical Biology, University of Pennsylvania, Philadelphia, PA19104
| |
Collapse
|
35
|
Cosmides L, Barbato MT, Sznycer D, Labarca MÁ, Guzmán RA. Reply to Greene: No version of the dual process model can explain rational performance by people who made compromise moral judgments. Proc Natl Acad Sci U S A 2023; 120:e2220909120. [PMID: 37279262 DOI: 10.1073/pnas.2220909120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023] Open
Affiliation(s)
- Leda Cosmides
- Department of Psychological and Brain Sciences, Center for Evolutionary Psychology, University of California, Santa Barbara, CA 93106-9660
| | - María Teresa Barbato
- Centro de Investigación en Complejidad Social, Facultad de Gobierno, Universidad del Desarrollo, Santiago 7610658, Chile
| | - Daniel Sznycer
- Department of Psychology, Oklahoma Center for Evolutionary Analysis, Oklahoma State University, Stillwater, OK 74078-3064
| | - Miguel Ángel Labarca
- Department of Psychological and Brain Sciences, Center for Evolutionary Psychology, University of California, Santa Barbara, CA 93106-9660
| | - Ricardo Andrés Guzmán
- Centro de Investigación en Complejidad Social, Facultad de Gobierno, Universidad del Desarrollo, Santiago 7610658, Chile
| |
Collapse
|
36
|
Abstract
Ribosomal DNA (rDNA) loci contain hundreds of tandemly repeated copies of ribosomal RNA genes needed to support cellular viability. This repetitiveness makes it highly susceptible to copy number (CN) loss due to intrachromatid recombination between rDNA copies, threatening multigenerational maintenance of rDNA. How this threat is counteracted to avoid extinction of the lineage has remained unclear. Here, we show that the rDNA-specific retrotransposon R2 is essential for restorative rDNA CN expansion to maintain rDNA loci in the Drosophila male germline. The depletion of R2 led to defective rDNA CN maintenance, causing a decline in fecundity over generations and eventual extinction. We find that double-stranded DNA breaks created by the R2 endonuclease, a feature of R2's rDNA-specific retrotransposition, initiate the process of rDNA CN recovery, which relies on homology-dependent repair of the DNA break at rDNA copies. This study reveals that an active retrotransposon provides an essential function for its host, contrary to transposable elements' reputation as entirely selfish. These findings suggest that benefiting host fitness can be an effective selective advantage for transposable elements to offset their threat to the host, which may contribute to retrotransposons' widespread success throughout taxa.
Collapse
Affiliation(s)
- Jonathan O Nelson
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142
- HHMI, Cambridge, MA 02142
| | - Alyssa Slicko
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142
- HHMI, Cambridge, MA 02142
| | - Yukiko M Yamashita
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142
- HHMI, Cambridge, MA 02142
- Department of Biology, School of Science, Massachusetts Institute of Technology, Cambridge, MA 02142
| |
Collapse
|
37
|
Cornwallis CK, Svensson-Coelho M, Lindh M, Li Q, Stábile F, Hansson LA, Rengefors K. Single-cell adaptations shape evolutionary transitions to multicellularity in green algae. Nat Ecol Evol 2023; 7:889-902. [PMID: 37081145 PMCID: PMC10250200 DOI: 10.1038/s41559-023-02044-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 03/22/2023] [Indexed: 04/22/2023]
Abstract
The evolution of multicellular life has played a pivotal role in shaping biological diversity. However, we know surprisingly little about the natural environmental conditions that favour the formation of multicellular groups. Here we experimentally examine how key environmental factors (predation, nitrogen and water turbulence) combine to influence multicellular group formation in 35 wild unicellular green algae strains (19 Chlorophyta species). All environmental factors induced the formation of multicellular groups (more than four cells), but there was no evidence this was adaptive, as multicellularity (% cells in groups) was not related to population growth rate under any condition. Instead, population growth was related to extracellular matrix (ECM) around single cells and palmelloid formation, a unicellular life-cycle stage where two to four cells are retained within a mother-cell wall after mitosis. ECM production increased with nitrogen levels resulting in more cells being in palmelloids and higher rates of multicellular group formation. Examining the distribution of 332 algae species across 478 lakes monitored over 55 years, showed that ECM and nitrogen availability also predicted patterns of obligate multicellularity in nature. Our results highlight that adaptations of unicellular organisms to cope with environmental challenges may be key to understanding evolutionary routes to multicellular life.
Collapse
Affiliation(s)
| | | | - Markus Lindh
- Swedish Meteorological and Hydrological Institute, Västra Frölunda, Sweden
| | - Qinyang Li
- Department of Biology, Lund University, Lund, Sweden
| | | | | | | |
Collapse
|
38
|
Wilson DS, Madhavan G, Gelfand MJ, Hayes SC, Atkins PWB, Colwell RR. Multilevel cultural evolution: From new theory to practical applications. Proc Natl Acad Sci U S A 2023; 120:e2218222120. [PMID: 37036975 PMCID: PMC10120078 DOI: 10.1073/pnas.2218222120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023] Open
Abstract
Evolutionary science has led to many practical applications of genetic evolution but few practical uses of cultural evolution. This is because the entire study of evolution was gene centric for most of the 20th century, relegating the study and application of human cultural change to other disciplines. The formal study of human cultural evolution began in the 1970s and has matured to the point of deriving practical applications. We provide an overview of these developments and examples for the topic areas of complex systems science and engineering, economics and business, mental health and well-being, and global change efforts.
Collapse
Affiliation(s)
- David Sloan Wilson
- ProSocial World, Austin, TX 78738
- Department of Biological Sciences, Binghamton University, State University of New York, Binghamton, NY 13902
| | - Guru Madhavan
- National Academy of Engineering, Washington, DC 20001
| | | | - Steven C Hayes
- Department of Psychology, University of Nevada, Reno, NV 89557
| | - Paul W B Atkins
- ProSocial World, Austin, TX 78738
- Crawford School of Public Policy, Australian National University, Canberra ACT 0200, Australia
| | - Rita R Colwell
- Department of Cell Biology and Molecular Genetics, University of Maryland Institute for Advanced Computer Studies, University of Maryland, College Park, MD 20742
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205
| |
Collapse
|
39
|
Robertson CE, Pröllochs N, Schwarzenegger K, Pärnamets P, Van Bavel JJ, Feuerriegel S. Negativity drives online news consumption. Nat Hum Behav 2023; 7:812-822. [PMID: 36928780 DOI: 10.1038/s41562-023-01538-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 01/06/2023] [Indexed: 03/18/2023]
Abstract
Online media is important for society in informing and shaping opinions, hence raising the question of what drives online news consumption. Here we analyse the causal effect of negative and emotional words on news consumption using a large online dataset of viral news stories. Specifically, we conducted our analyses using a series of randomized controlled trials (N = 22,743). Our dataset comprises ~105,000 different variations of news stories from Upworthy.com that generated ∼5.7 million clicks across more than 370 million overall impressions. Although positive words were slightly more prevalent than negative words, we found that negative words in news headlines increased consumption rates (and positive words decreased consumption rates). For a headline of average length, each additional negative word increased the click-through rate by 2.3%. Our results contribute to a better understanding of why users engage with online media.
Collapse
Affiliation(s)
| | - Nicolas Pröllochs
- Department of Business and Economics, University of Giessen, Giessen, Germany
| | - Kaoru Schwarzenegger
- Department of Management, Technology and Economics, ETH Zurich, Zurich, Switzerland
| | - Philip Pärnamets
- Division of Psychology, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Jay J Van Bavel
- Department of Psychology, New York University, New York, NY, USA.
- Center for Neural Science, New York University, New York, NY, USA.
| | - Stefan Feuerriegel
- Department of Management, Technology and Economics, ETH Zurich, Zurich, Switzerland.
- LMU Munich School of Management, LMU Munich, Munich, Germany.
| |
Collapse
|
40
|
Kocher CD, Dill KA. Darwinian evolution as a dynamical principle. Proc Natl Acad Sci U S A 2023; 120:e2218390120. [PMID: 36881627 PMCID: PMC10089213 DOI: 10.1073/pnas.2218390120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 02/03/2023] [Indexed: 03/08/2023] Open
Abstract
Darwinian evolution (DE)-biology's powerful process of adaptation-is remarkably different from other known dynamical processes. It is antithermodynamic, driving away from equilibrium; it has persisted for 3.5 billion years; and its target, fitness, can seem like "Just So" stories. For insights, we make a computational model. In the Darwinian Evolution Machine (DEM) model, resource-driven duplication and competition operate inside a cycle of search/compete/choose. We find the following: 1) DE requires multiorganism coexistence for its long-term persistence and ability to cross fitness valleys. 2) DE is driven by resource dynamics, like booms and busts, not just by mutational change. And, 3) fitness ratcheting requires a mechanistic separation between variation and selection steps, perhaps explaining biology's use of separate polymers, DNA and proteins.
Collapse
Affiliation(s)
- Charles D. Kocher
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY11794
- Department of Physics and Astronomy, Stony Brook University, Stony Brook, NY11794
| | - Ken A. Dill
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY11794
- Department of Physics and Astronomy, Stony Brook University, Stony Brook, NY11794
- Department of Chemistry, Stony Brook University, Stony Brook, NY11794
| |
Collapse
|
41
|
Abstract
The goal of deliberation is to separate between options so that we can commit to one and leave the other behind. However, deliberation can, paradoxically, also form an association in memory between the chosen and unchosen options. Here, we consider this possibility and examine its consequences for how outcomes affect not only the value of the options we chose, but also, by association, the value of options we did not choose. In five experiments (total n = 612), including a preregistered experiment (n = 235), we found that the value assigned to unchosen options is inversely related to their chosen counterparts. Moreover, this inverse relationship was associated with participants' memory of the pairs they chose between. Our findings suggest that deciding between options does not end the competition between them. Deliberation binds choice options together in memory such that the learned value of one can affect the inferred value of the other.
Collapse
Affiliation(s)
- Natalie Biderman
- Department of Psychology and Mortimer B. Zuckerman Mind, Brain, Behavior Institute, Columbia University, New York, NY, USA.
| | - Daphna Shohamy
- Department of Psychology and Mortimer B. Zuckerman Mind, Brain, Behavior Institute, Columbia University, New York, NY, USA.
- The Kavli Institute for Brain Science, Columbia University, New York, NY, USA.
| |
Collapse
|
42
|
Dideriksen KB, Schmieg R, Zugenmaier M, Polzik ES. Room-temperature single-photon source with near-millisecond built-in memory. Nat Commun 2021; 12:3699. [PMID: 34140508 PMCID: PMC8211654 DOI: 10.1038/s41467-021-24033-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 05/28/2021] [Indexed: 11/26/2022] Open
Abstract
Non-classical photon sources are a crucial resource for distributed quantum networks. Photons generated from matter systems with memory capability are particularly promising, as they can be integrated into a network where each source is used on-demand. Among all kinds of solid state and atomic quantum memories, room-temperature atomic vapours are especially attractive due to their robustness and potential scalability. To-date room-temperature photon sources have been limited either in their memory time or the purity of the photonic state. Here we demonstrate a single-photon source based on room-temperature memory. Following heralded loading of the memory, a single photon is retrieved from it after a variable storage time. The single-photon character of the retrieved field is validated by the strong suppression of the two-photon component with antibunching as low as [Formula: see text]. Non-classical correlations between the heralding and the retrieved photons are maintained for up to [Formula: see text], more than two orders of magnitude longer than previously demonstrated with other room-temperature systems. Correlations sufficient for violating Bell inequalities exist for up to τBI = (0.15 ± 0.03) ms.
Collapse
Affiliation(s)
| | - Rebecca Schmieg
- Niels Bohr Institute, University of Copenhagen, Copenhagen Ø, Denmark
| | | | - Eugene S Polzik
- Niels Bohr Institute, University of Copenhagen, Copenhagen Ø, Denmark.
| |
Collapse
|
43
|
Chandru K, Jia TZ, Mamajanov I, Bapat N, Cleaves HJ. Prebiotic oligomerization and self-assembly of structurally diverse xenobiological monomers. Sci Rep 2020; 10:17560. [PMID: 33067516 PMCID: PMC7567815 DOI: 10.1038/s41598-020-74223-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Accepted: 09/22/2020] [Indexed: 02/07/2023] Open
Abstract
Prebiotic chemists often study how modern biopolymers, e.g., peptides and nucleic acids, could have originated in the primitive environment, though most contemporary biomonomers don't spontaneously oligomerize under mild conditions without activation or catalysis. However, life may not have originated using the same monomeric components that it does presently. There may be numerous non-biological (or "xenobiological") monomer types that were prebiotically abundant and capable of facile oligomerization and self-assembly. Many modern biopolymers degrade abiotically preferentially via processes which produce thermodynamically stable ring structures, e.g. diketopiperazines in the case of proteins and 2', 3'-cyclic nucleotide monophosphates in the case of RNA. This weakness is overcome in modern biological systems by kinetic control, but this need not have been the case for primitive systems. We explored here the oligomerization of a structurally diverse set of prebiotically plausible xenobiological monomers, which can hydrolytically interconvert between cyclic and acyclic forms, alone or in the presence of glycine under moderate temperature drying conditions. These monomers included various lactones, lactams and a thiolactone, which varied markedly in their stability, propensity to oligomerize and apparent modes of initiation, and the oligomeric products of some of these formed self-organized microscopic structures which may be relevant to protocell formation.
Collapse
Affiliation(s)
- Kuhan Chandru
- Space Science Center (ANGKASA), Institute of Climate Change, Level 3, Research Complex, National University of Malaysia, UKM, 43600, Bangi, Selangor, Malaysia.
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Technicka 5, 16628, Prague 6-Dejvice, Czech Republic.
| | - Tony Z Jia
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
- Blue Marble Space Institute for Science, 1001 4th Ave, Suite 3201, Seattle, WA, 98154, USA
| | - Irena Mamajanov
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Niraja Bapat
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
- Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune, Maharashtra, 411 008, India
| | - H James Cleaves
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
- Blue Marble Space Institute for Science, 1001 4th Ave, Suite 3201, Seattle, WA, 98154, USA
- Institute for Advanced Study, 1 Einstein Drive, Princeton, NJ, 08540, USA
| |
Collapse
|
44
|
Abstract
To date we know little about natural emotion word repertoires, and whether or how they are associated with emotional functioning. Principles from linguistics suggest that the richness or diversity of individuals' actively used emotion vocabularies may correspond with their typical emotion experiences. The current investigation measures active emotion vocabularies in participant-generated natural speech and examined their relationships to individual differences in mood, personality, and physical and emotional well-being. Study 1 analyzes stream-of-consciousness essays by 1,567 college students. Study 2 analyzes public blogs written by over 35,000 individuals. The studies yield consistent findings that emotion vocabulary richness corresponds broadly with experience. Larger negative emotion vocabularies correlate with more psychological distress and poorer physical health. Larger positive emotion vocabularies correlate with higher well-being and better physical health. Findings support theories linking language use and development with lived experience and may have future clinical implications pending further research.
Collapse
Affiliation(s)
- Vera Vine
- University of Pittsburgh, Pittsburgh, PA, USA.
| | | | | |
Collapse
|
45
|
Weinberger AB, Gallagher NM, Warren ZJ, English GA, Moghaddam FM, Green AE. Implicit pattern learning predicts individual differences in belief in God in the United States and Afghanistan. Nat Commun 2020; 11:4503. [PMID: 32908145 PMCID: PMC7481241 DOI: 10.1038/s41467-020-18362-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 08/13/2020] [Indexed: 11/11/2022] Open
Abstract
Most humans believe in a god, but many do not. Differences in belief have profound societal impacts. Anthropological accounts implicate bottom-up perceptual processes in shaping religious belief, suggesting that individual differences in these processes may help explain variation in belief. Here, in findings replicated across socio-religiously disparate samples studied in the U.S. and Afghanistan, implicit learning of patterns/order within visuospatial sequences (IL-pat) in a strongly bottom-up paradigm predict 1) stronger belief in an intervening/ordering god, and 2) increased strength-of-belief from childhood to adulthood, controlling for explicit learning and parental belief. Consistent with research implicating IL-pat as a basis of intuition, and intuition as a basis of belief, mediation models support a hypothesized effect pathway whereby IL-pat leads to intuitions of order which, in turn, lead to belief in ordering gods. The universality and variability of human IL-pat may thus contribute to the global presence and variability of religious belief.
Collapse
Affiliation(s)
- Adam B Weinberger
- Georgetown University, Washington, DC, 20057, USA.
- University of Pennsylvania, Philadelphia, PA, 19104, USA.
| | - Natalie M Gallagher
- Georgetown University, Washington, DC, 20057, USA
- Northwestern University, Evanston, IL, 60208, USA
| | - Zachary J Warren
- Georgetown University, Washington, DC, 20057, USA
- The Asia Foundation, 1779 Massachusetts Ave NW #815, Washington, DC, 20036, USA
| | - Gwendolyn A English
- Georgetown University, Washington, DC, 20057, USA
- ETH Zurich, 8092, Zurich, CH-8092, Switzerland
| | | | - Adam E Green
- Georgetown University, Washington, DC, 20057, USA.
| |
Collapse
|
46
|
Denervaud S, Fornari E, Yang XF, Hagmann P, Immordino-Yang MH, Sander D. An fMRI study of error monitoring in Montessori and traditionally-schooled children. NPJ Sci Learn 2020; 5:11. [PMID: 32699649 PMCID: PMC7367880 DOI: 10.1038/s41539-020-0069-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 06/05/2020] [Indexed: 06/11/2023]
Abstract
The development of error monitoring is central to learning and academic achievement. However, few studies exist on the neural correlates of children's error monitoring, and no studies have examined its susceptibility to educational influences. Pedagogical methods differ on how they teach children to learn from errors. Here, 32 students (aged 8-12 years) from high-quality Swiss traditional or Montessori schools performed a math task with feedback during fMRI. Although the groups' accuracies were similar, Montessori students skipped fewer trials, responded faster and showed more neural activity in right parietal and frontal regions involved in math processing. While traditionally-schooled students showed greater functional connectivity between the ACC, involved in error monitoring, and hippocampus following correct trials, Montessori students showed greater functional connectivity between the ACC and frontal regions following incorrect trials. The findings suggest that pedagogical experience influences the development of error monitoring and its neural correlates, with implications for neurodevelopment and education.
Collapse
Affiliation(s)
- Solange Denervaud
- Swiss Center for Affective Sciences (CISA), Campus Biotech, University of Geneva, 1202 Geneva, Switzerland
- Connectomics Lab, Department of Radiology, Lausanne University Hospital and University of Lausanne (CHUV-UNIL), 1011 Lausanne, Switzerland
- The Laboratory for Investigative Neurophysiology (The LINE), Department of Radiology and Department of Clinical Neurosciences, Lausanne University Hospital and University of Lausanne (CHUV-UNIL), 1011 Lausanne, Switzerland
| | - Eleonora Fornari
- Biomedical Imaging Center (CIBM), Department of Radiology, Lausanne University Hospital and University of Lausanne (CHUV-UNIL), 1011 Lausanne, Switzerland
| | - Xiao-Fei Yang
- Center for Affective Neuroscience, Development, Learning and Education (CANDLE); Brain and Creativity Institute, Rossier School of Education, University of Southern California, Los Angeles, CA 90089 USA
| | - Patric Hagmann
- Connectomics Lab, Department of Radiology, Lausanne University Hospital and University of Lausanne (CHUV-UNIL), 1011 Lausanne, Switzerland
| | - Mary Helen Immordino-Yang
- Center for Affective Neuroscience, Development, Learning and Education (CANDLE); Brain and Creativity Institute, Rossier School of Education, University of Southern California, Los Angeles, CA 90089 USA
- Neuroscience Graduate Program, University of Southern California, Los Angeles, CA USA
| | - David Sander
- Swiss Center for Affective Sciences (CISA), Campus Biotech, University of Geneva, 1202 Geneva, Switzerland
- Laboratory for the Study of Emotion Elicitation and Expression, Department of Psychology, Faculty of Psychology and Educational Sciences (FPSE), University of Geneva, 1205 Geneva, Switzerland
| |
Collapse
|
47
|
Poderini D, Agresti I, Marchese G, Polino E, Giordani T, Suprano A, Valeri M, Milani G, Spagnolo N, Carvacho G, Chaves R, Sciarrino F. Experimental violation of n-locality in a star quantum network. Nat Commun 2020; 11:2467. [PMID: 32424194 PMCID: PMC7235259 DOI: 10.1038/s41467-020-16189-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 04/21/2020] [Indexed: 11/24/2022] Open
Abstract
The launch of a satellite capable of distributing entanglement through long distances and the first loophole-free violation of Bell inequalities are milestones indicating a clear path for the establishment of quantum networks. However, nonlocality in networks with independent entanglement sources has only been experimentally verified in simple tripartite networks, via the violation of bilocality inequalities. Here, by using a scalable photonic platform, we implement star-shaped quantum networks consisting of up to five distant nodes and four independent entanglement sources. We exploit this platform to violate the chained n-locality inequality and thus witness, in a device-independent way, the emergence of nonlocal correlations among the nodes of the implemented networks. These results open new perspectives for quantum information processing applications in the relevant regime where the observed correlations are compatible with standard local hidden variable models but are non-classical if the independence of the sources is taken into account.
Collapse
Affiliation(s)
- Davide Poderini
- Dipartimento di Fisica, Sapienza Università di Roma, P.le Aldo Moro 5, I-00185, Roma, Italy
| | - Iris Agresti
- Dipartimento di Fisica, Sapienza Università di Roma, P.le Aldo Moro 5, I-00185, Roma, Italy
| | - Guglielmo Marchese
- Dipartimento di Fisica, Sapienza Università di Roma, P.le Aldo Moro 5, I-00185, Roma, Italy
| | - Emanuele Polino
- Dipartimento di Fisica, Sapienza Università di Roma, P.le Aldo Moro 5, I-00185, Roma, Italy
| | - Taira Giordani
- Dipartimento di Fisica, Sapienza Università di Roma, P.le Aldo Moro 5, I-00185, Roma, Italy
| | - Alessia Suprano
- Dipartimento di Fisica, Sapienza Università di Roma, P.le Aldo Moro 5, I-00185, Roma, Italy
| | - Mauro Valeri
- Dipartimento di Fisica, Sapienza Università di Roma, P.le Aldo Moro 5, I-00185, Roma, Italy
| | - Giorgio Milani
- Dipartimento di Fisica, Sapienza Università di Roma, P.le Aldo Moro 5, I-00185, Roma, Italy
| | - Nicolò Spagnolo
- Dipartimento di Fisica, Sapienza Università di Roma, P.le Aldo Moro 5, I-00185, Roma, Italy
| | - Gonzalo Carvacho
- Dipartimento di Fisica, Sapienza Università di Roma, P.le Aldo Moro 5, I-00185, Roma, Italy
| | - Rafael Chaves
- International Institute of Physics & School of Science and Technology, Federal University of Rio Grande do Norte, 59078-970, P. O. Box 1613, Natal, Brazil
| | - Fabio Sciarrino
- Dipartimento di Fisica, Sapienza Università di Roma, P.le Aldo Moro 5, I-00185, Roma, Italy.
| |
Collapse
|
48
|
Tang C, Xie Y, Yu T, Liu N, Wang Z, Woolsey RJ, Tang Y, Zhang X, Qin W, Zhang Y, Song G, Zheng W, Wang J, Chen W, Wei X, Xie Z, Klukovich R, Zheng H, Quilici DR, Yan W. m 6A-dependent biogenesis of circular RNAs in male germ cells. Cell Res 2020; 30:211-228. [PMID: 32047269 PMCID: PMC7054367 DOI: 10.1038/s41422-020-0279-8] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 01/14/2020] [Indexed: 12/15/2022] Open
Abstract
The majority of circular RNAs (circRNAs) spliced from coding genes contain open reading frames (ORFs) and thus, have protein coding potential. However, it remains unknown what regulates the biogenesis of these ORF-containing circRNAs, whether they are actually translated into proteins and what functions they play in specific physiological contexts. Here, we report that a large number of circRNAs are synthesized with increasing abundance when late pachytene spermatocytes develop into round and then elongating spermatids during murine spermatogenesis. For a subset of circRNAs, the back splicing appears to occur mostly at m6A-enriched sites, which are usually located around the start and stop codons in linear mRNAs. Consequently, approximately a half of these male germ cell circRNAs contain large ORFs with m6A-modified start codons in their junctions, features that have been recently shown to be associated with protein-coding potential. Hundreds of peptides encoded by the junction sequences of these circRNAs were detected using liquid chromatography coupled with mass spectrometry, suggesting that these circRNAs can indeed be translated into proteins in both developing (spermatocytes and spermatids) and mature (spermatozoa) male germ cells. The present study discovered not only a novel role of m6A in the biogenesis of coding circRNAs, but also a potential mechanism to ensure stable and long-lasting protein production in the absence of linear mRNAs, i.e., through production of circRNAs containing large ORFs and m6A-modified start codons in junction sequences.
Collapse
Affiliation(s)
- Chong Tang
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, 89557, USA.
- BGI Co. Ltd., Shenzhen, 518083, China.
| | - Yeming Xie
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, 89557, USA
| | - Tian Yu
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, 89557, USA
| | - Na Liu
- BGI Co. Ltd., Shenzhen, 518083, China
| | - Zhuqing Wang
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, 89557, USA
| | - Rebekah J Woolsey
- Nevada Proteomics Center, University of Nevada, Reno, Reno, NV, 89557, USA
| | - Yunge Tang
- Key Laboratory of Male Reproduction and Genetics, National Health and Family Planning Commission, No. 17 Meidong Road, Yuexiu District, Guangzhou, 510600, China
- Family Planning Research Institute of Guangdong Province, No. 17 Meidong Road, Yuexiu District, Guangzhou, 510600, China
| | - Xinzong Zhang
- Key Laboratory of Male Reproduction and Genetics, National Health and Family Planning Commission, No. 17 Meidong Road, Yuexiu District, Guangzhou, 510600, China
- Family Planning Research Institute of Guangdong Province, No. 17 Meidong Road, Yuexiu District, Guangzhou, 510600, China
| | - Weibing Qin
- Key Laboratory of Male Reproduction and Genetics, National Health and Family Planning Commission, No. 17 Meidong Road, Yuexiu District, Guangzhou, 510600, China
- Family Planning Research Institute of Guangdong Province, No. 17 Meidong Road, Yuexiu District, Guangzhou, 510600, China
| | - Ying Zhang
- Key Laboratory of Male Reproduction and Genetics, National Health and Family Planning Commission, No. 17 Meidong Road, Yuexiu District, Guangzhou, 510600, China
- Family Planning Research Institute of Guangdong Province, No. 17 Meidong Road, Yuexiu District, Guangzhou, 510600, China
| | - Ge Song
- Key Laboratory of Male Reproduction and Genetics, National Health and Family Planning Commission, No. 17 Meidong Road, Yuexiu District, Guangzhou, 510600, China
- Family Planning Research Institute of Guangdong Province, No. 17 Meidong Road, Yuexiu District, Guangzhou, 510600, China
| | - Weiwei Zheng
- Key Laboratory of Male Reproduction and Genetics, National Health and Family Planning Commission, No. 17 Meidong Road, Yuexiu District, Guangzhou, 510600, China
- Family Planning Research Institute of Guangdong Province, No. 17 Meidong Road, Yuexiu District, Guangzhou, 510600, China
| | - Juan Wang
- BGI Co. Ltd., Shenzhen, 518083, China
| | | | | | - Zhe Xie
- BGI Co. Ltd., Shenzhen, 518083, China
- Department of Cell Biology and Physiology, University of Copenhagen 13, 2100, Copenhagen, Denmark
| | - Rachel Klukovich
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, 89557, USA
| | - Huili Zheng
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, 89557, USA
| | - David R Quilici
- Nevada Proteomics Center, University of Nevada, Reno, Reno, NV, 89557, USA
| | - Wei Yan
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, 89557, USA.
- Department of Obstetrics and Gynecology, University of Nevada, Reno, School of Medicine, Reno, NV, 89557, USA.
- Department of Biology, University of Nevada, Reno, Reno, NV, 89557, USA.
| |
Collapse
|
49
|
Harden KP, Domingue BW, Belsky DW, Boardman JD, Crosnoe R, Malanchini M, Nivard M, Tucker-Drob EM, Harris KM. Genetic associations with mathematics tracking and persistence in secondary school. NPJ Sci Learn 2020; 5:1. [PMID: 32047651 PMCID: PMC7002519 DOI: 10.1038/s41539-020-0060-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 01/09/2020] [Indexed: 05/11/2023]
Abstract
Maximizing the flow of students through the science, technology, engineering, and math (STEM) pipeline is important to promoting human capital development and reducing economic inequality. A critical juncture in the STEM pipeline is the highly cumulative sequence of secondary school math courses. Students from disadvantaged schools are less likely to complete advanced math courses. Here, we conduct an analysis of how the math pipeline differs across schools using student polygenic scores, which are DNA-based indicators of propensity to succeed in education. We integrated genetic and official school transcript data from over 3000 European-ancestry students from U.S. high schools. We used polygenic scores as a molecular tracer to understand how the flow of students through the high school math pipeline differs in socioeconomically advantaged versus disadvantaged schools. Students with higher education polygenic scores were tracked to more advanced math already at the beginning of high school and persisted in math for more years. Analyses using genetics as a molecular tracer revealed that the dynamics of the math pipeline differed by school advantage. Compared to disadvantaged schools, advantaged schools buffered students with low polygenic scores from dropping out of math. Across all schools, even students with exceptional polygenic scores (top 2%) were unlikely to take the most advanced math classes, suggesting substantial room for improvement in the development of potential STEM talent. These results link new molecular genetic discoveries to a common target of educational-policy reforms.
Collapse
Affiliation(s)
- K. Paige Harden
- Department of Psychology and Population Research Center, University of Texas at Austin, Austin, TX USA
| | | | - Daniel W. Belsky
- Department of Epidemiology, Columbia University Mailman School of Public Health, New York, NY USA
| | - Jason D. Boardman
- Department of Sociology and Institute of Behavioral Science, University of Colorado at Boulder, Boulder, CA USA
| | - Robert Crosnoe
- Department of Sociology and Population Research Center, University of Texas at Austin, Austin, TX USA
| | - Margherita Malanchini
- Department of Psychology and Population Research Center, University of Texas at Austin, Austin, TX USA
| | - Michel Nivard
- Biological Psychology, VU University Amsterdam, Amsterdam, The Netherlands
| | - Elliot M. Tucker-Drob
- Department of Psychology and Population Research Center, University of Texas at Austin, Austin, TX USA
| | - Kathleen Mullan Harris
- Department of Sociology and Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| |
Collapse
|
50
|
Abstract
A fundamental puzzle of human evolution is how we evolved to cooperate with genetically unrelated strangers in transient interactions. Group-level selection on culturally differentiated populations is one proposed explanation. We evaluate a central untested prediction of Cultural Group Selection theory, by assessing whether readiness to cooperate between individuals from different groups corresponds to the degree of cultural similarity between those groups. We documented the normative beliefs and cooperative dispositions of 759 individuals spanning nine clans nested within four pastoral ethnic groups of Kenya-the Turkana, Samburu, Rendille and Borana. We find that cooperation between groups is predicted by how culturally similar they are, suggesting that norms of cooperation in these societies have evolved under the influence of group-level selection on cultural variation. Such selection acting over human evolutionary history may explain why we cooperate readily with unrelated and unfamiliar individuals, and why humans' unprecedented cooperative flexibility is nevertheless culturally parochial.
Collapse
Affiliation(s)
- Carla Handley
- School of Human Evolution and Social Change, Arizona State University, P.O. Box 872402, Tempe, AZ, 85287, USA
- Institute of Human Origins, Arizona State University, Tempe, AZ, 85287, USA
| | - Sarah Mathew
- School of Human Evolution and Social Change, Arizona State University, P.O. Box 872402, Tempe, AZ, 85287, USA.
- Institute of Human Origins, Arizona State University, Tempe, AZ, 85287, USA.
| |
Collapse
|