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Belcher LJ, Dewar AE, Hao C, Katz Z, Ghoul M, West SA. SOCfinder: a genomic tool for identifying social genes in bacteria. Microb Genom 2023; 9:001171. [PMID: 38117204 PMCID: PMC10763506 DOI: 10.1099/mgen.0.001171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 12/08/2023] [Indexed: 12/21/2023] Open
Abstract
Bacteria cooperate by working collaboratively to defend their colonies, share nutrients, and resist antibiotics. Nevertheless, our understanding of these remarkable behaviours primarily comes from studying a few well-characterized species. Consequently, there is a significant gap in our understanding of microbial social traits, particularly in natural environments. To address this gap, we can use bioinformatic tools to identify genes that control cooperative or otherwise social traits. Existing tools address this challenge through two approaches. One approach is to identify genes that encode extracellular proteins, which can provide benefits to neighbouring cells. An alternative approach is to predict gene function using annotation tools. However, these tools have several limitations. Not all extracellular proteins are cooperative, and not all cooperative behaviours are controlled by extracellular proteins. Furthermore, existing functional annotation methods frequently miss known cooperative genes. We introduce SOCfinder as a new tool to find bacterial genes that control cooperative or otherwise social traits. SOCfinder combines information from several methods, considering if a gene is likely to [1] code for an extracellular protein [2], have a cooperative functional annotation, or [3] be part of the biosynthesis of a cooperative secondary metabolite. We use data on two extensively-studied species (P. aeruginosa and B. subtilis) to show that SOCfinder is better at finding known cooperative genes than existing tools. We also use theory from population genetics to identify a signature of kin selection in SOCfinder cooperative genes, which is lacking in genes identified by existing tools. SOCfinder opens up a number of exciting directions for future research, and is available to download from https://github.com/lauriebelch/SOCfinder.
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Affiliation(s)
| | - Anna E. Dewar
- Department of Biology, University of Oxford, Oxford, OX1 3SZ, UK
| | - Chunhui Hao
- Department of Biology, University of Oxford, Oxford, OX1 3SZ, UK
| | - Zohar Katz
- Department of Biology, University of Oxford, Oxford, OX1 3SZ, UK
| | - Melanie Ghoul
- Department of Biology, University of Oxford, Oxford, OX1 3SZ, UK
| | - Stuart A. West
- Department of Biology, University of Oxford, Oxford, OX1 3SZ, UK
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Belcher LJ, Dewar AE, Hao C, Ghoul M, West SA. Signatures of kin selection in a natural population of the bacteria Bacillus subtilis. Evol Lett 2023; 7:315-330. [PMID: 37829498 PMCID: PMC10565896 DOI: 10.1093/evlett/qrad029] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 06/14/2023] [Accepted: 07/07/2023] [Indexed: 10/14/2023] Open
Abstract
Laboratory experiments have suggested that bacteria perform a range of cooperative behaviors, which are favored because they are directed toward relatives (kin selection). However, there is a lack of evidence for cooperation and kin selection in natural bacterial populations. Molecular population genetics offers a promising method to study natural populations because the theory predicts that kin selection will lead to relaxed selection, which will result in increased polymorphism and divergence at cooperative genes. Examining a natural population of Bacillus subtilis, we found consistent evidence that putatively cooperative traits have higher polymorphism and greater divergence than putatively private traits expressed at the same rate. In addition, we were able to eliminate alternative explanations for these patterns and found more deleterious mutations in genes controlling putatively cooperative traits. Overall, our results suggest that cooperation is favored by kin selection, with an average relatedness of r = .79 between interacting individuals.
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Affiliation(s)
| | - Anna E Dewar
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Chunhui Hao
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Melanie Ghoul
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Stuart A West
- Department of Biology, University of Oxford, Oxford, United Kingdom
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Scott TW, West SA, Dewar AE, Wild G. Is cooperation favored by horizontal gene transfer? Evol Lett 2023; 7:113-120. [PMID: 37251586 PMCID: PMC10210433 DOI: 10.1093/evlett/qrad003] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 01/18/2023] [Accepted: 01/31/2023] [Indexed: 05/31/2023] Open
Abstract
It has been hypothesized that horizontal gene transfer on plasmids can facilitate the evolution of cooperation, by allowing genes to jump between bacteria, and hence increase genetic relatedness at the cooperative loci. However, we show theoretically that horizontal gene transfer only appreciably increases relatedness when plasmids are rare, where there are many plasmid-free cells available to infect (many opportunities for horizontal gene transfer). In contrast, when plasmids are common, there are few opportunities for horizontal gene transfer, meaning relatedness is not appreciably increased, and so cooperation is not favored. Plasmids, therefore, evolve to be rare and cooperative, or common and noncooperative, meaning plasmid frequency and cooperativeness are never simultaneously high. The overall level of plasmid-mediated cooperation, given by the product of plasmid frequency and cooperativeness, is therefore consistently negligible or low.
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Affiliation(s)
- Thomas W Scott
- Corresponding author: Department of Biology, University of Oxford; Oxford, OX1 3SZ, United Kingdom.
| | - Stuart A West
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Anna E Dewar
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Geoff Wild
- Department of Mathematics, University of Western Ontario, London, Ontario, Canada
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Multiple social encounters can eliminate Crozier's paradox and stabilise genetic kin recognition. Nat Commun 2022; 13:3902. [PMID: 35794146 PMCID: PMC9259605 DOI: 10.1038/s41467-022-31545-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 06/22/2022] [Indexed: 11/28/2022] Open
Abstract
Crozier’s paradox suggests that genetic kin recognition will not be evolutionarily stable. The problem is that more common tags (markers) are more likely to be recognised and helped. This causes common tags to increase in frequency, and hence eliminates the genetic variability that is required for genetic kin recognition. It has therefore been assumed that genetic kin recognition can only be stable if there is some other factor maintaining tag diversity, such as the advantage of rare alleles in host-parasite interactions. We show that allowing for multiple social encounters before each social interaction can eliminate Crozier’s paradox, because it allows individuals with rare tags to find others with the same tag. We also show that rare tags are better indicators of relatedness, and hence better at helping individuals avoid interactions with non-cooperative cheats. Consequently, genetic kin recognition provides an advantage to rare tags that maintains tag diversity, and stabilises itself. Crozier’s paradox suggests that genetic kin recognition will not be evolutionarily stable. Here, the authors show that allowing for multiple social encounters before each social interaction can eliminate Crozier’s paradox and stabilise genetic kin recognition.
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Plasmids do not consistently stabilize cooperation across bacteria but may promote broad pathogen host-range. Nat Ecol Evol 2021; 5:1624-1636. [PMID: 34750532 PMCID: PMC7612097 DOI: 10.1038/s41559-021-01573-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 09/27/2021] [Indexed: 11/24/2022]
Abstract
Horizontal gene transfer via plasmids could favour cooperation in bacteria, because transfer of a cooperative gene turns non-cooperative cheats into cooperators. This hypothesis has received support from theoretical, genomic and experimental analyses. In contrast, we show here, with a comparative analysis across 51 diverse species, that genes for extracellular proteins, which are likely to act as cooperative ‘public goods’, were not more likely to be carried on either: (i) plasmids compared to chromosomes; or (ii) plasmids that transfer at higher rates. Our results were supported by theoretical modelling which showed that while horizontal gene transfer can help cooperative genes initially invade a population, it has less influence on the longer-term maintenance of cooperation. Instead, we found that genes for extracellular proteins were more likely to be on plasmids when they coded for pathogenic virulence traits, in pathogenic bacteria with a broad host-range.
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West SA, Cooper GA, Ghoul MB, Griffin AS. Ten recent insights for our understanding of cooperation. Nat Ecol Evol 2021; 5:419-430. [PMID: 33510431 PMCID: PMC7612052 DOI: 10.1038/s41559-020-01384-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 12/11/2020] [Indexed: 01/29/2023]
Abstract
Since Hamilton published his seminal papers in 1964, our understanding of the importance of cooperation for life on Earth has evolved beyond recognition. Early research was focused on altruism in the social insects, where the problem of cooperation was easy to see. In more recent years, research into cooperation has expanded across the entire tree of life, and has been revolutionized by advances in genetic, microbiological and analytical techniques. We highlight ten insights that have arisen from these advances, which have illuminated generalizations across different taxa, making the world simpler to explain. Furthermore, progress in these areas has opened up numerous new problems to solve, suggesting exciting directions for future research.
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Affiliation(s)
- Stuart A West
- Department of Zoology, University of Oxford, Oxford, UK.
| | - Guy A Cooper
- Department of Zoology, University of Oxford, Oxford, UK
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Gerber L, Wittwer S, Allen SJ, Holmes KG, King SL, Sherwin WB, Wild S, Willems EP, Connor RC, Krützen M. Cooperative partner choice in multi-level male dolphin alliances. Sci Rep 2021; 11:6901. [PMID: 33767258 PMCID: PMC7994371 DOI: 10.1038/s41598-021-85583-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 02/22/2021] [Indexed: 12/28/2022] Open
Abstract
Investigations into cooperative partner choice should consider both potential and realised partners, allowing for the comparison of traits across all those available. Male bottlenose dolphins form persisting multi-level alliances. Second-order alliances of 4–14 males are the core social unit, within which 2–3 males form first-order alliances to sequester females during consortships. We compared social bond strength, relatedness and age similarity of potential and realised partners of individual males in two age periods: (i) adolescence, when second-order alliances are formed from all available associates, and (ii) adulthood, when first-order allies are selected from within second-order alliances. Social bond strength during adolescence predicted second-order alliance membership in adulthood. Moreover, males preferred same-aged or older males as second-order allies. Within second-order alliances, non-mating season social bond strength predicted first-order partner preferences during mating season consortships. Relatedness did not influence partner choice on either alliance level. There is thus a striking resemblance between male dolphins, chimpanzees and humans, where closely bonded non-relatives engage in higher-level, polyadic cooperative acts. To that end, our study extends the scope of taxa in which social bonds rather than kinship explain cooperation, providing the first evidence that such traits might have evolved independently in marine and terrestrial realms.
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Affiliation(s)
- Livia Gerber
- Evolutionary Genetics Group, Department of Anthropology, University of Zurich, 8057, Zurich, Switzerland.
| | - Samuel Wittwer
- Evolutionary Genetics Group, Department of Anthropology, University of Zurich, 8057, Zurich, Switzerland
| | - Simon J Allen
- Evolutionary Genetics Group, Department of Anthropology, University of Zurich, 8057, Zurich, Switzerland.,School of Biological Sciences, University of Bristol, Bristol, BS8 1TQ, UK.,School of Biological Sciences and Oceans Institute, University of Western Australia, Crawley, WA, 6009, Australia
| | - Kathryn G Holmes
- School of Biological Sciences and Oceans Institute, University of Western Australia, Crawley, WA, 6009, Australia
| | - Stephanie L King
- School of Biological Sciences, University of Bristol, Bristol, BS8 1TQ, UK.,School of Biological Sciences and Oceans Institute, University of Western Australia, Crawley, WA, 6009, Australia
| | - William B Sherwin
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - Sonja Wild
- Centre for the Advanced Study of Collective Behaviour, University of Konstanz, 78464, Konstanz, Germany.,Cognitive and Cultural Ecology Research Group, Max Planck Institute of Animal Behavior, 78315, Radolfzell, Germany
| | - Erik P Willems
- Evolutionary Genetics Group, Department of Anthropology, University of Zurich, 8057, Zurich, Switzerland
| | - Richard C Connor
- Biology Department, UMASS Dartmouth, North Dartmouth, MA, 02747, USA
| | - Michael Krützen
- Evolutionary Genetics Group, Department of Anthropology, University of Zurich, 8057, Zurich, Switzerland
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Simonet C, McNally L. Kin selection explains the evolution of cooperation in the gut microbiota. Proc Natl Acad Sci U S A 2021; 118:e2016046118. [PMID: 33526674 PMCID: PMC8017935 DOI: 10.1073/pnas.2016046118] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Through the secretion of "public goods" molecules, microbes cooperatively exploit their habitat. This is known as a major driver of the functioning of microbial communities, including in human disease. Understanding why microbial species cooperate is therefore crucial to achieve successful microbial community management, such as microbiome manipulation. A leading explanation is that of Hamilton's inclusive-fitness framework. A cooperator can indirectly transmit its genes by helping the reproduction of an individual carrying similar genes. Therefore, all else being equal, as relatedness among individuals increases, so should cooperation. However, the predictive power of relatedness, particularly in microbes, is surrounded by controversy. Using phylogenetic comparative analyses across the full diversity of the human gut microbiota and six forms of cooperation, we find that relatedness is predictive of the cooperative gene content evolution in gut-microbe genomes. Hence, relatedness is predictive of cooperation over broad microbial taxonomic levels that encompass variation in other life-history and ecology details. This supports the generality of Hamilton's central insights and the relevance of relatedness as a key parameter of interest to advance microbial predictive and engineering science.
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Affiliation(s)
- Camille Simonet
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom;
| | - Luke McNally
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
- Centre for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
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Abstract
Stu West and Melanie Ghoul introduce the special issue on conflict and cooperation.
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Faragalla KM, Chernyshova AM, Gallo AJ, Thompson GJ. From gene list to gene network: Recognizing functional connections that regulate behavioral traits. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2018; 330:317-329. [DOI: 10.1002/jez.b.22829] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 09/10/2018] [Indexed: 12/27/2022]
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Kasper C, Hebert FO, Aubin-Horth N, Taborsky B. Divergent brain gene expression profiles between alternative behavioural helper types in a cooperative breeder. Mol Ecol 2018; 27:4136-4151. [DOI: 10.1111/mec.14837] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 07/21/2018] [Accepted: 08/07/2018] [Indexed: 01/17/2023]
Affiliation(s)
- Claudia Kasper
- Behavioural Ecology; University of Bern; Hinterkappelen Switzerland
| | - Francois Olivier Hebert
- Département de Biologie et Institut de Biologie Intégrative et des Systèmes; Université Laval; Québec Québec Canada
| | - Nadia Aubin-Horth
- Département de Biologie et Institut de Biologie Intégrative et des Systèmes; Université Laval; Québec Québec Canada
| | - Barbara Taborsky
- Behavioural Ecology; University of Bern; Hinterkappelen Switzerland
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