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Cited by 3Evolutionary Game Theory and CooperationBacterial Genetics and BiotechnologyEvolution and Genetic Dynamics

Genes for cooperation are not more likely to be carried by plasmids

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Dewar, Anna E., Belcher, Laurence J., Scott, Thomas W., West, Stuart A.·2024·Proceedings of the Royal Society B: Biological Sciences
DOI 10.1098/rspb.2023.2549PMC PMC10898968
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Abstract

Cooperation is prevalent across bacteria, but risks being exploited by non-cooperative cheats. Horizontal gene transfer, particularly via plasmids, has been suggested as a mechanism to stabilize cooperation. A key prediction of this hypothesis is that genes which are more likely to be transferred, such as those on plasmids, should be more likely to code for cooperative traits. Testing this prediction requires identifying all genes for cooperation in bacterial genomes. However, previous studies used a method which likely misses some of these genes for cooperation. To solve this, we used a new genomics tool, SOCfinder, which uses three distinct modules to identify all kinds of genes for cooperation. We compared where these genes were located across 4648 genomes from 146 bacterial species. In contrast to the prediction of the hypothesis, we found no evidence that plasmid genes are more likely to code for cooperative traits. Instead, we found the opposite—that genes for cooperation were more likely to be carried on chromosomes. Overall, the vast majority of genes for cooperation are not located on plasmids, suggesting that the more general mechanism of kin selection is sufficient to explain the prevalence of cooperation across bacteria.

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  • The problem of species not being independent can be exacerbated by additional levels of non-independence, including genes within genomes and genomes of the same or closely related species.

    “In genomic datasets, data points can correspond to genomes or even individual genes, meaning the problem of species not being independent can be exacerbated by additional levels of non-independence, including genes within genomes, such as those carried on the same replicon, and genomes of the same or closely related species16,19,21–26.”

    From A phylogenetic approach to comparative genomics (2025) · cites this paper as [23]

    The Methods (Data and statistical analyses; page unavailable) warn against grouping genes from multiple genomes or species, use genomes as data points, and account for species and phylogenetic similarity. This supports non-independence across genomes of the same or related species, but the paper does not specifically identify genes on the same replicon as an additional source of non-independence. (LLM, conf=0.82)

    Experimental — accuracy not yet measured

  • The problem of non-independence can be exacerbated when examining genomes or genes.

    “This problem of non-independence can be exacerbated when examining genomes or genes.”

    From A phylogenetic approach to comparative genomics (2025) · cites this paper as [23]

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Cited by

Sorted by citations

Authors
Dewar, A. E., Belcher, L. J., Scott, T. W., & West, S. A.
Affiliations
University of Oxford (GB)
Corresponding author
Dewar, Anna E.
ORCID
Venue
Proceedings of the Royal Society B: Biological Sciences
Publisher
The Royal Society
Published
2024-02-28
Volume
291
Issue
2017
Pages
20232549-20232549
ISSN
  • 0080-4649 (ISSN-L)
  • 0962-8452
  • 1471-2954
DOI
10.1098/rspb.2023.2549
PMC
PMC10898968
OpenAlex
W4392771631
Cited by
3
References
1
Citations by year
2026: 1 · 2025: 1 · 2024: 1
FWCI
1.58
Type
journal article
Language
en
Open access
Licence
Locations
  • Proceedings of the Royal Society B Biological Sciences (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • eScholarship (California Digital Library) (submittedVersion, cc-by)
  • Oxford University Research Archive (ORA) (University of Oxford) (submittedVersion, cc-by)
Funders
  • Natural Environment Research Council (NE/V011537/1)
  • European Research Council (834164)
Topics
  • Social Sciences › Sociology and Political Science › Evolutionary Game Theory and Cooperation
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
Keywords
bacterial cooperation, plasmids, horizontal gene transfer, kin selection, bacterial genomes, cheating
MeSH terms
Bacteria, Plasmids, Genome, Bacterial, Gene Transfer, Horizontal, Genomics

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