CoChat
Sign Up
Cited by 13Bacterial biofilms and quorum sensingGenomics and Phylogenetic StudiesBacterial Genetics and Biotechnology

SOCfinder: a genomic tool for identifying social genes in bacteria

Open access
Belcher, Laurence J., Dewar, Anna E., Hao, Chunhui, Katz, Zohar, Ghoul, Melanie, West, Stuart A.·2023·Microbial Genomics
DOI 10.1099/mgen.0.001171PMC PMC10763506
Open this paper in CoChat — free account

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 [] code for an extracellular protein [], have a cooperative functional annotation, or [] 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.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1099/mgen.0.001171

Cites

4 of 4 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • Particularly successful areas, such as the evolution of sex ratios and cooperation, have produced comparative studies that can explain 20-40% of the variation in data across species.

    “Particularly successful areas, such as the evolution of sex ratios and cooperation, have produced comparative studies that can explain 20–40% of the variation in data across species124,125.”

    From A phylogenetic approach to comparative genomics (2025) · cites this paper as [124]

    The Introduction discusses comparing cooperative genes across species, and the Results describe an analysis of genomes from 47 bacterial species. Neither passage says that comparative studies of cooperation or sex ratios explain 20–40% of variation across species. Searches for that figure and for sex-ratio comparative studies found no supporting passage in our copy. (LLM, conf=0.72)

    Experimental — accuracy not yet measured

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Cites

Flagged first, then by citations

Research works printed but not linked: 90

  1. [1]West SA Griffin AS Gardner A Diggle SP Social evolution theory for microorganisms Nat Rev Microbiol 2006 4 597 607 10.1038/nrmicro1461 16845430 · DOI
  2. [2]Strassmann JE Gilbert OM Queller DC Kin discrimination and cooperation in microbes Annu Rev Microbiol 2011 65 349 367 10.1146/annurev.micro.112408.134109 21682642 · DOI
  3. [3]Ghoul M Andersen SB West SA Sociomics: using omic approaches to understand social evolution Trends Genet 2017 33 408 419 10.1016/j.tig.2017.03.009 28506494 · DOI · Paper page
  4. [4]Mitri S Foster KR The genotypic view of social interactions in microbial communities Annu Rev Genet 2013 47 247 273 10.1146/annurev-genet-111212-133307 24016192 · DOI
  5. [5]West SA Cooper GA Ghoul MB Griffin AS Ten recent insights for our understanding of cooperation Nat Ecol Evol 2021 5 419 430 10.1038/s41559-020-01384-x 33510431 PMC7612052 · DOI
  6. [6]Kümmerli R Santorelli LA Granato ET Dumas Z Dobay A et al Co-evolutionary dynamics between public good producers and cheats in the bacterium Pseudomonas aeruginosa J Evol Biol 2015 28 2264 2274 10.1111/jeb.12751 26348785 · DOI
  7. [8]Harrison F Buckling A Siderophore production and biofilm formation as linked social traits ISME J 2009 3 632 634 10.1038/ismej.2009.9 19225554 · DOI
  8. [9]Kümmerli R Ross-Gillespie A Explaining the sociobiology of pyoverdin producing Pseudomonas: a comment on Zhang and Rainey (2013) Evolution 2014 68 3337 3343 10.1111/evo.12311 24219572 · DOI
  9. [10]O’Brien S Hodgson DJ Buckling A Social evolution of toxic metal bioremediation in Pseudomonas aeruginosa Proc Biol Sci 2014 281 20140858 10.1098/rspb.2014.0858 24898376 PMC4071558 · DOI
  10. [11]Kümmerli R Griffin AS West SA Buckling A Harrison F Viscous medium promotes cooperation in the pathogenic bacterium Pseudomonas aeruginosa Proc R Soc B Biol Sci 2009 276 3531 3538 10.1098/rspb.2009.0861 19605393 PMC2817189 · DOI
  11. [12]Dragoš A Kiesewalter H Martin M Hsu C-Y Hartmann R et al Division of labor during biofilm matrix production Curr Biol 2018 28 1903 1913 10.1016/j.cub.2018.04.046 29887307 PMC6331042 · DOI
  12. [13]Chai Y Chu F Kolter R Losick R Bistability and biofilm formation in Bacillus subtilis Mol Microbiol 2008 67 254 263 10.1111/j.1365-2958.2007.06040.x 18047568 PMC2430929 · DOI
  13. [14]O’Brien S Luján AM Paterson S Cant MA Buckling A Adaptation to public goods cheats in Pseudomonas aeruginosa Proc R Soc B Biol Sci 2017 284 20171089 10.1098/rspb.2017.1089 28747481 PMC5543229 · DOI
  14. [16]Cordero OX Ventouras L-A DeLong EF Polz MF Public good dynamics drive evolution of iron acquisition strategies in natural bacterioplankton populations Proc Natl Acad Sci U S A 2012 109 20059 20064 10.1073/pnas.1213344109 23169633 PMC3523850 · DOI
  15. [18]Chen R Déziel E Groleau M-C Schaefer AL Greenberg EP Social cheating in a Pseudomonas aeruginosa quorum-sensing variant Proc Natl Acad Sci U S A 2019 116 7021 7026 10.1073/pnas.1819801116 30846553 PMC6452681 · DOI
  16. [19]van Gestel J Weissing FJ Kuipers OP Kovács AT Density of founder cells affects spatial pattern formation and cooperation in Bacillus subtilis biofilms ISME J 2014 8 2069 2079 10.1038/ismej.2014.52 24694715 PMC4184017 · DOI
  17. [20]Yu NY Wagner JR Laird MR Melli G Rey S et al PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes Bioinformatics 2010 26 1608 1615 10.1093/bioinformatics/btq249 20472543 PMC2887053 · DOI
  18. [21]Törönen P Holm L PANNZER-a practical tool for protein function prediction Protein Sci 2022 31 118 128 10.1002/pro.4193 34562305 PMC8740830 · DOI
  19. [22]Taglialegna A Lasa I Valle J Amyloid structures as biofilm matrix scaffolds J Bacteriol 2016 198 2579 2588 10.1128/JB.00122-16 27185827 PMC5019065 · DOI
  20. [23]Bruce JB West SA Griffin AS Functional amyloids promote retention of public goods in bacteria Proc R Soc B Biol Sci 2019 286 20190709 10.1098/rspb.2019.0709 31138071 PMC6545082 · DOI
  21. [24]Ringel MT Brüser T The biosynthesis of pyoverdines Microb Cell 2018 5 424 437 10.15698/mic2018.10.649 30386787 PMC6206403 · DOI
  22. [25]Sandoz KM Mitzimberg SM Schuster M Social cheating in Pseudomonas aeruginosa quorum sensing Proc Natl Acad Sci U S A 2007 104 15876 15881 10.1073/pnas.0705653104 17898171 PMC2000394 · DOI · Paper page
  23. [26]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 10.1073/pnas.2016046118 33526674 PMC8017935 · DOI
  24. [27]Nogueira T Touchon M Rocha EPC Rapid evolution of the sequences and gene repertoires of secreted proteins in bacteria PLoS One 2012 7 1 10 10.1371/journal.pone.0049403 23189144 PMC3506625 · DOI
  25. [28]Nogueira T Rankin DJ Touchon M Taddei F Brown SP et al Horizontal gene transfer of the secretome drives the evolution of bacterial cooperation and virulence Curr Biol 2009 19 1683 1691 10.1016/j.cub.2009.08.056 19800234 PMC2773837 · DOI
  26. [29]Garcia-Garcera M Rocha EPC Community diversity and habitat structure shape the repertoire of extracellular proteins in bacteria Nat Commun 2020 11 1 11 10.1038/s41467-020-14572-x 32029728 PMC7005277 · DOI · Paper page
  27. [30]Hao C Dewar AE West SA Ghoul M Gene transferability and sociality do not correlate with gene connectivity Proc R Soc B Biol Sci 2022 289 20221819 10.1098/rspb.2022.1819 36448285 PMC9709509 · DOI
  28. [31]Dewar AE Thomas JL Scott TW Wild G Griffin AS et al Plasmids do not consistently stabilize cooperation across bacteria but may promote broad pathogen host-range Nat Ecol Evol 2021 5 1624 1636 10.1038/s41559-021-01573-2 34750532 PMC7612097 · DOI · Paper page
  29. [32]Belcher LJ Dewar AE Ghoul M West SA Kin selection for cooperation in natural bacterial populations Proc Natl Acad Sci U S A 2022 119 e2119070119 10.1073/pnas.2119070119 35193981 PMC8892524 · DOI · Paper page
  30. [33]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 1 21 10.1093/evlett/qrad029 37829498 PMC10565896 · DOI
  31. [34]Tai J-S Mukherjee S Nero T Olson R Tithof J et al Social evolution of shared biofilm matrix components Proc Natl Acad Sci U S A 2022 119 e2123469119 10.1073/pnas.2123469119 35771939 PMC9271185 · DOI
  32. [35]Pollak S Omer-Bendori S Even-Tov E Lipsman V Bareia T et al Facultative cheating supports the coexistence of diverse quorum-sensing alleles Proc Natl Acad Sci U S A 2016 113 2152 2157 10.1073/pnas.1520615113 26787913 PMC4776494 · DOI
  33. [37]West SA Griffin AS Gardner A Evolutionary explanations for cooperation Curr Biol 2007 17 R661 R672 10.1016/j.cub.2007.06.004 17714660 · DOI
  34. [38]Ghoul M Griffin AS West SA Toward an evolutionary definition of cheating Evolution 2014 68 318 331 10.1111/evo.12266 24131102 · DOI
  35. [39]Hamilton WD The genetical evolution of social behaviour. II J Theor Biol 1964 7 17 52 10.1016/0022-5193(64)90039-6 5875340 · DOI
  36. [40]Oster GF Wilson E Caste and Ecology in the Social Insects Princeton University Press 1978 740003
  37. [41]Wilkinson GS Reciprocal food sharing in the vampire bat Nature 1984 308 181 184 10.1038/308181a0 · DOI
  38. [42]Clutton-Brock TH Brotherton PN Russell AF O’Riain MJ Gaynor D et al Cooperation, control, and concession in meerkat groups Science 2001 291 478 481 10.1126/science.291.5503.478 11161200 · DOI
  39. [43]West SA Buckling A Cooperation, virulence and siderophore production in bacterial parasites Proc R Soc B Biol Sci 2003 270 37 44 10.1098/rspb.2002.2209 12590769 PMC1691207 · DOI
  40. [44]Schuster M Sexton DJ Hense BA Why quorum sensing controls private goods Front Microbiol 2017 8 1 16 10.3389/fmicb.2017.00885 28579979 PMC5437708 · DOI
  41. [45]Ghoul M West SA Johansen HK Molin S Harrison OB et al Bacteriocin-mediated competition in cystic fibrosis lung infections Proc R Soc B Biol Sci 2015 282 20150972 10.1098/rspb.2015.0972 26311664 PMC4571691 · DOI
  42. [46]Granato ET Meiller-Legrand TA Foster KR Meiller-Legrand TA Foster KR The evolution and ecology of bacterial warfare Curr Biol 2019 29 1 39 10.1016/j.cub.2019.04.024 31163166 · DOI
  43. [47]Kessler E Safrin M Gustin JK Ohman DE Elastase and the LasA protease of Pseudomonas aeruginosa are secreted with their propeptides J Biol Chem 1998 273 30225 30231 10.1074/jbc.273.46.30225 9804780 · DOI
  44. [48]Diggle SP Griffin AS Campbell GS West SA Cooperation and conflict in quorum-sensing bacterial populations Nature 2007 450 411 414 10.1038/nature06279 18004383 · DOI
  45. [49]Özkaya Ö Balbontín R Gordo I Xavier KB Cheating on cheaters stabilizes cooperation in Pseudomonas aeruginosa Curr Biol 2018 28 2070 2080 10.1016/j.cub.2018.04.093 30008329 · DOI
  46. [50]Jautzus T van Gestel J Kovács ÁT Complex extracellular biology drives surface competition during colony expansion in Bacillus subtilis ISME J 2022 16 2320 2328 10.1038/s41396-022-01279-8 35790818 PMC9477810 · DOI
  47. [51]Gardner A Hardy ICW Taylor PD West SA Spiteful soldiers and sex ratio conflict in polyembryonic parasitoid wasps Am Nat 2007 169 519 533 10.1086/512107 17427122 · DOI
  48. [52]McNally L Viana M Brown SP Cooperative secretions facilitate host range expansion in bacteria Nat Commun 2014 5 4594 10.1038/ncomms5594 25091146 PMC4143932 · DOI
  49. [53]Aramaki T Blanc-Mathieu R Endo H Ohkubo K Kanehisa M et al KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold Bioinformatics 2020 36 2251 2252 10.1093/bioinformatics/btz859 31742321 PMC7141845 · DOI · Paper page
  50. [54]Cantalapiedra CP Hernández-Plaza A Letunic I Bork P Huerta-Cepas J eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale Mol Biol Evol 2021 38 5825 5829 10.1093/molbev/msab293 34597405 PMC8662613 · DOI
  51. [55]Velicer GJ Vos M Sociobiology of the Myxobacteria Annu Rev Microbiol 2009 63 599 623 10.1146/annurev.micro.091208.073158 19575567 · DOI
  52. [56]Vos M Velicer GJ Social conflict in centimeter-and global-scale populations of the bacterium Myxococcus xanthus Curr Biol 2009 19 1763 1767 10.1016/j.cub.2009.08.061 19879146 PMC2858270 · DOI
  53. [57]Kessin RH Dictyostelium: Evolution, Cell Biology, and the Development of Multicellularity Cambridge University Press 2001 10.1017/CBO9780511525315 · DOI
  54. [58]Strassmann JE Queller DC Evolution of cooperation and control of cheating in a social microbe Proc Natl Acad Sci U S A 2011 108 10855 10862 10.1073/pnas.1102451108 21690338 PMC3131822 · DOI
  55. [59]Strassmann JE Zhu Y Queller DC Altruism and social cheating in the social amoeba Dictyostelium discoideum Nature 2000 408 965 967 10.1038/35050087 11140681 · DOI
  56. [60]Madgwick PG Stewart B Belcher LJ Thompson CRL Wolf JB Strategic investment explains patterns of cooperation and cheating in a microbe Proc Natl Acad Sci U S A 2018 115 E4823 E4832 10.1073/pnas.1716087115 29735672 PMC6003509 · DOI
  57. [61]Belcher LJ Madgwick PG Kuwana S Stewart B Thompson CRL et al Developmental constraints enforce altruism and avert the tragedy of the commons in a social microbe Proc Natl Acad Sci U S A 2022 119 e2111233119 10.1073/pnas.2111233119 35858311 PMC9303850 · DOI
  58. [62]de Oliveira JL Morales AC Stewart B Gruenheit N Engelmoer J et al Conditional expression explains molecular evolution of social genes in a microbe Nat Commun 2019 10 3284 10.1038/s41467-019-11237-2 31337766 PMC6650454 · DOI
  59. [63]Warner MR Mikheyev AS Linksvayer TA Genomic signature of kin selection in an ant with obligately sterile workers Mol Biol Evol 2017 34 1780 1787 10.1093/molbev/msx123 28419349 PMC5455959 · DOI
  60. [64]Imrit MA Dogantzis KA Harpur BA Zayed A Eusociality influences the strength of negative selection on insect genomes: negative selection in social genomes Proc R Soc B Biol Sci 2020 287 1 7 10.1098/rspb.2020.1512 PMC7482261 32811314 · DOI
  61. [65]Sharrar AM Crits-Christoph A Méheust R Diamond S Starr EP et al Bacterial secondary metabolite biosynthetic potential in soil varies with phylum, depth, and vegetation type mBio 2020 11 e00416-20 10.1128/mBio.00416-20 32546614 PMC7298704 · DOI
  62. [66]Blin K Shaw S Kloosterman AM Charlop-Powers Z van Wezel GP et al antiSMASH 6.0: improving cluster detection and comparison capabilities Nucleic Acids Res 2021 49 W29 W35 10.1093/nar/gkab335 33978755 PMC8262755 · DOI
  63. [67]Wang H Fewer DP Holm L Rouhiainen L Sivonen K Atlas of nonribosomal peptide and polyketide biosynthetic pathways reveals common occurrence of nonmodular enzymes Proc Natl Acad Sci U S A 2014 111 9259 9264 10.1073/pnas.1401734111 24927540 PMC4078802 · DOI
  64. [68]Zhang S Mukherji R Chowdhury S Reimer L Stallforth P Lipopeptide-mediated bacterial interaction enables cooperative predator defense Proc Natl Acad Sci U S A 2021 118 e2013759118 10.1073/pnas.2013759118 33526668 PMC8017672 · DOI
  65. [69]Kanehisa M Sato Y Kawashima M Furumichi M Tanabe M KEGG as a reference resource for gene and protein annotation Nucleic Acids Res 2016 44 D457 D462 10.1093/nar/gkv1070 26476454 PMC4702792 · DOI · Paper page
  66. [70]McNally L Bernardy E Thomas J Kalziqi A Pentz J et al Killing by Type VI secretion drives genetic phase separation and correlates with increased cooperation Nat Commun 2017 8 14371 10.1038/ncomms14371 28165005 PMC5303878 · DOI
  67. [71]Linksvayer TA Wade MJ Genes with social effects are expected to harbor more sequence variation within and between species Evolution 2009 63 1685 1696 10.1111/j.1558-5646.2009.00670.x 19245396 PMC3151725 · DOI
  68. [72]Linksvayer TA Wade MJ Theoretical predictions for sociogenomic data: the effects of Kin selection and sex-limited expression on the evolution of social insect genomes Front Ecol Evol 2016 4 1 10 10.3389/fevo.2016.00065 · DOI
  69. [73]Van Dyken JD Wade MJ Detecting the molecular signature of social conflict: theory and a test with bacterial quorum sensing genes Am Nat 2012 179 436 450 10.1086/664609 22437174 PMC4098724 · DOI
  70. [74]Van Dyken JD Linksvayer TA Wade MJ Kin selection-mutation balance: a model for the origin, maintenance, and consequences of social cheating Am Nat 2011 177 288 300 10.1086/658365 21460538 · DOI
  71. [75]Hall DW Goodisman MAD The effects of kin selection on rates of molecular evolution in social insects Evolution 2012 66 2080 2093 10.1111/j.1558-5646.2012.01602.x 22759286 · DOI
  72. [76]Schuster M Lostroh CP Ogi T Greenberg EP Identification, timing, and signal specificity of Pseudomonas aeruginosa quorum-controlled genes: a transcriptome analysis J Bacteriol 2003 185 2066 2079 10.1128/JB.185.7.2066-2079.2003 12644476 PMC151497 · DOI
  73. [77]Comella N Grossman AD Conservation of genes and processes controlled by the quorum response in bacteria: characterization of genes controlled by the quorum-sensing transcription factor ComA in Bacillus subtilis Mol Microbiol 2005 57 1159 1174 10.1111/j.1365-2958.2005.04749.x 16091051 · DOI
  74. [78]Molle V Fujita M Jensen ST Eichenberger P González-Pastor JE et al The Spo0A regulon of Bacillus subtilis Mol Microbiol 2003 50 1683 1701 10.1046/j.1365-2958.2003.03818.x 14651647 · DOI
  75. [79]Kobayashi K Gradual activation of the response regulator DegU controls serial expression of genes for flagellum formation and biofilm formation in Bacillus subtilis Mol Microbiol 2007 66 395 409 10.1111/j.1365-2958.2007.05923.x 17850253 · DOI
  76. [80]Chong RA Park H Moran NA Genome evolution of the obligate endosymbiont Buchnera aphidicola Mol Biol Evol 2019 36 1481 1489 10.1093/molbev/msz082 30989224 · DOI
  77. [81]Stelzner K Vollmuth N Rudel T Intracellular lifestyle of Chlamydia trachomatis and host-pathogen interactions Nat Rev Microbiol 2023 21 448 462 10.1038/s41579-023-00860-y 36788308 · DOI
  78. [82]Hansen AK Moran NA Aphid genome expression reveals host-symbiont cooperation in the production of amino acids Proc Natl Acad Sci U S A 2011 108 2849 2854 10.1073/pnas.1013465108 21282658 PMC3041126 · DOI
  79. [83]Elwell C Mirrashidi K Engel J Chlamydia cell biology and pathogenesis Nat Rev Microbiol 2016 14 385 400 10.1038/nrmicro.2016.30 27108705 PMC4886739 · DOI
  80. [84]Blackwell GA Hunt M Malone KM Lima L Horesh G et al Exploring bacterial diversity via a curated and searchable snapshot of archived DNA sequences PLoS Biol 2021 19 e3001421 10.1371/journal.pbio.3001421 34752446 PMC8577725 · DOI · Paper page
  81. [85]Blin K Kim HU Medema MH Weber T Recent development of antiSMASH and other computational approaches to mine secondary metabolite biosynthetic gene clusters Brief Bioinform 2018 20 1103 1113 10.1093/bib/bbx146 29112695 PMC6781578 · DOI
  82. [86]Blin K Shaw S Augustijn HE Reitz ZL Biermann F et al antiSMASH 7.0: new and improved predictions for detection, regulation, chemical structures and visualisation Nucleic Acids Res 2023 51 W46 W50 10.1093/nar/gkad344 37140036 PMC10320115 · DOI
  83. [87]Smith EE Sims EH Spencer DH Kaul R Olson MV Evidence for diversifying selection at the pyoverdine locus of Pseudomonas aeruginosa J Bacteriol 2005 187 2138 2147 10.1128/JB.187.6.2138-2147.2005 15743962 PMC1064051 · DOI
  84. [88]Lee W van Baalen M Jansen VAA An evolutionary mechanism for diversity in siderophore-producing bacteria Ecol Lett 2012 15 119 125 10.1111/j.1461-0248.2011.01717.x 22151214 · DOI
  85. [89]Ostrowski EA Shen Y Tian X Sucgang R Jiang H et al Genomic signatures of cooperation and conflict in the social amoeba Curr Biol 2015 25 1661 1665 10.1016/j.cub.2015.04.059 26051890 PMC4591038 · DOI
  86. [91]Brandis G Hughes D The selective advantage of synonymous codon usage bias in Salmonella PLoS Genet 2016 1 16 10.1371/journal.pgen.1005926 26963725 PMC4786093 · DOI
  87. [92]Madgwick PG Belcher LJ Wolf JB Greenbeard genes: theory and reality Trends Ecol Evol 2019 34 1 12 10.1016/j.tree.2019.08.001 31488327 · DOI
  88. [93]Dawkins R The Selfish Gene Oxford University Press 1976
  89. [94]Scott TW Grafen A West SA Multiple social encounters can eliminate Crozier’s paradox and stabilise genetic kin recognition Nat Commun 2022 13 3902 10.1038/s41467-022-31545-4 35794146 PMC9259605 · DOI
  90. [95]Grafen A Do animals really recognize kin? Anim Behav 1990 39 42 54 10.1016/S0003-3472(05)80724-9 · DOI

Cited by

Sorted by citations

Authors
Belcher, L. J., Dewar, A. E., Hao, C., Katz, Z., Ghoul, M., & West, S. A.
Affiliations
University of Oxford (GB)
Corresponding author
Belcher, Laurence J.
ORCID
Venue
Microbial Genomics
Publisher
Microbiology Society
Published
2023-12-20
Volume
9
Issue
12
ISSN
2057-5858 (ISSN-L)
DOI
10.1099/mgen.0.001171
PMC
PMC10763506
OpenAlex
W4389993468
Cited by
13
References
4
Citations by year
2026: 5 · 2025: 5 · 2024: 3
FWCI
1.15
Type
journal article
Language
en
Open access
Licence
Locations
  • Microbial Genomics (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
Funders
  • European Research Council (834164)
  • BBSRC
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bacterial biofilms and quorum sensing
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
Keywords
bacterial cooperation, extracellular proteins, gene function prediction, kin selection, population genetics, Pseudomonas aeruginosa, Bacillus subtilis, bioinformatics software
MeSH terms
Anti-Bacterial Agents, Bacteria, Genes, Bacterial, Pseudomonas aeruginosa, Computational Biology, Genomics

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review