Recombination Facilitates Adaptive Evolution in Rhizobial Soil Bacteria.
adaptive evolution
beneficial mutations
recombination
rhizobium
Journal
Molecular biology and evolution
ISSN: 1537-1719
Titre abrégé: Mol Biol Evol
Pays: United States
ID NLM: 8501455
Informations de publication
Date de publication:
09 12 2021
09 12 2021
Historique:
pubmed:
20
8
2021
medline:
29
3
2022
entrez:
19
8
2021
Statut:
ppublish
Résumé
Homologous recombination is expected to increase natural selection efficacy by decoupling the fate of beneficial and deleterious mutations and by readily creating new combinations of beneficial alleles. Here, we investigate how the proportion of amino acid substitutions fixed by adaptive evolution (α) depends on the recombination rate in bacteria. We analyze 3,086 core protein-coding sequences from 196 genomes belonging to five closely related species of the genus Rhizobium. These genes are found in all species and do not display any signs of introgression between species. We estimate α using the site frequency spectrum (SFS) and divergence data for all pairs of species. We evaluate the impact of recombination within each species by dividing genes into three equally sized recombination classes based on their average level of intragenic linkage disequilibrium. We find that α varies from 0.07 to 0.39 across species and is positively correlated with the level of recombination. This is both due to a higher estimated rate of adaptive evolution and a lower estimated rate of nonadaptive evolution, suggesting that recombination both increases the fixation probability of advantageous variants and decreases the probability of fixation of deleterious variants. Our results demonstrate that homologous recombination facilitates adaptive evolution measured by α in the core genome of prokaryote species in agreement with studies in eukaryotes.
Identifiants
pubmed: 34410427
pii: 6355043
doi: 10.1093/molbev/msab247
pmc: PMC8662638
doi:
Substances chimiques
Soil
0
Banques de données
figshare
['10.6084/m9.figshare.11568894.v5']
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
5480-5490Informations de copyright
© The Author(s) 2021. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
Références
Genetics. 1964 Jan;49(1):49-67
pubmed: 17248194
Mol Biol Evol. 2007 Aug;24(8):1792-800
pubmed: 17545186
Open Biol. 2015 Jan;5(1):140133
pubmed: 25589577
Mol Biol Evol. 2014 Apr;31(4):1010-28
pubmed: 24489114
Genetics. 2011 Dec;189(4):1427-37
pubmed: 21954160
Proc Natl Acad Sci U S A. 2003 Dec 23;100(26):15754-7
pubmed: 14660790
Mol Biol Evol. 2009 Sep;26(9):2097-108
pubmed: 19535738
Curr Biol. 2005 Sep 20;15(18):1651-6
pubmed: 16169487
Evol Lett. 2019 May 01;3(3):299-312
pubmed: 31171985
Evolution. 2008 Jan;62(1):39-49
pubmed: 17976191
ISME J. 2009 Feb;3(2):199-208
pubmed: 18830278
Genome Biol. 2006;7(4):R34
pubmed: 16640791
Theor Popul Biol. 1976 Dec;10(3):254-75
pubmed: 1013905
FEMS Microbiol Ecol. 2010 Sep;73(3):563-76
pubmed: 20533948
Mol Biol Evol. 2006 Jul;23(7):1348-56
pubmed: 16621913
Bioinformatics. 2009 Jun 1;25(11):1422-3
pubmed: 19304878
Mol Syst Biol. 2011 Oct 11;7:539
pubmed: 21988835
Mol Biol Evol. 2000 Jan;17(1):32-43
pubmed: 10666704
ISME J. 2017 Jan;11(1):248-262
pubmed: 27420027
Phys Rev Lett. 2005 Mar 11;94(9):098102
pubmed: 15784005
Bioinformatics. 2014 May 1;30(9):1312-3
pubmed: 24451623
Curr Opin Microbiol. 2011 Oct;14(5):615-23
pubmed: 21856213
PLoS One. 2014 Aug 19;9(8):e105015
pubmed: 25137074
Genetics. 1974 Oct;78(2):737-56
pubmed: 4448362
Nature. 2012 Feb 08;482(7384):173-8
pubmed: 22318601
Cold Spring Harb Symp Quant Biol. 2009;74:177-86
pubmed: 19734202
Trends Microbiol. 2010 Jul;18(7):315-22
pubmed: 20452218
Genetics. 2001 Jul;158(3):1227-34
pubmed: 11454770
FEMS Microbiol Rev. 2011 Sep;35(5):957-76
pubmed: 21711367
Genetics. 2000 Jun;155(2):929-44
pubmed: 10835411
Microb Genom. 2020 Apr;6(4):
pubmed: 32176601
Genet Res. 1966 Dec;8(3):269-94
pubmed: 5980116
J Comput Biol. 2012 May;19(5):455-77
pubmed: 22506599
J Mol Evol. 1995 Feb;40(2):190-226
pubmed: 7699723
Science. 2003 Aug 8;301(5634):785-9
pubmed: 12907787
PLoS Biol. 2007 Sep;5(9):e225
pubmed: 17713986
PLoS Comput Biol. 2015 Feb 12;11(2):e1004041
pubmed: 25675341
PLoS Genet. 2009 Aug;5(8):e1000601
pubmed: 19680442
Nat Rev Genet. 2007 Aug;8(8):610-8
pubmed: 17637733
Genes (Basel). 2021 Jan 18;12(1):
pubmed: 33477547
Mol Biol Evol. 2016 Feb;33(2):442-55
pubmed: 26494843
Genetics. 2017 Nov;207(3):1103-1119
pubmed: 28951530
Philos Trans R Soc Lond B Biol Sci. 2006 Nov 29;361(1475):1929-40
pubmed: 17062412
PLoS Genet. 2016 Jan 11;12(1):e1005774
pubmed: 26752180
Genome Res. 2010 Mar;20(3):291-300
pubmed: 20067940
Mol Biol Evol. 2019 Sep 1;36(9):2013-2028
pubmed: 31147689
Genetics. 2006 Jun;173(2):891-900
pubmed: 16547091
Mol Biol Evol. 2010 Apr;27(4):848-61
pubmed: 20008457
Genetics. 2018 Mar;208(3):1247-1260
pubmed: 29330348
Curr Biol. 2009 Apr 28;19(8):655-60
pubmed: 19285399
Bioinformatics. 2014 Jul 15;30(14):2068-9
pubmed: 24642063
Trends Microbiol. 2010 Apr;18(4):141-8
pubmed: 20080407
Nature. 2000 May 18;405(6784):299-304
pubmed: 10830951
Genetics. 2005 Feb;169(2):533-8
pubmed: 15545641
Science. 2010 Jan 22;327(5964):469-74
pubmed: 20093474