Inferring Long-Term Effective Population Size with Mutation-Selection Models.
codon models
life-history traits
mutation rate
mutation–selection models
phylogenetic
population genetic
population size
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:
27 09 2021
27 09 2021
Historique:
pubmed:
1
7
2021
medline:
26
3
2022
entrez:
30
6
2021
Statut:
ppublish
Résumé
Mutation-selection phylogenetic codon models are grounded on population genetics first principles and represent a principled approach for investigating the intricate interplay between mutation, selection, and drift. In their current form, mutation-selection codon models are entirely characterized by the collection of site-specific amino-acid fitness profiles. However, thus far, they have relied on the assumption of a constant genetic drift, translating into a unique effective population size (Ne) across the phylogeny, clearly an unrealistic assumption. This assumption can be alleviated by introducing variation in Ne between lineages. In addition to Ne, the mutation rate (μ) is susceptible to vary between lineages, and both should covary with life-history traits (LHTs). This suggests that the model should more globally account for the joint evolutionary process followed by all of these lineage-specific variables (Ne, μ, and LHTs). In this direction, we introduce an extended mutation-selection model jointly reconstructing in a Bayesian Monte Carlo framework the fitness landscape across sites and long-term trends in Ne, μ, and LHTs along the phylogeny, from an alignment of DNA coding sequences and a matrix of observed LHTs in extant species. The model was tested against simulated data and applied to empirical data in mammals, isopods, and primates. The reconstructed history of Ne in these groups appears to correlate with LHTs or ecological variables in a way that suggests that the reconstruction is reasonable, at least in its global trends. On the other hand, the range of variation in Ne inferred across species is surprisingly narrow. This last point suggests that some of the assumptions of the model, in particular concerning the assumed absence of epistatic interactions between sites, are potentially problematic.
Identifiants
pubmed: 34191010
pii: 6311666
doi: 10.1093/molbev/msab160
pmc: PMC8476147
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
4573-4587Informations de copyright
© The Author(s) 2021. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
Références
Proc Natl Acad Sci U S A. 2010 Nov 23;107(47):20423-8
pubmed: 21059910
Syst Biol. 2002 Oct;51(5):729-39
pubmed: 12396587
BMC Evol Biol. 2018 Feb 8;18(1):17
pubmed: 29422024
PLoS Genet. 2011 Mar;7(3):e1001342
pubmed: 21436896
Syst Biol. 2002 Oct;51(5):689-702
pubmed: 12396584
Proc Natl Acad Sci U S A. 2007 Aug 14;104(33):13390-5
pubmed: 17679693
Proc Natl Acad Sci U S A. 1979 Jul;76(7):3440-4
pubmed: 16592684
Mol Biol Evol. 1994 Sep;11(5):725-36
pubmed: 7968486
Mol Ecol. 2008 Dec;17(24):5349-63
pubmed: 19121002
Mol Biol Evol. 2007 Jan;24(1):228-35
pubmed: 17041152
Curr Opin Genet Dev. 2003 Dec;13(6):562-8
pubmed: 14638315
Bioinformatics. 2014 Nov 1;30(21):3020-8
pubmed: 25053744
Nat Ecol Evol. 2017 Dec;1(12):1923-1930
pubmed: 29062121
J Mol Evol. 2008 Oct;67(4):418-26
pubmed: 18818860
Mol Biol Evol. 2011 Jan;28(1):729-44
pubmed: 20926596
J Mol Evol. 1981;17(6):368-76
pubmed: 7288891
Genome Biol Evol. 2013;5(7):1273-90
pubmed: 23711670
Proc Natl Acad Sci U S A. 1999 Apr 13;96(8):4482-7
pubmed: 10200288
Proc Natl Acad Sci U S A. 2010 Mar 9;107(10):4629-34
pubmed: 20176949
Mol Biol Evol. 2017 Jan;34(1):204-214
pubmed: 27744408
J Mol Evol. 1998 Apr;46(4):409-18
pubmed: 9541535
Mol Ecol. 2013 Nov;22(22):5685-99
pubmed: 24102689
Proc Natl Acad Sci U S A. 2015 Jun 23;112(25):E3226-35
pubmed: 26056312
Mol Biol Evol. 2008 Mar;25(3):568-79
pubmed: 18178545
Proteins. 2011 May;79(5):1396-407
pubmed: 21337623
Genome Biol Evol. 2021 Aug 3;13(8):
pubmed: 34190972
Biol Direct. 2017 Jan 17;12(1):1
pubmed: 28095902
G3 (Bethesda). 2014 Jul 03;4(9):1667-70
pubmed: 24996580
Genetics. 2020 Oct;216(2):559-572
pubmed: 32839240
Mol Biol Evol. 2007 Aug;24(8):1586-91
pubmed: 17483113
Mol Biol Evol. 2017 Feb 1;34(2):391-407
pubmed: 28110273
PLoS Genet. 2011 Dec;7(12):e1002395
pubmed: 22144911
PLoS Biol. 2016 Jan 13;14(1):e1002355
pubmed: 26761240
Mol Biol Evol. 2017 Jul 1;34(7):1812-1819
pubmed: 28387841
PLoS One. 2013 Sep 27;8(9):e76213
pubmed: 24086709
J Theor Biol. 1965 Mar;8(2):357-66
pubmed: 5876245
Bioinformatics. 2017 Feb 1;33(3):354-362
pubmed: 28172542
J Evol Biol. 2009 Aug;22(8):1770-4
pubmed: 19522730
Genome Biol Evol. 2013;5(9):1584-93
pubmed: 23884461
Genetics. 2011 Dec;189(4):1389-402
pubmed: 21954163
Genetics. 2012 Mar;190(3):1101-15
pubmed: 22209901
Proc Natl Acad Sci U S A. 2014 Apr 15;111(15):E1450
pubmed: 24706894
Mol Biol Evol. 2018 Dec 1;35(12):2900-2912
pubmed: 30247705
Mol Biol Evol. 2016 Jun;33(6):1517-27
pubmed: 26944704
Trends Ecol Evol. 2014 Jan;29(1):33-41
pubmed: 24148292
Mol Biol Evol. 1998 May;15(5):568-73
pubmed: 9580986
BMC Evol Biol. 2007 Nov 30;7:241
pubmed: 18053139
Science. 2011 Oct 28;334(6055):521-4
pubmed: 21940861
Nature. 2014 Nov 13;515(7526):261-3
pubmed: 25141177
Biol Lett. 2015 Apr;11(4):20141031
pubmed: 25854546
Genome Biol. 2019 Jan 7;20(1):5
pubmed: 30616647
Protein Sci. 2016 Jul;25(7):1354-62
pubmed: 27028523
Mol Biol Evol. 2003 Aug;20(8):1231-9
pubmed: 12777508
Nucleic Acids Res. 2013 Jan;41(Database issue):D1027-33
pubmed: 23193293
PLoS Genet. 2008 Aug 01;4(8):e1000144
pubmed: 18670650
Mol Biol Evol. 2015 Apr;32(4):1097-108
pubmed: 25576365
Mol Biol Evol. 2019 Apr 1;36(4):861-862
pubmed: 30698751
Nat Rev Genet. 2015 Jul;16(7):409-20
pubmed: 26055156
Nat Rev Genet. 2007 Aug;8(8):610-8
pubmed: 17637733
Mol Biol Evol. 2012 Jul;29(7):1861-74
pubmed: 22319139
J Comput Biol. 2014 Sep;21(9):676-90
pubmed: 24918812
Genetics. 2016 Jun;203(2):847-62
pubmed: 27052568
Evolution. 2012 Jun;66(6):1773-87
pubmed: 22671546
Trends Genet. 2009 Mar;25(3):111-9
pubmed: 19232770
Bioinformatics. 2014 Apr 1;30(7):1020-1
pubmed: 24351710
Genetics. 1998 Oct;150(2):911-9
pubmed: 9755219
PLoS Genet. 2016 Jan 11;12(1):e1005774
pubmed: 26752180
Nat Rev Genet. 2011 Jan;12(1):32-42
pubmed: 21102527
Nat Rev Genet. 2016 Feb;17(2):109-21
pubmed: 26781812
Proc Natl Acad Sci U S A. 2012 May 22;109(21):E1352-9
pubmed: 22547823
PLoS Comput Biol. 2006 Jun 23;2(6):e69
pubmed: 16789817
Mol Biol Evol. 1998 Jul;15(7):910-7
pubmed: 9656490
Nature. 2011 Jul 13;475(7357):493-6
pubmed: 21753753
Mol Biol Evol. 1994 Sep;11(5):715-24
pubmed: 7968485
Bioinformatics. 2008 Jan 1;24(1):56-62
pubmed: 18003644
Annu Rev Ecol Evol Syst. 2014 Nov 1;45:179-201
pubmed: 26740803
Genetics. 2014 May;197(1):257-71
pubmed: 24532780
Mol Biol Evol. 2004 Jul;21(7):1201-13
pubmed: 15014159