Population-Genomic Analysis Identifies a Low Rate of Global Adaptive Fixation in the Proteins of the Cyclical Parthenogen Daphnia magna.
Daphnia magna
McDonald–Kreitman
RNA interference
adaptive evolution
arms race
distribution of fitness effects
immune genes
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:
02 03 2022
02 03 2022
Historique:
pubmed:
5
3
2022
medline:
30
4
2022
entrez:
4
3
2022
Statut:
ppublish
Résumé
Daphnia are well-established ecological and evolutionary models, and the interaction between D. magna and its microparasites is widely considered a paragon of the host-parasite coevolutionary process. Like other well-studied arthropods such as Drosophila melanogaster and Anopheles gambiae, D. magna is a small, widespread, and abundant species that is therefore expected to display a large long-term population size and high rates of adaptive protein evolution. However, unlike these other species, D. magna is cyclically asexual and lives in a highly structured environment (ponds and lakes) with moderate levels of dispersal, both of which are predicted to impact upon long-term effective population size and adaptive protein evolution. To investigate patterns of adaptive protein fixation, we produced the complete coding genomes of 36 D. magna clones sampled from across the European range (Western Palaearctic), along with draft sequences for the close relatives D. similis and D. lumholtzi, used as outgroups. We analyzed genome-wide patterns of adaptive fixation, with a particular focus on genes that have an a priori expectation of high rates, such as those likely to mediate immune responses, RNA interference against viruses and transposable elements, and those with a strongly male-biased expression pattern. We find that, as expected, D. magna displays high levels of diversity and that this is highly structured among populations. However, compared with Drosophila, we find that D. magna proteins appear to have a high proportion of weakly deleterious variants and do not show evidence of pervasive adaptive fixation across its entire range. This is true of the genome as a whole, and also of putative 'arms race' genes that often show elevated levels of adaptive substitution in other species. In addition to the likely impact of extensive, and previously documented, local adaptation, we speculate that these findings may reflect reduced efficacy of selection associated with cyclical asexual reproduction.
Identifiants
pubmed: 35244177
pii: 6542319
doi: 10.1093/molbev/msac048
pmc: PMC8963301
pii:
doi:
Substances chimiques
DNA Transposable Elements
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Informations de copyright
© The Author(s) 2022. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
Références
J Evol Biol. 2009 Mar;22(3):515-26
pubmed: 19170822
Nature. 2002 Feb 28;415(6875):1022-4
pubmed: 11875568
BMC Evol Biol. 2012 May 11;12:63
pubmed: 22577801
Mol Biol Evol. 2020 Sep 1;37(9):2661-2678
pubmed: 32413142
Science. 2008 Jun 20;320(5883):1632-5
pubmed: 18566285
Bioinformatics. 2009 Jul 15;25(14):1754-60
pubmed: 19451168
Ecotoxicology. 2011 May;20(3):552-62
pubmed: 21380530
BMC Genomics. 2008 Nov 04;9:524
pubmed: 18983662
G3 (Bethesda). 2018 May 4;8(5):1523-1533
pubmed: 29535148
Genome Res. 2016 Jan;26(1):60-9
pubmed: 26518480
Proc Natl Acad Sci U S A. 2001 May 22;98(11):6256-60
pubmed: 11353872
Mol Biol Evol. 2008 Jun;25(6):1007-15
pubmed: 18195052
Bioinformatics. 2014 Apr 1;30(7):923-30
pubmed: 24227677
Proc Biol Sci. 2019 Jul 24;286(1907):20190929
pubmed: 31337313
Nature. 1991 Jun 20;351(6328):652-4
pubmed: 1904993
Genetics. 2000 Dec;156(4):1879-88
pubmed: 11102381
Mol Ecol. 2010 Aug;19(15):3076-87
pubmed: 20609079
Genetics. 2006 Oct;174(2):893-900
pubmed: 16951084
Nucleic Acids Res. 2002 Jul 15;30(14):3059-66
pubmed: 12136088
Mol Ecol. 2015 Jul;24(14):3529-45
pubmed: 25943689
Bioinformatics. 2008 Mar 1;24(5):637-44
pubmed: 18218656
Mol Biol Evol. 2013 Apr;30(4):772-80
pubmed: 23329690
Bioinformatics. 2013 Nov 1;29(21):2669-77
pubmed: 23990416
Genetics. 2019 May;212(1):287-303
pubmed: 30923166
Mol Biol Evol. 2018 May 1;35(5):1092-1103
pubmed: 29390090
Genetics. 2009 May;182(1):313-23
pubmed: 19299338
Nature. 2007 Dec 6;450(7171):870-3
pubmed: 18004303
PLoS Genet. 2014 Sep 25;10(9):e1004622
pubmed: 25255320
Yale J Biol Med. 2016 Dec 23;89(4):499-512
pubmed: 28018141
Heredity (Edinb). 2008 Jan;100(1):19-31
pubmed: 17878920
BMC Genomics. 2014 Oct 04;15:859
pubmed: 25282344
Genetics. 2018 Jul;209(3):897-906
pubmed: 29769282
Genetics. 2012 Jan;190(1):5-22
pubmed: 22219506
PLoS Genet. 2020 Apr 6;16(4):e1008668
pubmed: 32251427
PLoS Genet. 2017 Sep 28;13(9):e1007023
pubmed: 28957326
Genome Res. 2010 Sep;20(9):1297-303
pubmed: 20644199
BMC Bioinformatics. 2011 Dec 22;12:491
pubmed: 22192575
Nat Ecol Evol. 2018 Jan;2(1):100-107
pubmed: 29180709
Proc Natl Acad Sci U S A. 2017 Apr 25;114(17):4465-4470
pubmed: 28400513
Mol Biol Evol. 2003 Jan;20(1):18-20
pubmed: 12519901
Science. 2011 Feb 4;331(6017):555-61
pubmed: 21292972
Bioinformatics. 2014 Aug 1;30(15):2114-20
pubmed: 24695404
Mol Biol Evol. 2009 Dec;26(12):2755-64
pubmed: 19713326
Trends Ecol Evol. 2006 Oct;21(10):569-75
pubmed: 16820244
Trends Genet. 2013 Sep;29(9):537-44
pubmed: 23790324
Genome Biol. 2014;15(12):550
pubmed: 25516281
G3 (Bethesda). 2017 May 5;7(5):1405-1416
pubmed: 28235826
Mol Biol Evol. 2017 Jun 1;34(6):1417-1428
pubmed: 28333215
Evolution. 2002 Dec;56(12):2368-73
pubmed: 12583577
Genetics. 2007 Nov;177(3):1321-35
pubmed: 18039869
Mol Phylogenet Evol. 2018 Dec;129:138-148
pubmed: 29920335
Proc Natl Acad Sci U S A. 2016 Apr 12;113(15):4110-5
pubmed: 26979956
Mol Biol Evol. 2007 Aug;24(8):1586-91
pubmed: 17483113
Genetics. 2016 Jan;202(1):297-312
pubmed: 26584902
G3 (Bethesda). 2018 Mar 28;8(4):1259-1272
pubmed: 29487186
Elife. 2016 May 17;5:
pubmed: 27187613
J Hered. 2009 Sep-Oct;100(5):605-17
pubmed: 19596713
Mol Biol Evol. 2020 Nov 1;37(11):3258-3266
pubmed: 32520985
PLoS Comput Biol. 2012;8(12):e1002806
pubmed: 23236270
Proc Natl Acad Sci U S A. 2013 May 21;110(21):8615-20
pubmed: 23650353
Mol Biol Evol. 2018 Jun 1;35(6):1366-1371
pubmed: 29722831
Genetics. 2007 Dec;177(4):2251-61
pubmed: 18073430
Genetics. 2005 Aug;170(4):1809-20
pubmed: 15937138
Am Nat. 2009 May;173(5):579-88
pubmed: 19272016
Genetics. 2006 Jun;173(2):821-37
pubmed: 16582427
Heredity (Edinb). 2020 Oct;125(4):173-183
pubmed: 32561843
Genetics. 2017 May;206(1):315-332
pubmed: 27932545
Mol Biol Evol. 2017 Jan;34(1):230-240
pubmed: 27702775
Mol Biol Evol. 2021 Apr 13;38(4):1512-1528
pubmed: 33258959
BMC Evol Biol. 2017 Jan 13;17(1):15
pubmed: 28086750
Mol Ecol. 2013 Jul;22(13):3567-79
pubmed: 23786714
Theor Appl Genet. 1968 Jun;38(6):226-31
pubmed: 24442307
BMC Genet. 2012 Apr 11;13:27
pubmed: 22494792
Nat Genet. 2011 May;43(5):491-8
pubmed: 21478889
Genetics. 2004 Jun;167(2):725-35
pubmed: 15238524
Mol Ecol. 2012 Feb;21(4):851-61
pubmed: 22221402
BMC Biol. 2017 Oct 30;15(1):98
pubmed: 29084517
Philos Trans R Soc Lond B Biol Sci. 2000 Dec 29;355(1404):1851-64
pubmed: 11205346
PLoS Genet. 2009 Oct;5(10):e1000698
pubmed: 19851448
Genome Res. 2003 Sep;13(9):2178-89
pubmed: 12952885
Sci Data. 2016 May 10;3:160030
pubmed: 27164179
Mol Biol Evol. 2013 Jun;30(6):1292-301
pubmed: 23412912
Trends Biochem Sci. 2016 Apr;41(4):324-337
pubmed: 26810602
Cold Spring Harb Perspect Biol. 2011 Nov 01;3(11):a002931
pubmed: 21730046
Curr Biol. 1999 Jul 15;9(14):747-50
pubmed: 10421576
J Lipid Res. 2016 Jun;57(6):925-42
pubmed: 27099397
PLoS Genet. 2018 Apr 25;14(4):e1007325
pubmed: 29694349
Genetics. 2011 Dec;189(4):1427-37
pubmed: 21954160
Trends Ecol Evol. 2014 Jan;29(1):33-41
pubmed: 24148292
Genetics. 2018 Apr;208(4):1585-1599
pubmed: 29437826
Mol Ecol. 2011 Mar;20(6):1083-91
pubmed: 21375616
Genome Biol Evol. 2012;4(5):658-67
pubmed: 22436998
PLoS Biol. 2005 Feb;3(2):e42
pubmed: 15678168
Comput Appl Biosci. 1997 Oct;13(5):555-6
pubmed: 9367129
Heredity (Edinb). 2015 Feb;114(2):241-8
pubmed: 25335558
Bioinformatics. 2013 Jan 1;29(1):15-21
pubmed: 23104886
Genome Res. 2008 Dec;18(12):1979-90
pubmed: 18757608
Mol Biol Evol. 2013 Feb;30(2):435-47
pubmed: 23104079
Mol Biol Evol. 2019 Jul 1;36(7):1405-1417
pubmed: 30865231
Mol Biol Evol. 2016 Dec;33(12):3308-3313
pubmed: 27687565
Bioessays. 2007 Apr;29(4):386-91
pubmed: 17373698
Mol Biol Evol. 2009 Sep;26(9):2097-108
pubmed: 19535738
Nat Genet. 2012 Jan 08;44(2):212-6
pubmed: 22231484
Proc Biol Sci. 2011 May 7;278(1710):1306-13
pubmed: 20943691
Proc Natl Acad Sci U S A. 2005 Jul 26;102(30):10557-62
pubmed: 16000407
Genetics. 2015 Apr;199(4):1229-41
pubmed: 25631317
Curr Protoc Bioinformatics. 2013;43:11.10.1-11.10.33
pubmed: 25431634
Genetics. 2013 Apr;193(4):1197-208
pubmed: 23341416
BMC Bioinformatics. 2010 Mar 08;11:119
pubmed: 20211023
Mol Biol Evol. 2016 Feb;33(2):442-55
pubmed: 26494843
Bioinformatics. 2009 Aug 15;25(16):2078-9
pubmed: 19505943
Genetics. 2017 Nov;207(3):1103-1119
pubmed: 28951530
PLoS Genet. 2016 Jan 11;12(1):e1005774
pubmed: 26752180
Heredity (Edinb). 2015 Feb;114(2):163-74
pubmed: 25227256
PLoS Genet. 2017 Feb 21;13(2):e1006596
pubmed: 28222092
BMC Genet. 2016 Oct 13;17(1):137
pubmed: 27737627
Mol Biol Evol. 2018 Mar 1;35(3):543-548
pubmed: 29220515
G3 (Bethesda). 2017 May 5;7(5):1569-1575
pubmed: 28341700
Proc Natl Acad Sci U S A. 2013 Sep 24;110(39):15740-5
pubmed: 23959868
BMC Res Notes. 2009 Dec 15;2:254
pubmed: 20003477
BMC Evol Biol. 2007 Feb 14;7:22
pubmed: 17300733