Highly Parallel Genomic Selection Response in Replicated Drosophila melanogaster Populations with Reduced Genetic Variation.
Drosophila melanogaster
evolve and resequence
experimental evolution
inbred strains
parallelism
polygenic trait
Journal
Genome biology and evolution
ISSN: 1759-6653
Titre abrégé: Genome Biol Evol
Pays: England
ID NLM: 101509707
Informations de publication
Date de publication:
05 11 2021
05 11 2021
Historique:
accepted:
21
10
2021
pubmed:
26
10
2021
medline:
1
4
2022
entrez:
25
10
2021
Statut:
ppublish
Résumé
Many adaptive traits are polygenic and frequently more loci contributing to the phenotype are segregating than needed to express the phenotypic optimum. Experimental evolution with replicated populations adapting to a new controlled environment provides a powerful approach to study polygenic adaptation. Because genetic redundancy often results in nonparallel selection responses among replicates, we propose a modified evolve and resequence (E&R) design that maximizes the similarity among replicates. Rather than starting from many founders, we only use two inbred Drosophila melanogaster strains and expose them to a very extreme, hot temperature environment (29 °C). After 20 generations, we detect many genomic regions with a strong, highly parallel selection response in 10 evolved replicates. The X chromosome has a more pronounced selection response than the autosomes, which may be attributed to dominance effects. Furthermore, we find that the median selection coefficient for all chromosomes is higher in our two-genotype experiment than in classic E&R studies. Because two random genomes harbor sufficient variation for adaptive responses, we propose that this approach is particularly well-suited for the analysis of polygenic adaptation.
Identifiants
pubmed: 34694407
pii: 6409861
doi: 10.1093/gbe/evab239
pmc: PMC8599828
pii:
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : Austrian Science Fund FWF
ID : P 29133
Pays : Austria
Informations de copyright
© The Author(s) 2021. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
Références
Genetics. 2018 Aug;209(4):1279-1303
pubmed: 29895560
Genetics. 2019 Mar;211(3):943-961
pubmed: 30593495
Heredity (Edinb). 2015 May;114(5):431-40
pubmed: 25269380
G3 (Bethesda). 2019 Nov 5;9(11):3715-3725
pubmed: 31690597
Bioinformatics. 2011 Nov 1;27(21):2987-93
pubmed: 21903627
J Theor Biol. 2018 Apr 7;442:123-128
pubmed: 29355539
Annu Rev Genomics Hum Genet. 2019 Aug 31;20:461-493
pubmed: 31283361
Genome Biol Evol. 2020 Mar 1;12(3):151-159
pubmed: 32159748
Nature. 2010 Apr 15;464(7291):1039-42
pubmed: 20393561
Nucleic Acids Res. 2019 Jan 8;47(D1):D759-D765
pubmed: 30364959
Heredity (Edinb). 1970 Feb;25(1):11-21
pubmed: 5004595
Trends Ecol Evol. 2020 Sep;35(9):809-822
pubmed: 32439075
Heredity (Edinb). 1968 Aug;23(3):433-42
pubmed: 5250124
Mol Biol Evol. 2019 Dec 1;36(12):2890-2905
pubmed: 31400203
Elife. 2019 Mar 21;8:
pubmed: 30895923
Theor Popul Biol. 2018 Jul;122:110-127
pubmed: 29246460
G3 (Bethesda). 2014 Sep 18;4(9):1623-33
pubmed: 25237114
Evolution. 2010 Mar 1;64(3):663-74
pubmed: 19796145
Genetics. 2020 Jan;214(1):3-48
pubmed: 31907300
Nat Rev Genet. 2009 Mar;10(3):195-205
pubmed: 19204717
Mol Ecol. 2014 Apr;23(7):1813-27
pubmed: 24372777
Nat Rev Genet. 2020 Dec;21(12):769-781
pubmed: 32601318
Mol Biol Evol. 2014 Feb;31(2):474-83
pubmed: 24214537
Am Nat. 2015 Oct;186 Suppl 1:S74-89
pubmed: 26656219
Nat Rev Genet. 2014 Nov;15(11):749-63
pubmed: 25246196
Genome Biol Evol. 2021 Aug 3;13(8):
pubmed: 34190980
Nat Genet. 2012 Sep;44(9):1015-9
pubmed: 22902787
Genetics. 1976 Aug;83(4):793-810
pubmed: 823074
Nat Rev Genet. 2010 Oct;11(10):665-7
pubmed: 20838407
Trends Genet. 2013 Sep;29(9):537-44
pubmed: 23790324
Elife. 2019 Mar 21;8:
pubmed: 30895926
Nucleic Acids Res. 1988 Feb 11;16(3):1215
pubmed: 3344216
PLoS Genet. 2014 Aug 07;10(8):e1004412
pubmed: 25102153
Mol Biol Evol. 2018 Mar 1;35(3):549-563
pubmed: 29029198
PLoS Genet. 2019 Mar 20;15(3):e1008035
pubmed: 30893299
PLoS Genet. 2011 Mar;7(3):e1001336
pubmed: 21437274
Genetics. 1974 Oct;78(2):737-56
pubmed: 4448362
PLoS Comput Biol. 2018 Aug 16;14(8):e1006413
pubmed: 30114186
Mol Biol Evol. 1983 Dec;1(1):84-93
pubmed: 6599962
Bioinformatics. 2015 Jul 1;31(13):2202-4
pubmed: 25701572
Genetics. 2015 Apr;199(4):991-1005
pubmed: 25672748
Nature. 1973 Nov 9;246(5428):96-8
pubmed: 4585855
PLoS Genet. 2012;8(10):e1002905
pubmed: 23071443
Mol Biol Evol. 2018 Jan 1;35(1):180-201
pubmed: 29069452
Genet Res. 1998 Oct;72(2):79-91
pubmed: 9883095
Theor Appl Genet. 1968 Jun;38(6):226-31
pubmed: 24442307
Bioinformatics. 2011 Aug 1;27(15):2156-8
pubmed: 21653522
Heredity (Edinb). 2017 Jan;118(1):42-51
pubmed: 27848948
J Exp Biol. 2010 Mar 15;213(6):870-80
pubmed: 20190112
Elife. 2019 Mar 21;8:
pubmed: 30895925
Curr Biol. 2010 Feb 23;20(4):R208-15
pubmed: 20178769
G3 (Bethesda). 2020 Sep 2;10(9):3213-3227
pubmed: 32646912
Mol Ecol. 2020 Sep;29(18):3466-3475
pubmed: 32762052
PLoS Genet. 2015 Feb 26;11(2):e1004883
pubmed: 25719753
Mol Biol Evol. 2014 Apr;31(4):1040-55
pubmed: 24441104
Nat Rev Genet. 2015 Oct;16(10):567-82
pubmed: 26347030
Genet Res. 1995 Apr;65(2):123-45
pubmed: 7605514
Genome Biol. 2019 Aug 15;20(1):169
pubmed: 31416462
Bioinformatics. 2009 Aug 15;25(16):2078-9
pubmed: 19505943
Genetics. 2006 Jul;173(3):1793-811
pubmed: 16702422
Genetica. 2021 Jun;149(3):143-153
pubmed: 33963492
Mol Ecol Resour. 2018 May;18(3):676-680
pubmed: 29171165
Bioinformatics. 2011 Dec 15;27(24):3435-6
pubmed: 22025480
Bioinformatics. 2010 Mar 15;26(6):841-2
pubmed: 20110278
Genetics. 2017 Feb;205(2):871-890
pubmed: 28007884
Mol Biol Evol. 2017 Nov 1;34(11):3023-3034
pubmed: 28961717
Mol Biol Evol. 2018 Jan 1;35(1):50-65
pubmed: 29309688
Mol Ecol. 2019 May;28(9):2136-2154
pubmed: 30963641
Mol Ecol Resour. 2017 Jan;17(1):44-53
pubmed: 27401132
PLoS Biol. 2019 Feb 4;17(2):e3000128
pubmed: 30716062
Proc Natl Acad Sci U S A. 2014 Apr 22;111(16):5938-43
pubmed: 24711428
Genetics. 2018 May;209(1):255-264
pubmed: 29500183
Nat Rev Genet. 2002 Apr;3(4):252-61
pubmed: 11967550
BMC Evol Biol. 2019 Feb 26;19(1):61
pubmed: 30808292