Hybridization Dynamics and Extensive Introgression in the Daphnia longispina Species Complex: New Insights from a High-Quality Daphnia galeata Reference Genome.
genome assembly
hybridization
introgression
resting eggs
species complex
whole-genome amplification
Journal
Genome biology and evolution
ISSN: 1759-6653
Titre abrégé: Genome Biol Evol
Pays: England
ID NLM: 101509707
Informations de publication
Date de publication:
01 12 2021
01 12 2021
Historique:
accepted:
24
11
2021
pubmed:
6
12
2021
medline:
1
4
2022
entrez:
5
12
2021
Statut:
ppublish
Résumé
Hybridization and introgression are recognized as an important source of variation that influence adaptive processes; both phenomena are frequent in the genus Daphnia, a keystone zooplankton taxon in freshwater ecosystems that comprises several species complexes. To investigate genome-wide consequences of introgression between species, we provide here the first high-quality genome assembly for a member of the Daphnia longispina species complex, Daphnia galeata. We further resequenced 49 whole genomes of three species of the complex and their interspecific hybrids both from genotypes sampled in the water column and from single resting eggs extracted from sediment cores. Populations from habitats with diverse ecological conditions offered an opportunity to study the dynamics of hybridization linked to ecological changes and revealed a high prevalence of hybrids. Using phylogenetic and population genomic approaches, we provide first insights into the intra- and interspecific genome-wide variability in this species complex and identify regions of high divergence. Finally, we assess the length of ancestry tracts in hybrids to characterize introgression patterns across the genome. Our analyses uncover a complex history of hybridization and introgression reflecting multiple generations of hybridization and backcrossing in the Daphnia longispina species complex. Overall, this study and the new resources presented here pave the way for a better understanding of ancient and contemporary gene flow in the species complex and facilitate future studies on resting egg banks accumulating in lake sediment.
Identifiants
pubmed: 34865004
pii: 6448229
doi: 10.1093/gbe/evab267
pmc: PMC8695838
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 29667
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
Zoology (Jena). 2021 Apr;145:125895
pubmed: 33561655
Ecol Lett. 2014 Mar;17(3):360-8
pubmed: 24400978
Mol Phylogenet Evol. 1996 Jun;5(3):495-510
pubmed: 8744763
Mol Ecol. 2018 Mar;27(6):1439-1456
pubmed: 29473242
Mol Biol Evol. 2018 Sep 1;35(9):2318-2326
pubmed: 29931083
Nat Ecol Evol. 2018 Mar;2(3):549-556
pubmed: 29335572
Trends Ecol Evol. 2008 Jan;23(1):38-44
pubmed: 18006185
Bioinformatics. 2009 Jul 15;25(14):1754-60
pubmed: 19451168
Proc Natl Acad Sci U S A. 2001 May 22;98(11):6256-60
pubmed: 11353872
J Evol Biol. 2016 Apr;29(4):720-35
pubmed: 26717418
Aquat Toxicol. 2019 May;210:69-84
pubmed: 30826642
Mol Ecol. 2021 Mar;30(5):1264-1280
pubmed: 33410230
Mol Ecol. 2014 Aug;23(16):4074-88
pubmed: 24724861
PeerJ. 2017 Mar 23;5:e3072
pubmed: 28348926
Proc Biol Sci. 2000 Sep 22;267(1455):1833-42
pubmed: 11052533
Mol Ecol. 2019 Feb;28(4):785-802
pubmed: 30582761
Bioinformatics. 2012 Dec 15;28(24):3326-8
pubmed: 23060615
Nature. 2009 Sep 24;461(7263):489-94
pubmed: 19779445
Bioinformatics. 2008 Mar 1;24(5):637-44
pubmed: 18218656
Genome Res. 2013 Nov;23(11):1817-28
pubmed: 24045163
Genome Biol. 2020 Sep 10;21(1):241
pubmed: 32912315
PLoS One. 2013 Jul 15;8(7):e69497
pubmed: 23869244
Syst Biol. 2017 May 01;66(3):320-337
pubmed: 27637567
Mol Phylogenet Evol. 2013 Nov;69(2):313-9
pubmed: 22982435
Bioinformatics. 2014 May 1;30(9):1236-40
pubmed: 24451626
Genome Res. 2010 Sep;20(9):1297-303
pubmed: 20644199
BMC Bioinformatics. 2011 Dec 22;12:491
pubmed: 22192575
Can J Microbiol. 1960 Dec;6:645-60
pubmed: 13788092
Science. 2011 Feb 4;331(6017):555-61
pubmed: 21292972
Bioinformatics. 2014 Aug 1;30(15):2114-20
pubmed: 24695404
G3 (Bethesda). 2017 May 5;7(5):1405-1416
pubmed: 28235826
PLoS Biol. 2020 Feb 27;18(2):e3000610
pubmed: 32108180
Mol Ecol. 2014 Mar;23(5):1124-36
pubmed: 24460929
Gigascience. 2015 Feb 25;4:7
pubmed: 25722852
Nat Biotechnol. 2019 Aug;37(8):907-915
pubmed: 31375807
Mol Biol Evol. 1993 Nov;10(6):1289-302
pubmed: 8277855
Genome Res. 2015 Nov;25(11):1656-65
pubmed: 26355005
New Phytol. 2019 Jan;221(1):515-526
pubmed: 30136727
Genome Biol Evol. 2014 Apr;6(4):886-96
pubmed: 24696399
Mol Phylogenet Evol. 2019 Aug;137:250-262
pubmed: 31125657
Mol Ecol. 2009 Apr;18(8):1616-28
pubmed: 19298264
PLoS Biol. 2019 Feb 7;17(2):e2006288
pubmed: 30730876
Bioinformatics. 2018 Sep 1;34(17):i884-i890
pubmed: 30423086
Mol Ecol. 2017 Apr;26(8):2212-2236
pubmed: 27997046
Nat Commun. 2018 Aug 14;9(1):3258
pubmed: 30108219
Bioinformatics. 2016 Sep 1;32(17):2577-81
pubmed: 27153665
Philos Trans R Soc Lond B Biol Sci. 2008 Sep 12;363(1505):2943-52
pubmed: 18508753
Oecologia. 1986 Mar;68(4):507-511
pubmed: 28311704
Microbiology (Reading). 2002 Jan;148(Pt 1):257-266
pubmed: 11782518
Evolution. 2016 Jul;70(7):1609-21
pubmed: 27196373
Nucleic Acids Res. 2005 Nov 28;33(20):6494-506
pubmed: 16314312
Evol Lett. 2020 Nov 06;5(1):86-100
pubmed: 33552538
BMC Bioinformatics. 2011 Jun 18;12:246
pubmed: 21682921
Bioinformatics. 2015 Oct 1;31(19):3210-2
pubmed: 26059717
Philos Trans R Soc Lond B Biol Sci. 2018 Oct 5;373(1757):
pubmed: 30150218
Mol Ecol. 2020 Mar;29(5):956-969
pubmed: 32034818
Mol Ecol. 2011 Mar;20(6):1191-207
pubmed: 21294799
Nucleic Acids Res. 2019 Jan 8;47(D1):D506-D515
pubmed: 30395287
Trends Ecol Evol. 2013 May;28(5):274-82
pubmed: 23395434
Evolution. 2011 Jul;65(7):1897-911
pubmed: 21729046
Mol Ecol Resour. 2018 Jan;18(1):118-127
pubmed: 28926213
New Phytol. 2014 Nov;204(3):693-703
pubmed: 25078531
Nat Ecol Evol. 2017 Feb 17;1(4):82
pubmed: 28812654
Mol Phylogenet Evol. 2009 Mar;50(3):423-36
pubmed: 19124080
J Biol. 2009 Oct 13;8(9):82
pubmed: 19833002
Evolution. 2014 Apr;68(4):935-49
pubmed: 24299519
Genome Biol Evol. 2016 Oct 23;8(10):3120-3139
pubmed: 27604882
Genetics. 2012 Nov;192(3):1065-93
pubmed: 22960212
Am J Hum Genet. 2009 Feb;84(2):210-23
pubmed: 19200528
Bioinformatics. 2016 Oct 1;32(19):3047-8
pubmed: 27312411
Bioinformatics. 2011 Nov 1;27(21):2987-93
pubmed: 21903627
Syst Biol. 2021 Aug 11;70(5):891-907
pubmed: 33404632
Mol Biol Evol. 2018 Oct 1;35(10):2582-2584
pubmed: 30165589
Bioinformatics. 2011 Aug 1;27(15):2156-8
pubmed: 21653522
J Evol Biol. 2016 Apr;29(4):810-23
pubmed: 26779592
Cladistics. 2011 Apr;27(2):171-180
pubmed: 34875773
Genes (Basel). 2018 May 18;9(5):
pubmed: 29783692
Bioinformatics. 2019 Sep 1;35(17):3194-3195
pubmed: 30668635
Mol Biol Evol. 2018 Feb 1;35(2):518-522
pubmed: 29077904
Proc Natl Acad Sci U S A. 2021 Apr 13;118(15):
pubmed: 33827928
Bioinformatics. 2013 Apr 15;29(8):1072-5
pubmed: 23422339
Syst Biol. 2016 Nov;65(6):997-1008
pubmed: 27121966
Mol Biol Evol. 2015 Jan;32(1):268-74
pubmed: 25371430
Nucleic Acids Res. 2019 Jun 20;47(11):e63
pubmed: 30864657
BMC Evol Biol. 2017 Nov 22;17(1):227
pubmed: 29166859
Proc Biol Sci. 2012 Aug 7;279(1740):2936-44
pubmed: 22513861
Bioinformatics. 2013 Nov 1;29(21):2790-1
pubmed: 23975764
F1000Res. 2018 Aug 24;7:1338
pubmed: 30254741
BMC Bioinformatics. 2014 Nov 25;15:356
pubmed: 25420514
Nat Commun. 2020 Mar 18;11(1):1433
pubmed: 32188850
Philos Trans R Soc Lond B Biol Sci. 2008 Sep 12;363(1505):2931-41
pubmed: 18508758
Proc Biol Sci. 2002 Feb 7;269(1488):281-7
pubmed: 11839197
Am J Bot. 2015 Jun;102(6):910-20
pubmed: 26101417
PLoS One. 2014 Nov 19;9(11):e112963
pubmed: 25409509
Bioinformatics. 2011 Mar 15;27(6):764-70
pubmed: 21217122
Curr Protoc Bioinformatics. 2013;43:11.10.1-11.10.33
pubmed: 25431634
BMC Bioinformatics. 2014 Jun 20;15:211
pubmed: 24950923
Proc Natl Acad Sci U S A. 2009 Mar 24;106(12):4758-63
pubmed: 19273852
Mol Ecol Resour. 2012 Jul;12(4):697-705
pubmed: 22487563
Nucleic Acids Res. 2013 Jul;41(13):e129
pubmed: 23661685
Nat Methods. 2017 Jun;14(6):587-589
pubmed: 28481363
Sci Rep. 2020 Aug 18;10(1):13956
pubmed: 32811858
Proc Biol Sci. 2012 May 22;279(1735):1873-82
pubmed: 22298849
Bioinformatics. 2018 Sep 15;34(18):3094-3100
pubmed: 29750242
Am Nat. 2005 Feb;165(2):274-80
pubmed: 15729656
J Exp Zool A Ecol Integr Physiol. 2017 Jan;327(1):53-65
pubmed: 29356401
BMC Bioinformatics. 2009 Dec 15;10:421
pubmed: 20003500
J Evol Biol. 2013 Feb;26(2):229-46
pubmed: 23323997
Syst Biol. 2021 Aug 11;70(5):908-921
pubmed: 33410870
Nucleic Acids Res. 2004 Mar 19;32(5):1792-7
pubmed: 15034147
BMC Evol Biol. 2014 Apr 12;14:80
pubmed: 24725969
Syst Biol. 2010 May;59(3):307-21
pubmed: 20525638
Nat Commun. 2017 Feb 10;8:14363
pubmed: 28186104
BMC Bioinformatics. 2004 May 14;5:59
pubmed: 15144565
Genetics. 2014 Jul;197(3):939-51
pubmed: 24788603