Whole-genome sequencing of Tarim red deer (
Arid-desert environment
Cervus elaphus
Environmental adaptability
Population demographic history
Tarim red deer
Whole genome sequencing
Journal
Frontiers in zoology
ISSN: 1742-9994
Titre abrégé: Front Zool
Pays: England
ID NLM: 101231669
Informations de publication
Date de publication:
2020
2020
Historique:
received:
16
06
2020
accepted:
02
10
2020
entrez:
19
10
2020
pubmed:
20
10
2020
medline:
20
10
2020
Statut:
epublish
Résumé
The initiation of desert conditions in the Tarim Basin in China since the late Miocene has led to the significant genetic structuring of local organisms. Tarim Red Deer ( We sequenced the whole genomes of 13 TRD individuals, conducted comparative genomic analyses, and estimated demographic fluctuation. The ∂a∂i model estimated that the TRD and Tule elk ( Our analyses highlight the role of historical global climates in the population dynamics of TRD. In light of ongoing global warming and the increasing incidence of droughts, our study offers insights into the genomic adaptations of animals, especially TRD, to extreme arid-desert environments and provides a valuable resource for future research on conservation design and biological adaptations to environmental change.
Sections du résumé
BACKGROUND
BACKGROUND
The initiation of desert conditions in the Tarim Basin in China since the late Miocene has led to the significant genetic structuring of local organisms. Tarim Red Deer (
RESULTS
RESULTS
We sequenced the whole genomes of 13 TRD individuals, conducted comparative genomic analyses, and estimated demographic fluctuation. The ∂a∂i model estimated that the TRD and Tule elk (
CONCLUSIONS
CONCLUSIONS
Our analyses highlight the role of historical global climates in the population dynamics of TRD. In light of ongoing global warming and the increasing incidence of droughts, our study offers insights into the genomic adaptations of animals, especially TRD, to extreme arid-desert environments and provides a valuable resource for future research on conservation design and biological adaptations to environmental change.
Identifiants
pubmed: 33072165
doi: 10.1186/s12983-020-00379-5
pii: 379
pmc: PMC7565370
doi:
Types de publication
Journal Article
Langues
eng
Pagination
31Informations de copyright
© The Author(s) 2020.
Déclaration de conflit d'intérêts
Competing interestsThe authors declare that they have no competing interests.
Références
Cell. 2014 May 8;157(4):785-94
pubmed: 24813606
Nature. 2012 Nov 1;491(7422):56-65
pubmed: 23128226
PLoS Genet. 2009 Oct;5(10):e1000695
pubmed: 19851460
Proc Natl Acad Sci U S A. 2012 Sep 4;109(36):E2382-90
pubmed: 22826254
Am J Physiol. 1996 Oct;271(4 Pt 2):R863-9
pubmed: 8897975
Ecol Lett. 2013 May;16 Suppl 1:94-105
pubmed: 23679011
Bioinformatics. 2009 Jul 15;25(14):1754-60
pubmed: 19451168
Front Genet. 2015 Apr 07;6:107
pubmed: 25904931
J Biol Chem. 2000 Feb 4;275(5):3305-12
pubmed: 10652318
Dermatol Clin. 2014 Apr;32(2):113-21
pubmed: 24679998
PLoS Biol. 2015 Apr 10;13(4):e1002112
pubmed: 25859758
J Exp Zool A Ecol Genet Physiol. 2015 Dec;323(10):696-703
pubmed: 26351085
Mol Biol Evol. 2019 Jul 02;:
pubmed: 31273382
Heredity (Edinb). 2016 Mar;116(3):255-64
pubmed: 26555032
Mol Biol Evol. 2014 Dec;31(12):3324-43
pubmed: 25249477
Pharmacogenetics. 1996 Feb;6(1):1-42
pubmed: 8845856
Genome Res. 2009 May;19(5):826-37
pubmed: 19307593
Nature. 2011 Nov 02;479(7373):359-64
pubmed: 22048313
Nat Commun. 2012;3:1202
pubmed: 23149746
Nat Commun. 2018 Mar 8;9(1):1005
pubmed: 29520061
Science. 2006 Jun 16;312(5780):1621
pubmed: 16778048
Curr Biol. 2017 Sep 25;27(18):R986-R988
pubmed: 28950089
BMC Genomics. 2019 May 17;20(1):384
pubmed: 31101010
Mol Biol Evol. 2016 May;33(5):1337-48
pubmed: 26823447
Mol Ecol. 2008 Oct;17(19):4186-96
pubmed: 18684136
Mol Biol Evol. 2019 Jan 1;36(1):4-14
pubmed: 30351418
Proc Natl Acad Sci U S A. 2017 Apr 18;114(16):4189-4194
pubmed: 28373541
F1000Res. 2017 Sep 15;6:1691
pubmed: 29333237
Exp Mol Med. 2002 Sep 30;34(4):273-7
pubmed: 12515392
Mol Phylogenet Evol. 2004 Jun;31(3):1064-83
pubmed: 15120401
Nature. 2007 Oct 18;449(7164):913-8
pubmed: 17943131
Am J Med Genet A. 2004 Oct 1;130A(2):138-45
pubmed: 15372515
J Biol Chem. 2004 Feb 20;279(8):6305-14
pubmed: 14660610
Nature. 2010 Sep 2;467(7311):43-51
pubmed: 20811450
Nature. 1989 Mar 16;338(6212):229-34
pubmed: 2922051
Evol Appl. 2018 Oct 09;11(10):2040-2053
pubmed: 30459847
Eur J Immunol. 2003 Apr;33(4):991-1000
pubmed: 12672065
Nucleic Acids Res. 2010 Sep;38(16):e164
pubmed: 20601685
Bioinformatics. 2019 May 15;35(10):1786-1788
pubmed: 30321304
Genome Res. 2014 Aug;24(8):1308-15
pubmed: 24721644
Philos Trans R Soc Lond B Biol Sci. 2010 Apr 27;365(1544):1245-53
pubmed: 20308100
Can J Microbiol. 2018 Jul;64(7):501-509
pubmed: 29562140
Genes Dev. 2010 Mar 1;24(5):423-31
pubmed: 20194435
J Invest Dermatol. 2016 May;136(5):1022-1030
pubmed: 26829034
Nature. 2000 Nov 2;408(6808):57-63
pubmed: 11081504
Sci Rep. 2016 Dec 12;6:38932
pubmed: 27941843
Bioinformatics. 2011 Aug 1;27(15):2156-8
pubmed: 21653522
G3 (Bethesda). 2017 Sep 7;7(9):3169-3176
pubmed: 28751500
Antonie Van Leeuwenhoek. 2019 Sep;112(9):1283-1296
pubmed: 30941531
J Smooth Muscle Res. 2005 Aug;41(4):175-93
pubmed: 16258232
Lancet. 2002 Oct 12;360(9340):1155-62
pubmed: 12387968
Nat Commun. 2013;4:1858
pubmed: 23673643
Proc Natl Acad Sci U S A. 2006 Jun 20;103(25):9381-6
pubmed: 16772383
Nature. 2013 Jul 4;499(7456):74-8
pubmed: 23803765
Genome Biol. 2017 Feb 20;18(1):34
pubmed: 28219390
Science. 2000 Sep 22;289(5487):2068-74
pubmed: 11000103
Science. 2014 Aug 29;345(6200):1074-1079
pubmed: 25170157
Jpn J Vet Res. 2001 Nov;49(3):231-7
pubmed: 11799907
Bioinformatics. 2005 Oct 1;21(19):3787-93
pubmed: 15817693
Allergy Asthma Immunol Res. 2016 Sep;8(5):466-70
pubmed: 27334786
Nat Genet. 2014 Dec;46(12):1303-10
pubmed: 25362486
Nat Genet. 2012 Jul 01;44(8):946-9
pubmed: 22751099
Front Physiol. 2011 Apr 20;2:15
pubmed: 21541253
Front Genet. 2018 Aug 14;9:318
pubmed: 30154830
Mol Genet Genomics. 2018 Jun;293(3):665-684
pubmed: 29294181
Mol Cell. 2007 Oct 12;28(1):79-90
pubmed: 17936706
Blood. 2009 Jan 1;113(1):175-85
pubmed: 18827186
Bioinformation. 2014 Aug 30;10(8):491-5
pubmed: 25258483
Evolution. 1984 Nov;38(6):1358-1370
pubmed: 28563791
Nat Genet. 2013 Jan;45(1):67-71
pubmed: 23242367
J Immunol. 2009 Sep 1;183(5):2966-73
pubmed: 19667091
Mol Biol Evol. 2016 Oct;33(10):2576-92
pubmed: 27401233
Nature. 2013 Jul 25;499(7459):471-5
pubmed: 23823723
Nat Rev Genet. 2004 Mar;5(3):202-12
pubmed: 14970822
Bioinformatics. 2009 Aug 15;25(16):2078-9
pubmed: 19505943
Conserv Biol. 2007 Oct;21(5):1353-5
pubmed: 17883501
Nat Commun. 2014 Oct 21;5:5188
pubmed: 25333821
Nature. 2011 Jul 13;475(7357):493-6
pubmed: 21753753