دورية أكاديمية
Genomic Analyses Capture the Human-Induced Demographic Collapse and Recovery in a Wide-Ranging Cervid.
| العنوان: | Genomic Analyses Capture the Human-Induced Demographic Collapse and Recovery in a Wide-Ranging Cervid. |
|---|---|
| المؤلفون: | Kessler C; Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada., Shafer ABA; Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada.; Department of Forensic Science, Trent University, Peterborough, Ontario, Canada. |
| المصدر: | Molecular biology and evolution [Mol Biol Evol] 2024 Mar 01; Vol. 41 (3). |
| نوع المنشور: | Journal Article |
| اللغة: | English |
| بيانات الدورية: | Publisher: Oxford University Press Country of Publication: United States NLM ID: 8501455 Publication Model: Print Cited Medium: Internet ISSN: 1537-1719 (Electronic) Linking ISSN: 07374038 NLM ISO Abbreviation: Mol Biol Evol Subsets: MEDLINE |
| أسماء مطبوعة: | Publication: 2003- : New York, NY : Oxford University Press Original Publication: [Chicago, Ill.] : University of Chicago Press, [c1983- |
| مواضيع طبية MeSH: | Genetics, Population* , Deer*/genetics, Humans ; Animals ; Genomics ; Demography ; Equidae |
| مستخلص: | The glacial cycles of the Quaternary heavily impacted species through successions of population contractions and expansions. Similarly, populations have been intensely shaped by human pressures such as unregulated hunting and land use changes. White-tailed and mule deer survived in different refugia through the Last Glacial Maximum, and their populations were severely reduced after the European colonization. Here, we analyzed 73 resequenced deer genomes from across their North American range to understand the consequences of climatic and anthropogenic pressures on deer demographic and adaptive history. We found strong signals of climate-induced vicariance and demographic decline; notably, multiple sequentially Markovian coalescent recovers a severe decline in mainland white-tailed deer effective population size (Ne) at the end of the Last Glacial Maximum. We found robust evidence for colonial overharvest in the form of a recent and dramatic drop in Ne in all analyzed populations. Historical census size and restocking data show a clear parallel to historical Ne estimates, and temporal Ne/Nc ratio shows patterns of conservation concern for mule deer. Signatures of selection highlight genes related to temperature, including a cold receptor previously highlighted in woolly mammoth. We also detected immune genes that we surmise reflect the changing land use patterns in North America. Our study provides a detailed picture of anthropogenic and climatic-induced decline in deer diversity and clues to understanding the conservation concerns of mule deer and the successful demographic recovery of white-tailed deer. (© The Author(s) 2024. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.) |
| References: | Nat Commun. 2021 Feb 16;12(1):965. (PMID: 33594059) Mol Ecol. 2005 Jul;14(8):2611-20. (PMID: 15969739) Evolution. 1994 Feb;48(1):122-136. (PMID: 28567797) Curr Biol. 2023 Aug 7;33(15):3272-3278.e3. (PMID: 37478865) Science. 2021 May 21;372(6544):860-864. (PMID: 34016781) Environ Sci Pollut Res Int. 2022 Sep;29(44):66010-66040. (PMID: 35908028) Evol Appl. 2022 Oct 25;15(12):2043-2053. (PMID: 36540642) PLoS One. 2022 Jan 18;17(1):e0262024. (PMID: 35041674) Bioinformatics. 2009 Jul 15;25(14):1754-60. (PMID: 19451168) PLoS Comput Biol. 2022 May 31;18(5):e1009123. (PMID: 35639788) Science. 2021 Sep 24;373(6562):1528-1531. (PMID: 34554787) Cell Rep. 2015 Jul 14;12(2):217-28. (PMID: 26146078) Nat Rev Genet. 2009 Mar;10(3):195-205. (PMID: 19204717) Mol Biol Evol. 2020 Dec 16;37(12):3642-3653. (PMID: 32642779) Nat Genet. 2015 May;47(5):555-9. (PMID: 25848749) Proc Biol Sci. 2013 Aug 07;280(1768):20131339. (PMID: 23926150) Mol Ecol. 2010 Nov;19(21):4589-621. (PMID: 20849561) Ecol Evol. 2019 Apr 16;9(10):5891-5905. (PMID: 31161006) Mol Biol Evol. 2022 Dec 5;39(12):. (PMID: 36322483) Nature. 2011 Nov 02;479(7373):359-64. (PMID: 22048313) GigaByte. 2021 Nov 22;2021:gigabyte34. (PMID: 36824347) Heredity (Edinb). 2023 Oct;131(4):273-281. (PMID: 37532838) Genome Res. 2010 Sep;20(9):1297-303. (PMID: 20644199) Mol Biol Evol. 1997 Nov;14(11):1154-66. (PMID: 9364773) Bioinformatics. 2014 Aug 1;30(15):2114-20. (PMID: 24695404) Mol Ecol. 2017 Oct;26(19):5245-5263. (PMID: 28748565) Proc Natl Acad Sci U S A. 2021 Jul 6;118(27):. (PMID: 34183409) Genetics. 2017 May;206(1):439-449. (PMID: 28341655) Gigascience. 2015 Feb 25;4:7. (PMID: 25722852) Bioinformatics. 2019 Feb 1;35(3):526-528. (PMID: 30016406) Science. 2019 Jun 21;364(6446):. (PMID: 31221828) Evol Appl. 2021 May 04;14(6):1673-1689. (PMID: 34178112) Nat Commun. 2020 Feb 21;11(1):1001. (PMID: 32081890) PLoS One. 2017 Oct 19;12(10):e0186512. (PMID: 29049389) PLoS Biol. 2006 Mar;4(3):e72. (PMID: 16494531) Curr Protoc Bioinformatics. 2016 Mar 24;53:1.29.1-1.29.15. (PMID: 27010333) J Comput Biol. 2015 Jun;22(6):498-509. (PMID: 25658651) Methods Mol Biol. 2020;2090:147-166. (PMID: 31975167) PLoS Genet. 2009 Oct;5(10):e1000695. (PMID: 19851460) PLoS Genet. 2014 Apr 17;10(4):e1004234. (PMID: 24743097) Nature. 2002 Oct 24;419(6909):832-7. (PMID: 12397357) Bioinformatics. 2018 Mar 1;34(5):867-868. (PMID: 29096012) Nature. 2021 Jun;594(7863):356-364. (PMID: 34135521) Mol Ecol. 2008 Aug;17(15):3428-47. (PMID: 19160474) Genetics. 2018 Oct;210(2):719-731. (PMID: 30131346) Evol Appl. 2021 Jun 01;14(7):1914-1925. (PMID: 34295372) Genet Res. 2007 Dec;89(5-6):491-503. (PMID: 18976539) Am J Hum Biol. 2019 May;31(3):e23243. (PMID: 31016798) Bioinformatics. 2016 Oct 1;32(19):3047-8. (PMID: 27312411) Sci Adv. 2015 Jun 19;1(5):e1400253. (PMID: 26601195) Mol Ecol. 2009 Apr;18(8):1730-45. (PMID: 19302464) Mol Ecol. 2016 Jan;25(1):170-84. (PMID: 26562485) Bioinformatics. 2011 Aug 1;27(15):2156-8. (PMID: 21653522) Curr Biol. 2022 Feb 28;32(4):R181-R196. (PMID: 35231416) PLoS Genet. 2020 Mar 9;16(3):e1008552. (PMID: 32150539) Mol Ecol Resour. 2015 Sep;15(5):1179-91. (PMID: 25684545) Nat Genet. 2014 Aug;46(8):919-25. (PMID: 24952747) Ecol Evol. 2016 Aug 18;6(18):6435-6451. (PMID: 27777720) Nat Commun. 2019 Aug 16;10(1):3713. (PMID: 31420542) Science. 2009 Aug 7;325(5941):710-4. (PMID: 19661421) Nat Ecol Evol. 2020 Aug;4(8):1095-1104. (PMID: 32514167) Genetics. 2013 Nov;195(3):693-702. (PMID: 24026093) Evolution. 2016 Jul;70(7):1486-500. (PMID: 27174031) Nat Commun. 2021 Feb 23;12(1):1199. (PMID: 33623046) Mol Ecol. 2024 Feb;33(3):e17230. (PMID: 38078558) Evol Appl. 2021 Dec 14;15(1):111-131. (PMID: 35126651) BMC Bioinformatics. 2014 Nov 25;15:356. (PMID: 25420514) Mol Ecol. 2020 May;29(9):1596-1610. (PMID: 31840921) Mol Ecol. 2015 Jan;24(2):328-45. (PMID: 25482153) Mol Ecol. 2023 Mar;32(5):1117-1132. (PMID: 36516402) Bioinformatics. 2024 Jan 2;40(1):. (PMID: 38180866) Science. 2023 Apr 28;380(6643):eabn5856. (PMID: 37104572) Mol Ecol. 2023 Apr;32(8):1943-1954. (PMID: 36704858) Mol Ecol. 2003 Dec;12(12):3237-52. (PMID: 14629342) Mol Ecol. 2020 Aug;29(15):2777-2792. (PMID: 32306438) Bioinformatics. 2009 Aug 15;25(16):2078-9. (PMID: 19505943) Proc Natl Acad Sci U S A. 2016 Jan 26;113(4):838-46. (PMID: 26811442) BMC Genomics. 2020 Dec 2;21(1):854. (PMID: 33267779) Mol Ecol. 2014 Jul;23(13):3171-90. (PMID: 24863151) Proc Natl Acad Sci U S A. 2020 Nov 17;117(46):28555-28563. (PMID: 33168739) Nat Commun. 2018 Mar 27;9(1):1100. (PMID: 29588441) Curr Biol. 2015 May 18;25(10):1395-400. (PMID: 25913407) G3 (Bethesda). 2020 Apr 9;10(4):1433-1441. (PMID: 32122960) Mol Ecol. 2021 Dec;30(23):6121-6143. (PMID: 34482596) Nat Commun. 2016 Nov 15;7:13175. (PMID: 27845766) Nature. 2011 Jul 13;475(7357):493-6. (PMID: 21753753) Proc Natl Acad Sci U S A. 2015 Apr 14;112(15):4531-40. (PMID: 25675493) Genome Biol. 2020 Nov 17;21(1):280. (PMID: 33203475) Mol Ecol. 2022 Jul;31(13):3548-3565. (PMID: 35560856) Heredity (Edinb). 2016 Oct;117(4):268-78. (PMID: 27530910) Bioinformatics. 2015 Jun 15;31(12):2032-4. (PMID: 25697820) Mol Ecol. 2006 Dec;15(14):4261-93. (PMID: 17107465) Proc Natl Acad Sci U S A. 2009 Jun 16;106 Suppl 1:9987-94. (PMID: 19528656) Proc Biol Sci. 2021 Feb 10;288(1944):20201945. (PMID: 33529556) |
| معلومات مُعتمدة: | International Graduate Scholarship; Ontario Graduate Scholarship; French American Charitable Trust Scholarship; RGPIN-2017- 03934 NSERC Discovery Grant; RRG gme-665-ab ComputeCanada Resources for Research Groups; Canadian Foundation for Innovation: John R. Evans Leaders Fund; #36905 Ontario Early Researcher Award |
| فهرسة مساهمة: | Keywords: Odocoileus; Last Glacial Maximum; deer; human impact; island population |
| SCR Organism: | Odocoileus virginianus |
| تواريخ الأحداث: | Date Created: 20240220 Date Completed: 20240328 Latest Revision: 20240331 |
| رمز التحديث: | 20240331 |
| مُعرف محوري في PubMed: | PMC10917209 |
| DOI: | 10.1093/molbev/msae038 |
| PMID: | 38378172 |
| قاعدة البيانات: | MEDLINE |
Full Text Finder | تدمد: | 1537-1719 |
|---|---|
| DOI: | 10.1093/molbev/msae038 |