دورية أكاديمية
أعرض في EDS

Contrasting whole-genome and reduced representation sequencing for population demographic and adaptive inference: an alpine mammal case study.

التفاصيل البيبلوغرافية
العنوان: Contrasting whole-genome and reduced representation sequencing for population demographic and adaptive inference: an alpine mammal case study.
المؤلفون: Martchenko D; Environmental and Life Sciences Graduate Program, Trent University, 2140 East Bank Drive, Peterborough, ON, K9J 7B8, Canada. dariamartchenko@trentu.ca., Shafer ABA; Environmental and Life Sciences Graduate Program, Trent University, 2140 East Bank Drive, Peterborough, ON, K9J 7B8, Canada.; Department of Forensics & Environmental and Life Sciences Graduate Program, Trent University, 2140 East Bank Drive, Peterborough, ON, K9J 7B8, Canada.
المصدر: Heredity [Heredity (Edinb)] 2023 Oct; Vol. 131 (4), pp. 273-281. Date of Electronic Publication: 2023 Aug 02.
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: Nature Publishing Group Country of Publication: England NLM ID: 0373007 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1365-2540 (Electronic) Linking ISSN: 0018067X NLM ISO Abbreviation: Heredity (Edinb) Subsets: MEDLINE
أسماء مطبوعة: Publication: <2003->: London : Nature Publishing Group
Original Publication: London, Oliver and Boyd.
مستخلص: Genomes capture the adaptive and demographic history of a species, but the choice of sequencing strategy and sample size can impact such inferences. We compared whole genome and reduced representation sequencing approaches to study the population demographic and adaptive signals of the North American mountain goat (Oreamnos americanus). We applied the restriction site-associated DNA sequencing (RADseq) approach to 254 individuals and whole genome resequencing (WGS) approach to 35 individuals across the species range at mid-level coverage (9X) and to 5 individuals at high coverage (30X). We used ANGSD to estimate the genotype likelihoods and estimated the effective population size (N e ), population structure, and explicitly modelled the demographic history with δaδi and MSMC2. The data sets were overall concordant in supporting a glacial induced vicariance and extremely low N e in mountain goats. We evaluated a set of climatic variables and geographic location as predictors of genetic diversity using redundancy analysis. A moderate proportion of total variance (36% for WGS and 21% for RADseq data sets) was explained by geography and climate variables; both data sets support a large impact of drift and some degree of local adaptation. The empirical similarities of WGS and RADseq presented herein reassuringly suggest that both approaches will recover large demographic and adaptive signals in a population; however, WGS offers several advantages over RADseq, such as inferring adaptive processes and calculating runs-of-homozygosity estimates. Considering the predicted climate-induced changes in alpine environments and the genetically depauperate mountain goat, the long-term adaptive capabilities of this enigmatic species are questionable.
(© 2023. The Author(s), under exclusive licence to The Genetics Society.)
References: Am Nat. 2021 Jun;197(6):658-676. (PMID: 33989142)
Genetics. 1943 Mar;28(2):114-38. (PMID: 17247074)
Conserv Biol. 2011 Jun;25(3):438-49. (PMID: 21284731)
Mol Ecol. 2013 Jun;22(11):3165-78. (PMID: 23110526)
Mol Ecol Resour. 2009 Jul;9(4):1121-6. (PMID: 21564850)
Proc Natl Acad Sci U S A. 2021 Nov 30;118(48):. (PMID: 34772759)
BMC Genomics. 2016 Feb 20;17:123. (PMID: 26897757)
Evolution. 2011 Jan;65(1):125-38. (PMID: 20731714)
Evolution. 2015 Jun;69(6):1501-1517. (PMID: 25903255)
BMC Bioinformatics. 2014 Nov 25;15:356. (PMID: 25420514)
Natl Sci Rev. 2020 Apr;7(4):798-814. (PMID: 34692098)
Mol Ecol. 2021 Dec;30(23):5966-5993. (PMID: 34250668)
Nat Commun. 2016 Oct 31;7:13195. (PMID: 27796282)
Evol Appl. 2022 Oct 25;15(12):2043-2053. (PMID: 36540642)
Mol Biol Evol. 2020 Dec 16;37(12):3642-3653. (PMID: 32642779)
Am J Hum Genet. 2007 Nov;81(5):1084-97. (PMID: 17924348)
Heredity (Edinb). 2016 Oct;117(4):233-40. (PMID: 27553452)
Proc Natl Acad Sci U S A. 2002 Jan 22;99(2):803-8. (PMID: 11792858)
Sci Total Environ. 2020 Dec 15;748:141344. (PMID: 32814293)
Mol Ecol. 2021 Sep;30(17):4147-4154. (PMID: 34191374)
CSH Protoc. 2006 Jun 01;2006(1):. (PMID: 22485786)
Syst Biol. 2016 Sep;65(5):910-24. (PMID: 27288477)
BMC Bioinformatics. 2013 Oct 02;14:289. (PMID: 24088262)
Heredity (Edinb). 2016 Feb;116(2):177-81. (PMID: 26374238)
Mol Ecol. 2013 Jun;22(11):3124-40. (PMID: 23701397)
Mol Ecol Resour. 2017 Mar;17(2):142-152. (PMID: 27860289)
Nat Biotechnol. 2008 Oct;26(10):1135-45. (PMID: 18846087)
Methods Mol Biol. 2020;2090:147-166. (PMID: 31975167)
PLoS Genet. 2009 Oct;5(10):e1000695. (PMID: 19851460)
G3 (Bethesda). 2020 Feb 6;10(2):437-442. (PMID: 31806764)
Genetics. 2010 Nov;186(3):983-95. (PMID: 20739713)
Ecol Evol. 2021 May 08;11(11):6119-6132. (PMID: 34141207)
Genetics. 2018 Oct;210(2):719-731. (PMID: 30131346)
Mol Ecol Resour. 2019 May;19(3):586-596. (PMID: 30633448)
Nat Rev Genet. 2016 Feb;17(2):81-92. (PMID: 26729255)
Mol Ecol. 2013 Jun;22(11):3151-64. (PMID: 23110438)
Mol Biol Evol. 2015 May;32(5):1296-309. (PMID: 25657328)
Mol Biol Evol. 2002 Dec;19(12):2092-100. (PMID: 12446801)
Mol Ecol Resour. 2017 Jul;17(4):631-641. (PMID: 27718335)
J Hered. 2012 May-Jun;103(3):371-9. (PMID: 22268162)
PLoS Genet. 2020 Mar 9;16(3):e1008552. (PMID: 32150539)
Proc Natl Acad Sci U S A. 2021 Mar 9;118(10):. (PMID: 33608481)
Mol Ecol Resour. 2017 May;17(3):362-365. (PMID: 28319339)
Nat Ecol Evol. 2020 Aug;4(8):1095-1104. (PMID: 32514167)
Genetics. 2013 Nov;195(3):693-702. (PMID: 24026093)
Mol Ecol. 2016 Mar;25(5):1058-72. (PMID: 26797914)
Mol Ecol. 2015 Jan;24(2):328-45. (PMID: 25482153)
Mol Ecol. 2023 Apr;32(8):1943-1954. (PMID: 36704858)
Nat Genet. 2013 Jan;45(1):67-71. (PMID: 23242367)
Mol Ecol Resour. 2019 Nov;19(6):1497-1515. (PMID: 31359622)
Mol Biol Evol. 2013 Sep;30(9):2209-23. (PMID: 23842528)
Nature. 2011 Jul 13;475(7357):493-6. (PMID: 21753753)
Science. 2022 May 27;376(6596):1012-1016. (PMID: 35617403)
Nat Ecol Evol. 2021 Oct;5(10):1350-1360. (PMID: 34373621)
Mol Ecol Resour. 2017 Jan;17(1):44-53. (PMID: 27401132)
Bioinformatics. 2015 Jun 15;31(12):2032-4. (PMID: 25697820)
Mol Ecol Resour. 2021 May;21(4):1085-1097. (PMID: 33434329)
Mol Ecol Resour. 2019 Sep;19(5):1205-1217. (PMID: 31058463)
تواريخ الأحداث: Date Created: 20230802 Latest Revision: 20231003
رمز التحديث: 20240628
مُعرف محوري في PubMed: PMC10539292
DOI: 10.1038/s41437-023-00643-4
PMID: 37532838
قاعدة البيانات: MEDLINE
الوصف
تدمد:1365-2540
DOI:10.1038/s41437-023-00643-4