Contrasting whole

Heredity (2023)Cite this article

Metrics details

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 (Ne), 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 Ne 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.

This is a preview of subscription content, access via your institution

Subscribe to this journal

Receive 12 print issues and online access

$259.00 per year

only $21.58 per issue

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

Prices may be subject to local taxes which are calculated during checkout

The raw DNA sequence data raw data have been deposited in the SRA under accession numbers PRJNA510081, PRJNA909333, PRJNA909334.

Aguirre-Liguori JA, Ramírez-Barahona S, Gaut BS (2021) The evolutionary genomics of species’ responses to climate change. Nat Ecol Evol 5:1350–1360. https://doi.org/10.1038/s41559-021-01526-9

Article PubMed Google Scholar

Andrews KR, Good JM, Miller MR, Luikart G, Hohenlohe PA (2016) Harnessing the power of RADseq for ecological and evolutionary genomics. Nat Rev Genet 17:81–92. https://doi.org/10.1038/nrg.2015.28

Article CAS PubMed PubMed Central Google Scholar

Andrews S (2010) Babraham Bioinformatics - FastQC - a quality control tool for high throughput sequence data. http://www.bioinformatics.babraham.ac.uk/projects/fastqc/. Accessed 25 Apr 2017

Beichman AC, Huerta-Sanchez E, Lohmueller KE (2018) Using genomic data to infer historic population dynamics of nonmodel organisms. Annu Rev Ecol Evol Syst 49:433–456. https://doi.org/10.1146/annurev-ecolsys-110617-062431

Article Google Scholar

Benjelloun B, Boyer F, Streeter I, Zamani W, Engelen S, Alberti A, Alberto FJ, BenBati M, Ibnelbachyr M, Chentouf M, Bechchari A, Rezaei HR, Naderi S, Stella A, Chikhi A, Clarke L, Kijas J, Flicek P, Taberlet P, Pompanon F (2019) An evaluation of sequencing coverage and genotyping strategies to assess neutral and adaptive diversity. Mol Ecol Resour 19:1497–1515. https://doi.org/10.1111/1755-0998.13070

Article CAS PubMed PubMed Central Google Scholar

Bertola LD, Sunnucks P, Bruford (SANBI) M, Brüniche-Olsen A, Cadena CD, Frankham D, Guayasamin JM, Grueber CE, Hoareau TB, Hoban S, Hohenlohe P, Hunter ME, Kershaw F, Kotze (SANBI) A, Lacy RC, Laikre L, MacDonald AJ, Meek MH, Mergeay J, Mittan C, O´Brien D, Orozco-terWengel P, Ogden R, Páez-Vacas M, Ralls K, Ramakrishnan U, Russo I-RM, Shaw RE, Stow A, Steeves T, Vernesi C, Waits L, Segelbacher G (2021) Genome-wide diversity is informative of extinction risk and critical for conservation: a response to Teixeira and Huber (2021)

Bohling J, Small M, Von Bargen J, Louden A, DeHaan P (2019) Comparing inferences derived from microsatellite and RADseq datasets: a case study involving threatened bull trout. Conserv Genet 20:329–342. https://doi.org/10.1007/s10592-018-1134-z

Article CAS Google Scholar

Bonnet T, Morrissey MB, de Villemereuil P, Alberts SC, Arcese P, Bailey LD, Boutin S, Brekke P, Brent LJN, Camenisch G, Charmantier A, Clutton-Brock TH, Cockburn A, Coltman DW, Courtiol A, Davidian E, Evans SR, Ewen JG, Festa-Bianchet M, de Franceschi C, Gustafsson L, Höner OP, Houslay TM, Keller LF, Manser M, McAdam AG, McLean E, Nietlisbach P, Osmond HL, Pemberton JM, Postma E, Reid JM, Rutschmann A, Santure AW, Sheldon BC, Slate J, Teplitsky C, Visser ME, Wachter B, Kruuk LEB (2022) Genetic variance in fitness indicates rapid contemporary adaptive evolution in wild animals. Science 376:1012–1016. https://doi.org/10.1126/science.abk0853

Article CAS PubMed Google Scholar

Brelsford A, Dufresnes C, Perrin N (2016) High-density sex-specific linkage maps of a European tree frog (Hyla arborea) identify the sex chromosome without information on offspring sex. Heredity 116:177–181. https://doi.org/10.1038/hdy.2015.83

Article CAS PubMed Google Scholar

Briñoccoli YF, Jardim de Queiroz L, Bogan S, Paracampo A, Posadas PE, Somoza GM, Montoya‐Burgos JI, Cardoso YP (2021) Processes that drive the population structuring of Jenynsia lineata (Cyprinidontiformes, Anablepidae) in the La Plata Basin. Ecol Evol 11:6119–6132. https://doi.org/10.1002/ece3.7427

Article PubMed PubMed Central Google Scholar

Browning SR, Browning BL (2007) Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. Am J Hum Genet 81:1084–1097. https://doi.org/10.1086/521987

Article CAS PubMed PubMed Central Google Scholar

Bushnell B (2018) BBTools. Available online at: https://jgi.doe.gov/data-and-tools/bbtools/

Catchen J, Hohenlohe PA, Bassham S, Amores A, Cresko WA (2013) Stacks: an analysis tool set for population genomics. Mol Ecol 22:3124. https://doi.org/10.1111/mec.12354

Article PubMed PubMed Central Google Scholar

Catchen JM, Hohenlohe PA, Bernatchez L, Funk WC, Andrews KR, Allendorf FW (2017) Unbroken: RADseq remains a powerful tool for understanding the genetics of adaptation in natural populations. Mol Ecol Resour 17:362–365. https://doi.org/10.1111/1755-0998.12669

Article CAS PubMed Google Scholar

Chikhi L, Sousa VC, Luisi P, Goossens B, Beaumont MA (2010) The confounding effects of population structure, genetic diversity and the sampling scheme on the detection and quantification of population size changes. Genetics 186:983–995. https://doi.org/10.1534/genetics.110.118661

Article PubMed PubMed Central Google Scholar

Côté SD, Festa-Bianchet M (2003) Mountain goat. In: Feldhamer GA, Thompson B, Chapman J (eds) Wild Mammals of North America: Biology, Management, Conservation. The John Hopkins University Press, Baltimore, Maryland

Davey JW, Cezard T, Fuentes‐Utrilla P, Eland C, Gharbi K, Blaxter ML (2013) Special features of RAD Sequencing data: implications for genotyping. Mol Ecol 22:3151–3164. https://doi.org/10.1111/mec.12084

Article CAS PubMed Google Scholar

Dedato M, Robert C, Taillon J, Shafer A, Cote S (2022) Demographic history and conservation genomics of caribou (Rangifer tarandus) in Québec. Evol Appl https://doi.org/10.1111/EVA.13495

DeWoody JA, Harder AM, Mathur S, Willoughby JR (2021) The long-standing significance of genetic diversity in conservation. Mol Ecol 30:4147–4154. https://doi.org/10.1111/mec.16051

Article PubMed Google Scholar

Earth Resources Observation And Science (EROS) Center (2017) Global 30 Arc-Second Elevation (GTOPO30) data. https://doi.org/10.5066/F7DF6PQS

Fick SE, Hijmans RJ (2017) WorldClim 2: new 1-km spatial resolution climate surfaces for global land areas. Int J Climatol 37:4302–4315. https://doi.org/10.1002/joc.5086

Article Google Scholar

Fisher RA (1930) The genetical theory of natural selection. Clarendon Press, Oxford, England

Gamble T, Coryell J, Ezaz T, Lynch J, Scantlebury DP, Zarkower D (2015) Restriction site-associated DNA sequencing (RAD-seq) reveals an extraordinary number of transitions among gecko sex-determining systems. Mol Biol Evol 32:1296–1309. https://doi.org/10.1093/molbev/msv023

Article CAS PubMed Google Scholar

Gautier M, Gharbi K, Cezard T, Foucaud J, Kerdelhué C, Pudlo P, Cornuet J-M, Estoup A (2013) The effect of RAD allele dropout on the estimation of genetic variation within and between populations. Mol Ecol 22:3165–3178. https://doi.org/10.1111/mec.12089

Article CAS PubMed Google Scholar

Gervais L, Perrier C, Bernard M, Merlet J, Pemberton JM, Pujol B, Quéméré E (2019) RAD-sequencing for estimating genomic relatedness matrix-based heritability in the wild: a case study in roe deer. Mol Ecol Resour 19:1205–1217. https://doi.org/10.1111/1755-0998.13031

Article CAS PubMed Google Scholar

Gower G, Tuke J, Rohrlach AB, Soubrier J, Llamas B, Bean N, Cooper A (2018) Population size history from short genomic scaffolds: how short is too short? 382036

Grabherr G, Gottfried M, Pauli H (2010) Climate change impacts in alpine environments. Geogr Compass 4:1133–1153. https://doi.org/10.1111/j.1749-8198.2010.00356.x

Article Google Scholar

Gutenkunst RN, Hernandez RD, Williamson SH, Bustamante CD (2009) Inferring the joint demographic History of multiple populations from multidimensional SNP frequency data. PLOS Genet 5:e1000695. https://doi.org/10.1371/journal.pgen.1000695

Article CAS PubMed PubMed Central Google Scholar

Hare MP, Nunney L, Schwartz MK, Ruzzante DE, Burford M, Waples RS, Ruegg K, Palstra F (2011) Understanding and estimating effective population size for practical application in marine species management. Conserv Biol J Soc 25:438–449. https://doi.org/10.1111/j.1523-1739.2010.01637.x

Article Google Scholar

Harvey MG, Smith BT, Glenn TC, Faircloth BC, Brumfield RT (2016) Sequence capture versus restriction site associated DNA sequencing for shallow systematics. Syst Biol 65:910–924. https://doi.org/10.1093/sysbio/syw036

Article CAS PubMed Google Scholar

Heller R, Nursyifa C, Garcia-Erill G, Salmona J, Chikhi L, Meisner J, Korneliussen TS, Albrechtsen A (2021) A reference-free approach to analyse RADseq data using standard next generation sequencing toolkits. Mol Ecol Resour 21(4):1085–1097. https://doi.org/10.1111/1755-0998.13324

Article CAS PubMed Google Scholar

Hu J-Y, Hao Z-Q, Frantz L, Wu S-F, Chen W, Jiang Y-F, Wu H, Kuang W-M, Li H, Zhang Y-P, Yu L (2020) Genomic consequences of population decline in critically endangered pangolins and their demographic histories. Natl Sci Rev 7:798–814. https://doi.org/10.1093/nsr/nwaa031

Article PubMed PubMed Central Google Scholar

Kardos M, Armstrong EE, Fitzpatrick SW, Hauser S, Hedrick PW, Miller JM, Tallmon DA, Funk WC (2021) The crucial role of genome-wide genetic variation in conservation. Proc Natl Acad Sci. 118. https://doi.org/10.1073/pnas.2104642118

Kingman JFC (1982) The coalescent. Stoch Process Their Appl 13:235–248. https://doi.org/10.1016/0304-4149(82)90011-4

Article Google Scholar

Kjeldsen SR, Zenger KR, Leigh K, Ellis W, Tobey J, Phalen D, Melzer A, FitzGibbon S, Raadsma HW (2016) Genome-wide SNP loci reveal novel insights into koala (Phascolarctos cinereus) population variability across its range. Conserv Genet 17:337–353. https://doi.org/10.1007/s10592-015-0784-3

Article Google Scholar

Knaus BJ, Grünwald NJ (2017) vcfr: a package to manipulate and visualize variant call format data in R. Mol Ecol Resour 17:44–53. https://doi.org/10.1111/1755-0998.12549

Article CAS PubMed Google Scholar

Korneliussen TS, Albrechtsen A, Nielsen R (2014) ANGSD: analysis of next generation sequencing data. BMC Bioinforma 15:356. https://doi.org/10.1186/s12859-014-0356-4

Article Google Scholar

Korneliussen TS, Moltke I, Albrechtsen A, Nielsen R (2013) Calculation of Tajima’s D and other neutrality test statistics from low depth next-generation sequencing data. BMC Bioinforma 14:289. https://doi.org/10.1186/1471-2105-14-289

Article CAS Google Scholar

Kumar S, Subramanian S (2002) Mutation rates in mammalian genomes. Proc Natl Acad Sci 99:803–808. https://doi.org/10.1073/pnas.022629899

Article CAS PubMed PubMed Central Google Scholar

Legendre P, Legendre L (2012) Chapter 11 - Canonical analysis. In: Legendre P, Legendre L (eds) Developments in Environmental Modelling. Elsevier, pp 625–710

Li H (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. ArXiv E-Prints 1303:arXiv:1303.3997

Li H, Durbin R (2011) Inference of human population history from individual whole-genome sequences. Nature 475:493–496. https://doi.org/10.1038/nature10231

Article CAS PubMed PubMed Central Google Scholar

Liu S, Hansen MM (2017) PSMC (pairwise sequentially Markovian coalescent) analysis of RAD (restriction site associated DNA) sequencing data. Mol Ecol Resour 17:631–641. https://doi.org/10.1111/1755-0998.12606

Article CAS PubMed Google Scholar

Lou RN, Jacobs A, Wilder AP, Therkildsen NO (2021) A beginner’s guide to low-coverage whole genome sequencing for population genomics. Mol Ecol 30:5966–5993. https://doi.org/10.1111/mec.16077

Article PubMed Google Scholar

Lowry DB, Hoban S, Kelley JL, Lotterhos KE, Reed LK, Antolin MF, Storfer A (2017) Breaking RAD: an evaluation of the utility of restriction site-associated DNA sequencing for genome scans of adaptation. Mol Ecol Resour 17:142–152. https://doi.org/10.1111/1755-0998.12635

Article CAS PubMed Google Scholar

MacLeod IM, Larkin DM, Lewin HA, Hayes BJ, Goddard ME (2013) Inferring demography from runs of homozygosity in whole-genome sequence, with correction for sequence errors. Mol Biol Evol 30:2209–2223. https://doi.org/10.1093/molbev/mst125

Article CAS PubMed PubMed Central Google Scholar

Martchenko D, Chikhi R, Shafer ABA (2020) Genome assembly and analysis of the North American mountain goat (Oreamnos americanus) reveals species-level responses to extreme environments. G3 Genes Genomes Genet 10:437–442. https://doi.org/10.1534/g3.119.400747

Article CAS Google Scholar

Martchenko D, White KS, Shafer ABA (2022) Long-term data reveal effects of climate, road access, and latitude on mountain goat horn size. J Wildl Manag 86:e22195. https://doi.org/10.1002/jwmg.22195

Article Google Scholar

Martin M, Patterson M, Garg S, Fischer OS, Pisanti N, Klau GW, Schöenhuth A, Marschall T (2016) WhatsHap: fast and accurate read-based phasing. bioRxiv 085050. https://doi.org/10.1101/085050

Meisner J, Albrechtsen A (2018) Inferring population structure and admixture proportions in low-depth NGS data. Genetics 210:719–731. https://doi.org/10.1534/genetics.118.301336

Article PubMed PubMed Central Google Scholar

Nadachowska-Brzyska K, Burri R, Smeds L, Ellegren H (2016) PSMC analysis of effective population sizes in molecular ecology and its application to black-and-white Ficedula flycatchers. Mol Ecol 25:1058–1072. https://doi.org/10.1111/mec.13540

Article PubMed PubMed Central Google Scholar

Oksanen J, Blanchet FG, Friendly M, Kindt R, Legendre P, McGlinn D, Minchin PR, O’Hara RB, Simpson GL, Solymos P, Stevens HH, Szoecs E, Wagner HH (2020) vegan: Community Ecology Package. R package version 2.5-7

Papadopoulou A, Knowles LL (2015) Genomic tests of the species-pump hypothesis: Recent island connectivity cycles drive population divergence but not speciation in Caribbean crickets across the Virgin Islands. Evolution 69:1501–1517. https://doi.org/10.1111/evo.12667

Article PubMed Google Scholar

Paris JR, Stevens JR, Catchen JM (2017) Lost in parameter space: a road map for stacks. Methods Ecol Evol 8:1360–1373. https://doi.org/10.1111/2041-210X.12775

Article Google Scholar

Peart CR, Tusso S, Pophaly SD et al. (2020) Determinants of genetic variation across eco-evolutionary scales in pinnipeds. Nat Ecol Evol 4:1095–1104. https://doi.org/10.1038/s41559-020-1215-5

Article PubMed Google Scholar

Poissant J, Shafer ABA, Davis CS, Mainguy J, Hogg JT, Côté S, Coltman DW (2009) Genome-wide cross-amplification of domestic sheep microsatellites in bighorn sheep and mountain goats. Mol Ecol Resour 9:1121–1126. https://doi.org/10.1111/j.1755-0998.2009.02575.x

Article CAS PubMed Google Scholar

Ramos-Onsins SE, Rozas J (2002) Statistical properties of new neutrality tests against population growth. Mol Biol Evol 19:2092–2100. https://doi.org/10.1093/oxfordjournals.molbev.a004034

Article CAS PubMed Google Scholar

Salmona J, Heller R, Lascoux M, Shafer A (2019) Inferring Demographic History Using Genomic Data. In: Rajora OP (ed) Population Genomics: Concepts, Approaches and Applications. Springer International Publishing, Cham, pp 511–537

Sambrook J, Russell DW (2006) Purification of nucleic acids by extraction with Phenol:chloroform. Cold Spring Harb Protoc https://doi.org/10.1101/pdb.prot4455

Santiago E, Novo I, Pardiñas AF, Saura M, Wang J, Caballero A (2020) Recent Demographic History inferred by high-resolution analysis of linkage disequilibrium. Mol Biol Evol 37:3642–3653. https://doi.org/10.1093/molbev/msaa169

Article CAS PubMed Google Scholar

Schiffels S, Wang K (2020) MSMC and MSMC2: The Multiple Sequentially Markovian Coalescent. In: Dutheil JY (ed) Statistical Population Genomics. Springer US, New York, NY, pp 147–166

Shafer ABA, Côté SD, Coltman DW (2011) Hot spots of genetic diversity descended from multiple Pleistocene refugia in an alpine ungulate. Evol Int J Org Evol 65:125–138. https://doi.org/10.1111/j.1558-5646.2010.01109.x

Article Google Scholar

Shafer ABA, Fan CW, Côté SD, Coltman DW (2012) (Lack of) genetic diversity in immune genes predates glacial isolation in the North American mountain goat (Oreamnos americanus). J Hered 103:371–379. https://doi.org/10.1093/jhered/esr138

Shafer ABA, Gattepaille LM, Stewart REA, Wolf JBW (2015) Demographic inferences using short-read genomic data in an approximate Bayesian computation framework: in silico evaluation of power, biases and proof of concept in Atlantic walrus. Mol Ecol 24:328–345. https://doi.org/10.1111/mec.13034

Article PubMed Google Scholar

Shafer ABA, Peart CR, Tusso S, Maayan I, Brelsford A, Wheat CW, Wolf JBW (2017) Bioinformatic processing of RAD-seq data dramatically impacts downstream population genetic inference. Methods Ecol Evol 8:907–917. https://doi.org/10.1111/2041-210X.12700

Article Google Scholar

Shendure J, Ji H (2008) Next-generation DNA sequencing. Nat Biotechnol 26:1135–1145. https://doi.org/10.1038/nbt1486

Article CAS PubMed Google Scholar

Sin SYW, Hoover B, Nevitt G, Edwards SV (2021) Demographic history, not mating system, explains signatures of inbreeding and inbreeding depression in a large outbred population. Am Nat. https://doi.org/10.1086/714079

Skotte L, Korneliussen TS, Albrechtsen A (2013) Estimating individual admixture proportions from next generation sequencing data. Genetics 195:693–702. https://doi.org/10.1534/genetics.113.154138

Article CAS PubMed PubMed Central Google Scholar

Subramanian S (2016) The effects of sample size on population genomic analyses – implications for the tests of neutrality. BMC Genom 17:123. https://doi.org/10.1186/s12864-016-2441-8

Article CAS Google Scholar

Tarasov A, Vilella AJ, Cuppen E, Nijman IJ, Prins P (2015) Sambamba: fast processing of NGS alignment formats. Bioinformatics 31:2032–2034. https://doi.org/10.1093/bioinformatics/btv098

Article CAS PubMed PubMed Central Google Scholar

Teixeira JC, Huber CD (2021) The inflated significance of neutral genetic diversity in conservation genetics. Proc Natl Acad Sci 118. https://doi.org/10.1073/pnas.2015096118

Verrall B, Pickering CM (2020) Alpine vegetation in the context of climate change: a global review of past research and future directions. Sci Total Environ 748:141344. https://doi.org/10.1016/j.scitotenv.2020.141344

Article CAS PubMed Google Scholar

Vijay N, Bossu CM, Poelstra JW, Weissensteiner MH, Suh A, Kryukov AP, Wolf JBW (2016) Evolution of heterogeneous genome differentiation across multiple contact zones in a crow species complex. Nat Commun 7:13195. https://doi.org/10.1038/ncomms13195

Article CAS PubMed PubMed Central Google Scholar

Wang K, Mathieson I, O’Connell J, Schiffels S (2020) Tracking human population structure through time from whole genome sequences. PLOS Genet 16:e1008552. https://doi.org/10.1371/journal.pgen.1008552

Article CAS PubMed PubMed Central Google Scholar

Waples RK, Larson WA, Waples RS (2016) Estimating contemporary effective population size in non-model species using linkage disequilibrium across thousands of loci. Heredity 117:233–240. https://doi.org/10.1038/hdy.2016.60

Article CAS PubMed PubMed Central Google Scholar

Warmuth VM, Ellegren H (2019) Genotype-free estimation of allele frequencies reduces bias and improves demographic inference from RADSeq data. Mol Ecol Resour 19:586–596. https://doi.org/10.1111/1755-0998.12990

Article CAS PubMed Google Scholar

Wootton E, Robert C, Taillon J, Côté S, Shafer ABA (2023) Genomic health is dependent on long-term population demographic history. Mol Ecol 32:1943–1954. https://doi.org/10.1111/mec.16863

Article CAS PubMed Google Scholar

Wright S (1943) Isolation by distance. Genetics 28:114–138

Article CAS PubMed PubMed Central Google Scholar

Zhao S, Zheng P, Dong S, Zhan X, Wu Q, Guo X, Hu Y, He W, Zhang S, Fan W, Zhu L, Li D, Zhang X, Chen Q, Zhang H, Zhang Z, Jin X, Zhang J, Yang H, Wang J, Wang J, Wei F (2013) Whole-genome sequencing of giant pandas provides insights into demographic history and local adaptation. Nat Genet 45:67–71. https://doi.org/10.1038/ng.2494

Article CAS PubMed Google Scholar

Download references

We thank Marty Kardos, Joanna R. Freeland, and Paul J. Wilson for comments on earlier versions of this manuscript.

This work was supported by a Natural Sciences and Engineering Research Council Discovery Grant, Canada Foundation for Innovation: John R. Evans Leaders Fund, and Compute Canada Awards to ABAS; Earth Rangers Bring Back the Wild grant and WCS Canada W. Garfield Weston Foundation 2017 and 2018 Fellowships for Northern Conservation to DM. DM was supported by the Ontario Graduate Scholarship. The samples were provided by Alaska Department of Fish and Game, BC Ministry of Forests, Lands, and Natural Resource Operations, BC Mountain Goat Conservation Society, Environment Yukon, Montana Fish, Wildlife and Parks, Alberta Fish and Wildlife and Washington Department of Fish and Wildlife.

Environmental and Life Sciences Graduate Program, Trent University, 2140 East Bank Drive, Peterborough, ON, K9J 7B8, Canada

Daria Martchenko & Aaron B. A. Shafer

Department of Forensics & Environmental and Life Sciences Graduate Program, Trent University, 2140 East Bank Drive, Peterborough, ON, K9J 7B8, Canada

Aaron B. A. Shafer

You can also search for this author in PubMed Google Scholar

You can also search for this author in PubMed Google Scholar

ABAS conceived the study. DM and ABAS analyzed the data and wrote the manuscript.

Correspondence to Daria Martchenko.

The authors declare no competing interests.

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Associate editor: Giorgio Bertorelle.

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and Permissions

Martchenko, D., Shafer, A.B.A. Contrasting whole-genome and reduced representation sequencing for population demographic and adaptive inference: an alpine mammal case study. Heredity (2023). https://doi.org/10.1038/s41437-023-00643-4

Download citation

Received: 22 October 2022

Revised: 22 July 2023

Accepted: 22 July 2023

Published: 02 August 2023

DOI: https://doi.org/10.1038/s41437-023-00643-4

Anyone you share the following link with will be able to read this content:

Sorry, a shareable link is not currently available for this article.

Provided by the Springer Nature SharedIt content-sharing initiative