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


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.

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Fig. 1: A map of the O. americanus tissue sample locations and extent of the species range.
Fig. 2: Folded site frequency spectra.
Fig. 3: Population structure inferred using PCA.
Fig. 4: Migration profiles from MSMC-IM between individuals from the extremes of species range.

Data availability

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


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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.

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

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Correspondence to Daria Martchenko.

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The authors declare no competing interests.

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Associate editor: Giorgio Bertorelle.

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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 131, 273–281 (2023).

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