DOI: 10.5061/dryad.8gtht76w4
title: Comparative population genomics of Arctic sled dogs reveals a deep and complex history

description: Recent evidence demonstrates genomic and morphological continuity in the
 Arctic ancestral lineage of dogs. Here, we use the Siberian Husky to
 investigate the genomic legacy of the northeast Eurasian Arctic lineage
 and model the deep population history using genome-wide SNPs. Utilizing
 ancient dog calibrated molecular clocks, we found that at least two
 distinct lineages of Arctic dogs existed in ancient Eurasia at the end of
 the Pleistocene. This pushes back the origin of sled dogs in the northeast
 Siberian Arctic with humans likely intentionally selecting dogs to perform
 different functions and keeping breeding populations that overlap in time
 and space relatively reproductively isolated. In modern Siberian Huskies,
 we found significant population structure based on how they are used by
 humans, recent European breed introgression in about half of the dogs that
 participate in races, moderate levels of inbreeding, and fewer potentially
 harmful variants in populations under strong selection for form and
 function (Show, Sled-Show, and Racing populations of Siberian Huskies). As
 the struggle to preserve unique evolutionary lineages while maintaining
 genetic health intensifies across pedigreed dogs, understanding the
 genomic history to guide policies and best practices for breed management
 is crucial to sustain these ancient lineages and their unique evolutionary
 identity.
description: # Comparative population genomics of Arctic sled dogs reveals a deep and
 complex history
 **[https://doi.org/10.5061/dryad.8gtht76w4](https://doi.org/10.5061/dryad.8gtht76w4)** This dataset contains the SNP genotype data in *Plink* ped and map format. ## Description of the data and file structure The dataset in these files contains the SNP genotype data for the canids used in this study including Alaskan sled dog (heritage, distance and sprint), Siberian Husky (Pet, Racing, Seppala, Show and Sled-Show), Alaskan Malamute, Chukotka Sled Dog, Greenland sled dog, Golden Retriever, German Shepherd, Saluki, Samoyed, German Shorthaired Pointer, North American Grey Wolf, and three ancient canids (Zhokhov dog, Port au choix pre-contact dog, and Yana wolf).  The QC.ped and QC.map files includes the 124905 variant dataset that has been filtered and pruned for to remove variants with missing call rates above 1%, individuals missing more than 33% genotype data, minor allele frequencies below 1%, singletons, and variants in linkage disequilibrium (--indep pairwise 200 100 0.9) for the 355 canids included in this study. This dataset was used for population structure and admixture analyses. The NeROH.ped and NeROH.map files includes the 135451 variant dataset that has been filtered to remove missing call rates above 1%, individuals missing more than 33% genotype data, and to exclude non-autosomal variants. This dataset only includes the Arctic dogs: Alaskan Sled dog, Siberian Huskies, Chukotka Sled Dog, Greenland sled dog, Alaskan Malamute and the Ancient Zhokhov dog. No linkage disequilibrium pruning was performed on this dataset. This dataset was used in effective population size and ROH analyses. ## **Sharing/Access Information** Port au choix pre-contact dog (AL3194) SNP data was obtained from the original article Ní Leathlobhair et al. (2018) available at [https://doi.org/10.5061/dryad.s1k47j4.](https://doi.org/10.5061/dryad.s1k47j4) Publicly available genomic sequences from nine Greenland sled dogs and two ancient canids, Zhokhov dog (Zh-03-97) and Yana wolf (Y06-NP-18994), were obtained from the original article Sinding et al. (2020) and are available from the Sequence Read Archive (Bioproject id: PRJNA608847). Website links to these download datasets below: GreenlandSledDog1 [https://www.ncbi.nlm.nih.gov/sra/SRX7813629\[accn](https://www.ncbi.nlm.nih.gov/sra/SRX7813629[accn)] GreenlandSledDog2 [https://www.ncbi.nlm.nih.gov/sra/SRX7813628\[accn](https://www.ncbi.nlm.nih.gov/sra/SRX7813628[accn)] GreenlandSledDog3 [https://www.ncbi.nlm.nih.gov/sra/SRX7813627\[accn](https://www.ncbi.nlm.nih.gov/sra/SRX7813627[accn)] GreenlandSledDog4 [https://www.ncbi.nlm.nih.gov/sra/SRX7813625\[accn](https://www.ncbi.nlm.nih.gov/sra/SRX7813625[accn)] GreenlandSledDog5 [https://www.ncbi.nlm.nih.gov/sra/SRX7813624\[accn](https://www.ncbi.nlm.nih.gov/sra/SRX7813624[accn)] GreenlandSledDog7 [https://www.ncbi.nlm.nih.gov/sra/SRX7813623\[accn](https://www.ncbi.nlm.nih.gov/sra/SRX7813623[accn)] GreenlandSledDog8 [https://www.ncbi.nlm.nih.gov/sra/SRX7813622\[accn](https://www.ncbi.nlm.nih.gov/sra/SRX7813622[accn)] GreenlandSledDog9 [https://www.ncbi.nlm.nih.gov/sra/SRX7813615\[accn](https://www.ncbi.nlm.nih.gov/sra/SRX7813615[accn)] GreenlandSledDog10 [https://www.ncbi.nlm.nih.gov/sra/SRX7813620\[accn](https://www.ncbi.nlm.nih.gov/sra/SRX7813620[accn)] Yana_wolf [https://www.ncbi.nlm.nih.gov/sra/SRX7813619\[accn](https://www.ncbi.nlm.nih.gov/sra/SRX7813619[accn)] Yana_wolf [https://www.ncbi.nlm.nih.gov/sra/SRX7813618\[accn](https://www.ncbi.nlm.nih.gov/sra/SRX7813618[accn)] Yana_wolf [https://www.ncbi.nlm.nih.gov/sra/SRX7813617\[accn](https://www.ncbi.nlm.nih.gov/sra/SRX7813617[accn)] Yana_wolf [https://www.ncbi.nlm.nih.gov/sra/SRX7813616\[accn](https://www.ncbi.nlm.nih.gov/sra/SRX7813616[accn)] Yana_wolf [https://www.ncbi.nlm.nih.gov/sra/SRX7813614\[accn](https://www.ncbi.nlm.nih.gov/sra/SRX7813614[accn)] Yana_wolf [https://www.ncbi.nlm.nih.gov/sra/SRX7813613\[accn](https://www.ncbi.nlm.nih.gov/sra/SRX7813613[accn)] Yana_wolf [https://www.ncbi.nlm.nih.gov/sra/SRX7813612\[accn](https://www.ncbi.nlm.nih.gov/sra/SRX7813612[accn)] Yana_wolf [https://www.ncbi.nlm.nih.gov/sra/SRX7813611\[accn](https://www.ncbi.nlm.nih.gov/sra/SRX7813611[accn)] Yana_wolf [https://www.ncbi.nlm.nih.gov/sra/SRX7813610\[accn](https://www.ncbi.nlm.nih.gov/sra/SRX7813610[accn)] Yana_wolf [https://www.ncbi.nlm.nih.gov/sra/SRX7813609\[accn](https://www.ncbi.nlm.nih.gov/sra/SRX7813609[accn)] Yana_wolf [https://www.ncbi.nlm.nih.gov/sra/SRX7813608\[accn](https://www.ncbi.nlm.nih.gov/sra/SRX7813608[accn)] Zhokhov_dog [https://www.ncbi.nlm.nih.gov/sra/SRX7813607\[accn](https://www.ncbi.nlm.nih.gov/sra/SRX7813607[accn)] Zhokhov_dog [https://www.ncbi.nlm.nih.gov/sra/SRX7813606\[accn](https://www.ncbi.nlm.nih.gov/sra/SRX7813606[accn)] Zhokhov_dog [https://www.ncbi.nlm.nih.gov/sra/SRX7813605\[accn](https://www.ncbi.nlm.nih.gov/sra/SRX7813605[accn)] Zhokhov_dog [https://www.ncbi.nlm.nih.gov/sra/SRX7813603\[accn](https://www.ncbi.nlm.nih.gov/sra/SRX7813603[accn)] Zhokhov_dog [https://www.ncbi.nlm.nih.gov/sra/SRX7813602\[accn](https://www.ncbi.nlm.nih.gov/sra/SRX7813602[accn)] Zhokhov_dog [https://www.ncbi.nlm.nih.gov/sra/SRX7813601\[accn](https://www.ncbi.nlm.nih.gov/sra/SRX7813601[accn)] Zhokhov_dog [https://www.ncbi.nlm.nih.gov/sra/SRX7813600\[accn](https://www.ncbi.nlm.nih.gov/sra/SRX7813600[accn)] Zhokhov_dog [https://www.ncbi.nlm.nih.gov/sra/SRX7813599\[accn](https://www.ncbi.nlm.nih.gov/sra/SRX7813599[accn)] Zhokhov_dog [https://www.ncbi.nlm.nih.gov/sra/SRX7813598\[accn](https://www.ncbi.nlm.nih.gov/sra/SRX7813598[accn)] Zhokhov_dog [https://www.ncbi.nlm.nih.gov/sra/SRX7813597\[accn](https://www.ncbi.nlm.nih.gov/sra/SRX7813597[accn)] Zhokhov_dog [https://www.ncbi.nlm.nih.gov/sra/SRX7813596\[accn](https://www.ncbi.nlm.nih.gov/sra/SRX7813596[accn)]