Origins and genetic legacy of prehistoric dogs

Abstract

Dogs were the first domestic animal, but little is known about their population history and to what extent it was linked to humans. We sequenced 27 ancient dog genomes and found that all dogs share a common ancestry distinct from present-day wolves, with limited gene flow from wolves since domestication but substantial dog-to-wolf gene flow. By 11,000 years ago, at least five major ancestry lineages had diversified, demonstrating a deep genetic history of dogs during the Paleolithic. Coanalysis with human genomes reveals aspects of dog population history that mirror humans, including Levant-related ancestry in Africa and early agricultural Europe. Other aspects differ, including the impacts of steppe pastoralist expansions in West and East Eurasia and a near-complete turnover of Neolithic European dog ancestry.

A Southeast Asian origin for present-day non-African human Y chromosomes

“…We assembled available sequences of C, D and FT lineages from worldwide surveys ensuring that common lineages were represented (Bergstrom et al 2020 ; Karmin et al 2015 ; Mallick et al 2016 ; Meyer et al 2012 ; Poznik et al 2016 ), and supplemented them with additional sequences from known rare lineages potentially relevant to early divergences, specifically, Australian C (Bergstrom et al 2016 ; Mallick et al 2016 ), West African D0 (Haber et al 2019 ), Andamanese D (Mondal et al 2017 ), and F chromosomes from China (Mallick et al 2016 ), Vietnam (Poznik et al 2016 ) and Singapore (Wong et al 2013 ): 1204 sequences in all. We then focussed on the phylogenetic structure of the early divergences within these three lineages, and their geographical distributions revealed by ancient DNA and present-day analyses.…”

“…Y-chromosomal data from high-coverage whole-genome sequenced samples were combined from the following publicly available or published datasets: the Simons Genome Diversity Project (SGDP) (Mallick et al 2016 ), Polaris ( https://github.com/Illumina/Polaris ), the Human Genome Diversity Project (HGDP) (Bergstrom et al 2020 ; Meyer et al 2012 ), the Andaman Islands samples (Mondal et al 2017 ), haplogroup D0 samples from Nigeria and additional haplogroup D samples from Tibet (Haber et al 2019 ), Australian haplogroup C samples (Bergstrom et al 2016 ) and a haplogroup F* Singapore Malay sample SSM072 (Wong et al 2013 ). Fifty low-coverage whole-genome sequenced samples from the 1000 Genomes Project dataset (Poznik et al 2016 ) were included to represent some of the deep-rooting lineages of haplogroups A, C, F, and H that were not present in other datasets.…”

“…The Y haplogroups of each sample were predicted from the all-site vcf file with the yHaplo software ( https://github.com/23andMe/yhaplo ) using a version where the marker coordinates in the relevant input files had been replaced to correspond to the GRCh38 assembly (Bergstrom et al 2020 ). The identified terminal SNV for each sample was used to update the haplogroup name to correspond to the International Society of Genetic Genealogy nomenclature (ISOGG, https://isogg.org , v03.10.19) (Supplementary Table 2).…”

A refined proposal for the origin of dogs: the case study of Gnirshöhle, a Magdalenian cave site

“…Second, the newly generated mitochondrial genomes from the Gnirshöhle canids introduce a yet unrecognized, ancient mitochondrial canid lineage that had survived into the Magdalenian. Several authors have now proposed that mitochondrial dog lineages in prehistoric Europe were replaced by expanding lineages arriving from the East 24,45,46 . This fate was possibly shared by the Gnirshöhle canids as an example of diversity that was replaced by the incoming lineages represented by today's dog clade A 43 .…”

“…This fate was possibly shared by the Gnirshöhle canids as an example of diversity that was replaced by the incoming lineages represented by today's dog clade A 43 . The age of the Gnirshöhle canids exceeds those of the samples analyzed by Frantz and colleagues 24 , and implies that with more samples, we may still discover divergent lineages representative of early dogs 47 , a prospect that helps to finally derive a more nuanced picture of modern wolf 's domestication history (see also Bergström and colleagues 46 ).…”