Ocean-wide genomic variation in Gray's beaked whales, Mesoplodon grayi

This is the final version. Available on open access from the Royal Society via the DOI in this recordData accessibility: Genbank accession codes for mitogenomes are MW645443-MW645463 and raw reads for nuclear genomes can be found in Genbank BioProject ID PRJNA702760. Additional Data and relevant code for this research work are stored in GitHub: https://github.com/Mvwestbury/Dstats-topology-test and have been archived within the Zenodo repository: https://doi.org/10.5281/zenodo.4320997The deep oceans of the Southern Hemisphere are home to several elusive and poorly studied marine megafauna. In the absence of robust observational data for these species, genetic data can aid inferences on population connectivity, demography and ecology. A previous investigation of genetic diversity and population structure in Gray's beaked whale (Mesoplodon grayi) from Western Australia and New Zealand found high levels of mtDNA diversity, no geographic structure and stable demographic history. To further investigate phylogeographic and demographic patterns across their range, we generated complete mitochondrial and partial nuclear genomes of 16 of the individuals previously analysed and included additional samples from South Africa (n = 2) and South Australia (n = 4), greatly expanding the spatial range of genomic data for the species. Gray's beaked whales are highly elusive and rarely observed, and our data represents a unique and geographically broad dataset. We find relatively high levels of diversity in the mitochondrial genome, despite an absence of population structure at the mitochondrial and nuclear level. Demographic analyses suggest these whales existed at stable levels over at least the past 1.1 million years, with an approximately twofold increase in female effective population size approximately 250 thousand years ago, coinciding with a period of increased Southern Ocean productivity, sea surface temperature and a potential expansion of suitable habitat. Our results suggest that Gray's beaked whales are likely to be resilient to near-future ecosystem changes, facilitating their conservation. Our study demonstrates the utility of low-effort shotgun sequencing in providing ecological information on highly elusive species.Lerner Grey Memorial Fund for Marine Research, American Natural History MuseumUniversity of Exeter European Network FundVillum Fonden Young Investigator ProgrammeCarlsberg FoundationIndependent Research Fund Denmark | Natural Sciences, Forskningsprojekt 1Rubicon-NW

Arctic-adapted dogs emerged at the Pleistocene-Holocene transitiond

Although sled dogs are one of the most specialized groups of dogs, their origin and evolution has received much less attention than many other dog groups. We applied a genomic approach to investigate their spatiotemporal emergence by sequencing the genomes of 10 modern Greenland sled dogs, an ~9500-year-old Siberian dog associated with archaeological evidence for sled technology, and an ~33,000-year-old Siberian wolf. We found noteworthy genetic similarity between the ancient dog and modern sled dogs. We detected gene flow from Pleistocene Siberian wolves, but not modern American wolves, to present-day sled dogs. The results indicate that the major ancestry of modern sled dogs traces back to Siberia, where sled dog–specific haplotypes of genes that potentially relate to Arctic adaptation were established by 9500 years ago