Gene flow from Neandertals has shaped the landscape of genetic and phenotypic variation in modern humans. We identify the location and size of introgressed Neandertal ancestry segments in more than 300 genomes spanning the last 50,000 years. We study how Neandertal ancestry is shared among individuals to infer the time and duration of the Neandertal gene flow. We find the correlation of Neandertal segment locations across individuals and their divergence to sequenced Neandertals, both support a model of a single major Neandertal gene flow. Our catalog of introgressed segments through time confirms that most natural selection–positive and negative–on Neandertal ancestry variants occurred immediately after the gene flow, and provides new insights into how contact with Neandertals shaped human origins and adaptation., We identified Neandertal introgressed segments in 59 ancient and 2118 present-day modern human individuals using an HMM approach called admixfrog., , # Neanderthal ancestry through time: Insights from genomes of ancient and present-day humans

https://doi.org/10.5061/dryad.zw3r228gg

In this study, we used 59 ancient and 2118 present-day modern human genomes. We called segments in the genome that are of Neandertal and Denisovan ancestry. In this data repository are all the files used for the analysis of the study. For a detailed description of how the data was generated see the supplementary section of the study.

Description of the data and file structure

In this data repository are 11 files in total. Most files are given or contain data for admixfrog runs. The genetic distances given in these files are from two different empirical genetic maps. Either from the Shared genetic map (these do not contain data on the X chromosome) or from the African-American map (this genetic map is specific to the African hot spot and not very precise for Eurasian populations but it contains the X chromos...

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 selectio..., , , # Comparative population genomics of Arctic sled dogs reveals a deep and complex history

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).Â

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%,...