DOI: 10.5061/dryad.cr1496b
title: Data from: Partial genomic survival of cave bears in living brown bears

description: Although many large mammal species went extinct at the end of the
 Pleistocene epoch, their DNA may persist due to past episodes of
 interspecies admixture. However, direct empirical evidence of the
 persistence of ancient alleles remains scarce. Here, we present multifold
 coverage genomic data from four Late Pleistocene cave bears (Ursus
 spelaeus complex) and show that cave bears hybridized with brown bears
 (Ursus arctos) during the Pleistocene. We develop an approach to assess
 both the directionality and relative timing of gene flow. We find that
 segments of cave bear DNA still persist in the genomes of living brown
 bears, with cave bears contributing 0.9 to 2.4% of the genomes of all
 brown bears investigated. Our results show that even though extinction is
 typically considered as absolute, following admixture, fragments of the
 gene pool of extinct species can survive for tens of thousands of years in
 the genomes of extant recipient species.
description: 191Y_arctos_Slovenia_haploidised_fastaHaploidised fasta sequence generated by mapping Illumina short reads to the reference genome assembly of the giant panda, then randomly selecting a single high quality nucleotide from the read stack for each position of the reference genome. See the original publication for full details. The raw sequencing data is also available from the European Nucleotide Archive. Note that this file will contain abundant errors in comparison to a consensus base call from high coverage data.191Y_rep1_all.fa.gz235_arctos_Russia_haploidised_fastaHaploidised fasta sequence generated by mapping Illumina short reads to the reference genome assembly of the giant panda, then randomly selecting a single high quality nucleotide from the read stack for each position of the reference genome. See the original publication for full details. The raw sequencing data is also available from the European Nucleotide Archive. Note that this file will contain abundant errors in comparison to a consensus base call from high coverage data.235_rep1_all.fa.gzAdm1_arctos_Admiralty_haploidised_fastaHaploidised fasta sequence generated by mapping Illumina short reads to the reference genome assembly of the giant panda, then randomly selecting a single high quality nucleotide from the read stack for each position of the reference genome. See the original publication for full details. The raw sequencing data is also available from the European Nucleotide Archive. Note that this file will contain abundant errors in comparison to a consensus base call from high coverage data.Adm1_rep1_all.fa.gzDen_arctos_Denali_haploidised_fastaHaploidised fasta sequence generated by mapping Illumina short reads to the reference genome assembly of the giant panda, then randomly selecting a single high quality nucleotide from the read stack for each position of the reference genome. See the original publication for full details. The raw sequencing data is also available from the European Nucleotide Archive. Note that this file will contain abundant errors in comparison to a consensus base call from high coverage data.Den_rep1_all.fa.gzE-VD-1838_spelaeus_Spain_haploidised_fastaHaploidised fasta sequence generated by mapping Illumina short reads to the reference genome assembly of the giant panda, then randomly selecting a single high quality nucleotide from the read stack for each position of the reference genome. See the original publication for full details. The raw sequencing data is also available from the European Nucleotide Archive. Note that this file will contain abundant errors in comparison to a consensus base call from high coverage data.E-VD-1838_rep1_all.fa.gzGe_arctos_Georgia_haploidised_fastaHaploidised fasta sequence generated by mapping Illumina short reads to the reference genome assembly of the giant panda, then randomly selecting a single high quality nucleotide from the read stack for each position of the reference genome. See the original publication for full details. The raw sequencing data is also available from the European Nucleotide Archive. Note that this file will contain abundant errors in comparison to a consensus base call from high coverage data.Ge_rep1_all.fa.gzGS136_ingressus_Austria_haploidised_fastaHaploidised fasta sequence generated by mapping Illumina short reads to the reference genome assembly of the giant panda, then randomly selecting a single high quality nucleotide from the read stack for each position of the reference genome. See the original publication for full details. The raw sequencing data is also available from the European Nucleotide Archive. Note that this file will contain abundant errors in comparison to a consensus base call from high coverage data.GS136_rep1_all.fa.gzHV74_kudarensis_Armenia_haploidised_fastaHaploidised fasta sequence generated by mapping Illumina short reads to the reference genome assembly of the giant panda, then randomly selecting a single high quality nucleotide from the read stack for each position of the reference genome. See the original publication for full details. The raw sequencing data is also available from the European Nucleotide Archive. Note that this file will contain abundant errors in comparison to a consensus base call from high coverage data.HV74_rep1_all.fa.gzLS039_arctos_Spain_haploidised_fastaHaploidised fasta sequence generated by mapping Illumina short reads to the reference genome assembly of the giant panda, then randomly selecting a single high quality nucleotide from the read stack for each position of the reference genome. See the original publication for full details. The raw sequencing data is also available from the European Nucleotide Archive. Note that this file will contain abundant errors in comparison to a consensus base call from high coverage data.LS039_rep1_all.fa.gzNB_maritimus_haploidised_fastaHaploidised fasta sequence generated by mapping Illumina short reads to the reference genome assembly of the giant panda, then randomly selecting a single high quality nucleotide from the read stack for each position of the reference genome. See the original publication for full details. The raw sequencing data is also available from the European Nucleotide Archive. Note that this file will contain abundant errors in comparison to a consensus base call from high coverage data.NB_rep1_all.fa.gzSB_maritimus_haploidised_fastaHaploidised fasta sequence generated by mapping Illumina short reads to the reference genome assembly of the giant panda, then randomly selecting a single high quality nucleotide from the read stack for each position of the reference genome. See the original publication for full details. The raw sequencing data is also available from the European Nucleotide Archive. Note that this file will contain abundant errors in comparison to a consensus base call from high coverage data.SB_rep1_all.fa.gzSwe_arctos_Sweden_haploidised_fastaHaploidised fasta sequence generated by mapping Illumina short reads to the reference genome assembly of the giant panda, then randomly selecting a single high quality nucleotide from the read stack for each position of the reference genome. See the original publication for full details. The raw sequencing data is also available from the European Nucleotide Archive. Note that this file will contain abundant errors in comparison to a consensus base call from high coverage data.Swe_rep1_all.fa.gzTornatus_haploidised_fastaHaploidised fasta sequence generated by mapping Illumina short reads to the reference genome assembly of the giant panda, then randomly selecting a single high quality nucleotide from the read stack for each position of the reference genome. See the original publication for full details. The raw sequencing data is also available from the European Nucleotide Archive. Note that this file will contain abundant errors in comparison to a consensus base call from high coverage data.Tornatus_all.fa.gzUamericanus_haploidised_fastaHaploidised fasta sequence generated by mapping Illumina short reads to the reference genome assembly of the giant panda, then randomly selecting a single high quality nucleotide from the read stack for each position of the reference genome. See the original publication for full details. The raw sequencing data is also available from the European Nucleotide Archive. Note that this file will contain abundant errors in comparison to a consensus base call from high coverage data.Uamericanus_all.fa.gzUap_arctos_Pleistocene_Austria_haploidised_fastaHaploidised fasta sequence generated by mapping Illumina short reads to the reference genome assembly of the giant panda, then randomly selecting a single high quality nucleotide from the read stack for each position of the reference genome. See the original publication for full details. The raw sequencing data is also available from the European Nucleotide Archive. Note that this file will contain abundant errors in comparison to a consensus base call from high coverage data.Uap_rep1_all.fa.gzUthibetanus_haploidised_fastaHaploidised fasta sequence generated by mapping Illumina short reads to the reference genome assembly of the giant panda, then randomly selecting a single high quality nucleotide from the read stack for each position of the reference genome. See the original publication for full details. The raw sequencing data is also available from the European Nucleotide Archive. Note that this file will contain abundant errors in comparison to a consensus base call from high coverage data.Uthibetanus_all.fa.gzWH2_maritimus_haploidised_fastaHaploidised fasta sequence generated by mapping Illumina short reads to the reference genome assembly of the giant panda, then randomly selecting a single high quality nucleotide from the read stack for each position of the reference genome. See the original publication for full details. The raw sequencing data is also available from the European Nucleotide Archive. Note that this file will contain abundant errors in comparison to a consensus base call from high coverage data.WH2_rep1_all.fa.gzWK01_eremus_Austria_haploidised_fastaHaploidised fasta sequence generated by mapping Illumina short reads to the reference genome assembly of the giant panda, then randomly selecting a single high quality nucleotide from the read stack for each position of the reference genome. See the original publication for full details. The raw sequencing data is also available from the European Nucleotide Archive. Note that this file will contain abundant errors in comparison to a consensus base call from high coverage data.WK01_rep1_all.fa.gz