DOI: 10.5061/dryad.qbzkh18pp
title: Holocene deglaciation drove rapid genetic diversification of Atlantic walrus

description: Rapid global warming is severely impacting Arctic ecosystems and is
 predicted to transform the abundance, distribution, and genetic diversity
 of Arctic species, though these linkages are poorly understood. We address
 this gap in knowledge using palaeogenomics to examine how earlier periods
 of global warming influenced the genetic diversity of Atlantic walrus
 (Odobenus rosmarus rosmarus), a species closely associated with sea ice
 and shallow-water habitats. We analysed 82 ancient and historical Atlantic
 walrus mitochondrial genomes (mitogenomes), including now-extinct
 populations in Iceland and the Canadian Maritimes, to reconstruct the
 Atlantic walrus’ response to Arctic deglaciation. Our results demonstrate
 that the phylogeography and genetic diversity of Atlantic walrus
 populations were initially shaped by the Last Glacial Maximum (LGM),
 surviving in distinct glacial refugia, and subsequently expanding rapidly
 in multiple migration waves during the late Pleistocene and early
 Holocene. The timing of diversification and establishment of distinct
 populations corresponds closely with the chronology of the glacial
 retreat, pointing to a strong link between walrus phylogeography and sea
 ice. Our results indicate that accelerated ice loss in the modern Arctic
 may trigger further dispersal events, likely increasing the connectivity
 of northern stocks while isolating more southerly stocks putatively caught
 in small pockets of suitable habitat. 
description: The 82 mitochondrial genomes were
 obtained from historical and ancient specimens collected from different
 museums around Europe and Canada. Of these, 28 were obtained from previous
 publications (Keighley et al. (2019)) and 10 samples originally from
 Svalbard obtained from Star et al. (2018). Ancient DNA laboratory work was
 undertaken at the Globe Institute from the University of Copenhagen,
 Denmark following stric aDNA laboratory guidelines. Shotgun sequencing was performed on a range of
 Illumina technologies (MiSeq, HiSeq 2500 and HiSeq 4000) at the Danish
 National High-throughput Sequencing Centre. Throughout all laboratory
 work, samples were randomly given a unique sample number, with different
 groupings for extraction, library build, amplification, and sequencing to
 ensure no clustering of samples from a particular locality or time period.
 Samples run on the Illumina HiSeq 4000 were dual-indexed due to the risk
 of index-hopping (Van der Valk et al.
 2020). Reads were trimmed, filtered, and aligned using
 the PALEOMIX (v1.2.13.4) BAM pipeline (Schubert et al.
 2014).
description: ## Holocene deglaciation drove rapid genetic diversification of Atlantic
 walrus The 82 mitogenomes content ancient and historical Atlantic walrus
 mitogenomes used to reconstruct Atlantic walrus’ responde to Artic
 deglaciation. All samples were obtained from different museums covering
 extinct and extanct Atlantic walrus subpopulations and 28 samples were
 obtained from previous studies. Further they were treated in specialized
 Ancient DNA laboratories at the University of Copenhagen, Denmark
 following Ancient DNA laboratory guidelines. Shotgun sequencing was
 performed on a range of Illumina technologies and output reads were
 trimmed, filtered and aligned using the PALEOMIX (v1.2.13.4) BAM pipeline.
 Our results demonstrate that the phylogeography and genetic diversity of
 Atlantic walrus populations was initially shaped by the Last Glacial
 Maximum (LGM), surviving in distinct glacial refugia, and subsequently
 expanding rapidly in multiple migration waves during the late Pleistocene
 and early Holocene. The timing of diversification and establishment of
 distinct populations corresponds closely with the chronology of the
 glacial retreat, pointing to a strong link between walrus phylogeography
 and sea ice. ## Description of the data and file structure 82 mitogenomes
 used in this study are uploaded in Dryad in .fasta format for further
 analysis. The first letters are the sample name as it is listed in the
 supplementary material information. ## Sharing/Access information Data is
 not shared on any other platform.  Data was derived from the following
 sources: *Data is not derived from any previous source ## Code/Software NA