Moose genomes reveal past glacial demography and the origin of modern lineages

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RESEARCH ARTICLE

Open Access

Moose genomes reveal past glacial demography and the origin of modern lineages Nicolas Dussex1,2,3* , Federica Alberti4,5, Matti T. Heino1,2,6,7, Remi-Andre Olsen8, Tom van der Valk1,2, Nils Ryman3, Linda Laikre3, Hans Ahlgren9, Igor V. Askeyev10, Oleg V. Askeyev10, Dilyara N. Shaymuratova10, Arthur O. Askeyev10, Doris Döppes5, Ronny Friedrich11, Susanne Lindauer11, Wilfried Rosendahl5,11, Jouni Aspi6, Michael Hofreiter4, Kerstin Lidén9, Love Dalén1,2 and David Díez-del-Molino1,2,3*

Abstract Background: Numerous megafauna species from northern latitudes went extinct during the Pleistocene/Holocene transition as a result of climate-induced habitat changes. However, several ungulate species managed to successfully track their habitats during this period to eventually flourish and recolonise the holarctic regions. So far, the genomic impacts of these climate fluctuations on ungulates from high latitudes have been little explored. Here, we assemble a de-novo genome for the European moose (Alces alces) and analyse it together with re-sequenced nuclear genomes and ancient and modern mitogenomes from across the moose range in Eurasia and North America. Results: We found that moose demographic history was greatly influenced by glacial cycles, with demographic responses to the Pleistocene/Holocene transition similar to other temperate ungulates. Our results further support that modern moose lineages trace their origin back to populations that inhabited distinct glacial refugia during the Last Glacial Maximum (LGM). Finally, we found that present day moose in Europe and North America show low to moderate inbreeding levels resulting from post-glacial bottlenecks and founder effects, but no evidence for recent inbreeding resulting from human-induced population declines. Conclusions: Taken together, our results highlight the dynamic recent evolutionary history of the moose and provide an important resource for further genomic studies. Keywords: Genomics, Moose, Ancient DNA, Phylogeny, Demography

* Correspondence: [email protected]; [email protected] 1 Centre for Palaeogenetics, Svante Arrhenius väg 20C, SE-106 91 Stockholm, Sweden Full list of author information is available at the end of the article © The Author(s). 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a