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

Nicolás Dussex ,Kerstin Lidén,Doris Döppes,Love Dalén,Susanne Lindauer,Jouni Aspi,Oleg Askeyev ,Ronny Friedrich,Linda Laikre,Remi‐André Olsen ,Federica Alberti,Arthur Askeyev ,Igor Askeyev ,Matti T J Heino ,Dilyara N Shaymuratova,Nils Ryman,Michael Hofreiter,Tom Van Der Valk,Hans Ahlgren,Wilfried Rosendahl,David Díez‐Del‐Molino

doi:10.1186/s12864-020-07208-3

Abstract

BackgroundNumerous 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.ResultsWe 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.ConclusionsTaken together, our results highlight the dynamic recent evolutionary history of the moose and provide an important resource for further genomic studies.

Highlights

Numerous megafauna species from northern latitudes went extinct during the Pleistocene/Holocene transition as a result of climate-induced habitat changes
The BUSCO analysis identified 164 (4%) and 317 (7.8%) missing, 221 (5.4%) and 256 (6.2%) fragmented, as well as 24 (0.6%) and 17 (0.4%) duplicated complete genes for the assemblies generated with ABySS and SOAPdenovo, respectively
We found low to moderate inbreeding for both Swedish and North American moose, with FROH ranging from 8 to 23% of their genome in runs of homozygosity (ROH) (≥0.5 Mb; Fig. S4; Table 1)

Summary

Introduction

Numerous megafauna species from northern latitudes went extinct during the Pleistocene/Holocene transition as a result of climate-induced habitat changes. While many large mammals from northern latitudes went extinct toward the end of the Quaternary, several ungulates survived and subsequently recolonized the Holarctic [2]. For these species, rather than leading to extinction, glacial cycles induced range shifts and geographical isolation in refugia which resulted in inter-specific diversification or allopatric speciation [3]. Ungulates inhabiting high-latitude habitats including tundra and boreal forests are ideal models to study biogeographical processes such as vicariance and recolonisation associated with these glacial cycles. Many Eurasian and North American ungulate species persisted south of the ice sheet or in southern refugia from where they recolonised areas following northward glacial retreat [6,7,8,9]

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Conclusion