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Demography and adaptation promoting evolutionary transitions in a mammalian genus that diversified during the Pleistocene

De Jong, M.; Li, Z.; Qin, Y.; Quemere, E.; Baker, K.; Wang, W.; Hoelzel, A.R.

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M. De Jong

Z. Li

Y. Qin

E. Quemere

Dr Karis Baker
Ancient-DNA Commercialisation Developer

W. Wang


Species that evolved in temperate regions during the Pleistocene experienced periods of extreme climatic transitions. Consequent population fragmentation and dynamics had the potential to generate small, isolated populations where the influence of genetic drift would be expected to be strong. We use comparative genomics to assess the evolutionary influence of historical demographics and natural selection through a series of transitions associated with the formation of the genus Capreolus, speciation within this genus during the Quaternary and during divergence among European roe deer (C. capreolus) populations. Our analyses were facilitated by the generation of a new high‐coverage reference genome for the Siberian roe deer (Capreolus pygargus). We find progressive reductions in effective population size (Ne), despite very large census sizes in modern C. capreolus populations and show that low Ne has impacted the C. capreolus genome, reducing diversity and increasing linkage disequilibrium. Even so, we find evidence for natural selection shared among C. capreolus populations, including a historically documented founder population that has been through a severe bottleneck. During each phylogenetic transition there is evidence for selection (e.g. using evidence from non‐synonymous change or population data), including at loci associated with diapause (delayed embryonic development), a phenotype restricted to this genus among the even‐toed ungulates. Together these data allow us to assess expectations for the origin and diversification of a mammalian genus during a period of extreme environmental change.

Journal Article Type Article
Acceptance Date Apr 3, 2020
Online Publication Date May 13, 2020
Publication Date 2020-08
Deposit Date Apr 5, 2020
Publicly Available Date Aug 11, 2020
Journal Molecular Ecology
Print ISSN 0962-1083
Electronic ISSN 1365-294X
Publisher Wiley
Peer Reviewed Peer Reviewed
Volume 29
Issue 15
Pages 2777-2792
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Copyright Statement
© 2020 The Authors. Molecular Ecology published by John Wiley & Sons Ltd. This is an open access article under the terms of the Creative Commons Attribution‐NonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.

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