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The population history of endogenous retroviruses in mule deer (Odocoileus heminous)

Journal of Heredity

By:
, , , , , and
DOI: 10.1093/jhered/est088

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Abstract

Mobile elements are powerful agents of genomic evolution and can be exceptionally informative markers for investigating species and population-level evolutionary history. While several studies have utilized retrotransposon-based insertional polymorphisms to resolve phylogenies, few population studies exist outside of humans. Endogenous retroviruses are LTR-retrotransposons derived from retroviruses that have become stably integrated in the host genome during past infections and transmitted vertically to subsequent generations. They offer valuable insight into host-virus co-evolution and a unique perspective on host evolutionary history because they integrate into the genome at a discrete point in time. We examined the evolutionary history of a cervid endogenous gammaretrovirus (CrERVγ) in mule deer (Odocoileus hemionus). We sequenced 14 CrERV proviruses (CrERV-in1 to -in14), and examined the prevalence and distribution of 13 proviruses in 262 deer among 15 populations from Montana, Wyoming, and Utah. CrERV absence in white-tailed deer (O. virginianus), identical 5′ and 3′ long terminal repeat (LTR) sequences, insertional polymorphism, and CrERV divergence time estimates indicated that most endogenization events occurred within the last 200000 years. Population structure inferred from CrERVs (F ST = 0.008) and microsatellites (θ = 0.01) was low, but significant, with Utah, northwestern Montana, and a Helena herd being particularly differentiated. Clustering analyses indicated regional structuring, and non-contiguous clustering could often be explained by known translocations. Cluster ensemble results indicated spatial localization of viruses, specifically in deer from northeastern and western Montana. This study demonstrates the utility of endogenous retroviruses to elucidate and provide novel insight into both ERV evolutionary history and the history of contemporary host populations.

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Additional Publication Details

Publication type:
Article
Publication Subtype:
Journal Article
Title:
The population history of endogenous retroviruses in mule deer (Odocoileus heminous)
Series title:
Journal of Heredity
DOI:
10.1093/jhered/est088
Volume
105
Issue:
2
Year Published:
2013
Language:
English
Publisher:
Oxford University Press
Publisher location:
Oxford, UK
Contributing office(s):
Northern Rocky Mountain Science Center
Description:
15 p.
Larger Work Type:
Article
Larger Work Subtype:
Journal Article
Larger Work Title:
Journal of Heredity
First page:
173
Last page:
187
Country:
United States
State:
Montana;Utah;Wyoming