The population history of endogenous retroviruses in mule deer (odocoileus hemionus)

Pauline L. Kamath, Daniel Elleder, Le Bao, Paul C. Cross, John H. Powell, Mary Poss

Research output: Contribution to journalArticle

8 Citations (Scopus)

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 (FST = 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.

Original languageEnglish (US)
Pages (from-to)173-187
Number of pages15
JournalJournal of Heredity
Volume105
Issue number2
DOIs
StatePublished - Oct 1 2014

Fingerprint

Gammaretrovirus
Endogenous Retroviruses
Deer
Equidae
History
Terminal Repeat Sequences
Proviruses
Retroelements
Population
Cluster Analysis
Genome
Viruses
Retroviridae
Phylogeny
Microsatellite Repeats
Infection

All Science Journal Classification (ASJC) codes

  • Biotechnology
  • Molecular Biology
  • Genetics
  • Genetics(clinical)

Cite this

Kamath, Pauline L. ; Elleder, Daniel ; Bao, Le ; Cross, Paul C. ; Powell, John H. ; Poss, Mary. / The population history of endogenous retroviruses in mule deer (odocoileus hemionus). In: Journal of Heredity. 2014 ; Vol. 105, No. 2. pp. 173-187.
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The population history of endogenous retroviruses in mule deer (odocoileus hemionus). / Kamath, Pauline L.; Elleder, Daniel; Bao, Le; Cross, Paul C.; Powell, John H.; Poss, Mary.

In: Journal of Heredity, Vol. 105, No. 2, 01.10.2014, p. 173-187.

Research output: Contribution to journalArticle

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