Data from: The population history of endogenous retroviruses in mule deer (Odocoileus hemionus)

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.