DOI: 10.5061/dryad.5c7c6
title: Data from: The population history of endogenous retroviruses in mule deer (Odocoileus hemionus)

description: 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.
description: CrERV-in1Sequence data for Odocoileus hemionus Cervid endogenous gammaretrovirus (CrERV-In1)CrERV-in2Sequence data for Odocoileus hemionus Cervid endogenous gammaretrovirus (CrERV-In2)CrERV-in3Sequence data for Odocoileus hemionus Cervid endogenous gammaretrovirus (CrERV-In3)CrERV-in4Sequence data for Odocoileus hemionus Cervid endogenous gammaretrovirus (CrERV-In4)CrERV-in5Sequence data for Odocoileus hemionus Cervid endogenous gammaretrovirus (CrERV-In5)CrERV-in6Sequence data for Odocoileus hemionus Cervid endogenous gammaretrovirus (CrERV-In6)CrERV-in7Sequence data for Odocoileus hemionus Cervid endogenous gammaretrovirus (CrERV-In7)CrERV-in8Sequence data for Odocoileus hemionus Cervid endogenous gammaretrovirus (CrERV-In8)CrERV-in9Sequence data for Odocoileus hemionus Cervid endogenous gammaretrovirus (CrERV-In9)CrERV-in10Sequence data for Odocoileus hemionus Cervid endogenous gammaretrovirus (CrERV-In10)CrERV-in11Sequence data for Odocoileus hemionus Cervid endogenous gammaretrovirus (CrERV-In11)CrERV-in12Sequence data for Odocoileus hemionus Cervid endogenous gammaretrovirus (CrERV-In12)CrERV-in13Sequence data for Odocoileus hemionus Cervid endogenous gammaretrovirus (CrERV-In13)CrERV-in14Sequence data for Odocoileus hemionus Cervid endogenous gammaretrovirus (CrERV-In14)White-tailed deer CrERV-in14Sequence data for Odocoileus virginianus Cervid endogenous gammaretrovirus (CrERV-In14)O.virginianus CrERV-in14.fastaMule Deer ERV Genotypes & Sampling LocationsGenotype data for presence/absence of CrERV in mule deer (n=259). Individuals samples across 15 "populations" in Montana (1-12, HLN: Helena) Wyoming (13) and Utah (UT). Sampling locations of individuals indicated in UTM coordinates (X,Y) and latitude/longitude. Population locations (average of sampled individuals) reported in a separate worksheet. Thirteen CrERVs genotyped (CrERV-in1 to -in13). Missing data indicated by "?".Mule Deer_ERVData_Locations.xlsxMule Deer Microsatellite DataMicrosatellite genotypes for 14 loci in mule deer (n=384). A subset of this data was also genotyped at 14 CrERV loci (see Mule Deer ERV genotype file). Individuals samples across 15 "populations" in Montana (1-12, HLN: Helena) Wyoming (13) and Utah (UT). Missing data indicated by "0".Mule Deer_Msat Data.xlsx