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.

可移动遗传元件（mobile elements）是基因组进化的关键驱动因子，亦是探究物种种群水平进化历史的极具信息价值的标记物。既往多项研究利用基于反转录转座子（retrotransposon）插入多态性的分析策略解析系统发育关系，但除人类以外的同类种群研究仍较为稀缺。内源性逆转录病毒（endogenous retroviruses, ERVs）是一类源自逆转录病毒的长末端重复序列反转录转座子（LTR-retrotransposon），它们在既往感染过程中稳定整合入宿主基因组，并经垂直传播传递给后代世代。这类元件可为宿主-病毒共进化研究提供宝贵见解，同时因其整合至宿主基因组的时间节点明确，亦能为宿主进化历史提供独特的解析视角。
本研究针对骡鹿（Odocoileus hemionus）体内的鹿科内源性γ逆转录病毒（cervid endogenous gammaretrovirus, CrERVγ）的进化历史展开探究。我们对14株CrERV前病毒（provirus）（CrERV-in1至-in14）进行了测序，并对采自美国蒙大拿州、怀俄明州与犹他州15个种群的262头鹿体内的13株前病毒的携带率与分布特征进行了检测。白尾鹿（O. virginianus）体内未检测到CrERV，结合其5′与3′端长末端重复序列（long terminal repeat, LTR）序列完全一致、插入多态性以及CrERV分化时间估算结果，表明多数内整合事件发生于近20万年内。
基于CrERV的群体结构分析（固定指数（fixation index, F_ST）= 0.008）与微卫星（microsatellites）分析结果显示，种群间遗传分化程度较低但具有统计学显著性，其中犹他州种群、蒙大拿州西北部种群以及海伦娜鹿群的分化尤为突出。聚类分析结果表明种群存在区域遗传结构，部分非连续聚类现象可通过已报道的鹿群易位事件得到合理解释。聚类集成分析结果显示病毒存在空间定位特征，尤其在蒙大拿州东北部与西部的鹿群中表现显著。本研究证实了内源性逆转录病毒可用于解析ERV自身的进化历史以及当代宿主种群的演化历史，并为相关研究提供全新的研究视角。