Evolution of endogenous retrovirus-like elements of the woolly mammoth (Mammuthus primigenius) and its relatives

Endogenous retrovirus-like elements characterizable by a leucine tRNA prime r (ERV-Ls) are reiterated genomic sequences known to be widespread in mamma ls, including humans. They may have arisen from an ancestral foamy virus-li ke element by successful germ line infection followed by copy number expans ion. However among mammals, only primates and rodents have thus far exhibit ed high copy number amplification and sequence diversification. Conventiona lly, empirical studies of proviral amplification and diversification have b een limited to extant species, but taxa havings good Quaternary fossil reco rds could potentially be investigated using the techniques of "ancient" DNA research. To examine evolutionary parameters of ERV-Ls across both time an d taxa, we characterized this proviral class in the extinct woolly mammoth (Mammuthus primigenius) and living elephants, as well as extant members of the larger clade to which they belong (Uranotheria, a group containing prob oscideans, sirenians, hyraxes, and their extinct relatives). Ungulates and carnivores previously analyzed demonstrated low copy numbers of ERV-L seque nces, and thus it was expected that uranotheres should as well. Here, we sh ow that all uranothere taxa exhibit unexpectedly numerous and diverse ERV-L sequence complements, indicating active expansion within this group of lin eages. Selection is the most parsimonious explanation for observed differen ces in ERV-L distribution and frequency, with relative success beings refle cted in the persistence of certain elements over a variety of sampled time depths (as can be observed by comparing sequences from fossil and extant el ephantid samples).