title: Evolution of endogenous retrovirus-like elements of the woolly mammoth (Mammuthus primigenius) and its relatives.
abstract: Endogenous retrovirus-like elements characterizable by a leucine tRNA primer (ERV-Ls) are reiterated genomic sequences known to be widespread in mammals, including humans. They may have arisen from an ancestral foamy virus-like element by successful germ line infection followed by copy number expansion. However, among mammals, only primates and rodents have thus far exhibited high copy number amplification and sequence diversification. Conventionally, empirical studies of proviral amplification and diversification have been limited to extant species, but taxa having good Quaternary fossil records could potentially be investigated using the techniques of "ancient" DNA research. To examine evolutionary parameters of ERV-Ls across both time and 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 proboscideans, sirenians, hyraxes, and their extinct relatives). Ungulates and carnivores previously analyzed demonstrated low copy numbers of ERV-L sequences, and thus it was expected that uranotheres should as well. Here, we show that all uranothere taxa exhibit unexpectedly numerous and diverse ERV-L sequence complements, indicating active expansion within this group of lineages. Selection is the most parsimonious explanation for observed differences in ERV-L distribution and frequency, with relative success being reflected in the persistence of certain elements over a variety of sampled time depths (as can be observed by comparing sequences from fossil and extant elephantid samples).
authors.affiliation: Division of Vertebrate Zoology, American Museum of Natural History, New York, New York 10024-5192, USA. alexgr@amnh.org
authors.forename: A D
authors.initials: AD
authors.lastname: Greenwood
authors.forename: F
authors.initials: F
authors.lastname: Lee
authors.forename: C
authors.initials: C
authors.lastname: Capelli
authors.forename: R
authors.initials: R
authors.lastname: DeSalle
authors.forename: A
authors.initials: A
authors.lastname: Tikhonov
authors.forename: P A
authors.initials: PA
authors.lastname: Marx
authors.forename: R D
authors.initials: RD
authors.lastname: MacPhee
mesh_terms: D000818:Animals; D001483:Base Sequence; D001842:Bone and Bones / Q000737:chemistry; D003001:Cloning, Molecular; D016384:Consensus Sequence; D003573:Cytochrome b Group / Q000235:genetics*; D003596:Cytosine / Q000737:chemistry; D004247:DNA / Q000097:blood / Q000235:genetics / Q000302:isolation & purification*; D004272:DNA, Mitochondrial / Q000235:genetics* / Q000302:isolation & purification; D004279:DNA, Viral / Q000032:analysis; D004606:Elephants / Q000097:blood / Q000145:classification / Q000235:genetics*; D020077:Endogenous Retroviruses / Q000235:genetics*; D019143:Evolution, Molecular; D005580:Fossils; D005814:Genes, Viral; D015751:Genes, pol; D015698:Genomic Library; D006151:Guanosine / Q000737:chemistry; D007043:Hyraxes / Q000235:genetics*; D018895:Microsatellite Repeats / Q000235:genetics*; D008969:Molecular Sequence Data; D009132:Muscles / Q000737:chemistry; D021141:Nucleic Acid Amplification Techniques; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D011533:Proviruses / Q000235:genetics* / Q000302:isolation & purification*; D012190:Retroviridae / Q000235:genetics* / Q000302:isolation & purification*; D017386:Sequence Homology, Amino Acid; D013045:Species Specificity; D014070:Tooth / Q000737:chemistry; D020457:Trichechus manatus / Q000097:blood / Q000235:genetics*
chemical_list: D003573:Cytochrome b Group; D004272:DNA, Mitochondrial; D004279:DNA, Viral; D006151:Guanosine; D003596:Cytosine; D004247:DNA