title: High copy number in human endogenous retrovirus families is associated with copying mechanisms in addition to reinfection.
abstract: There are at least 31 families of human endogenous retroviruses (HERVs), each derived from an independent infection by an exogenous virus. Using evidence of purifying selection on HERV genes, we have shown previously that reinfection by replication-competent elements was the predominant mechanism of copying in some families. Here we analyze the evolution of 17 HERV families using d(N)/d(S) ratios and find a positive relationship between copy number and the use of additional copying mechanisms. All families with more than 200 elements have also used one or more of the following mechanisms: (1) complementation in trans (elements copied by other elements of the same family; HERV-H and ERV-9), (2) retrotransposition in cis (elements copying themselves) within germ-line cells (HERV-K(HML3)), and (3) being copied by non-HERV machinery (HERV-W). We discuss why these other mechanisms are rare in most families and suggest why complementation in trans is significant only in the larger families.
authors.forename: Robert
authors.initials: R
authors.lastname: Belshaw
authors.forename: Aris
authors.initials: A
authors.lastname: Katzourakis
authors.forename: Jan
authors.initials: J
authors.lastname: Paces
authors.forename: Austin
authors.initials: A
authors.lastname: Burt
authors.forename: Michael
authors.initials: M
authors.lastname: Tristem
mesh_terms: D020077:Endogenous Retroviruses / Q000145:classification / Q000235:genetics*; D016013:Likelihood Functions; D010802:Phylogeny; D012091:Repetitive Sequences, Nucleic Acid; D012192:Retroviridae Infections / Q000235:genetics*; D016662:Virus Integration