title: Phylogeny, rates of evolution, and patterns of codon usage among sea urchin retroviral-like elements, with implications for the recognition of horizontal transfer.
abstract: Phylogenetic relationships, rates of evolution, and codon usage were investigated in a family of retrotransposons (SURL elements) found in echinoids. The phylogeny of SURL element reverse transcriptase sequences from 10 echinoid species clearly shows the phylogenetic signature of the host taxa as well as paralogous sequences that diverged prior to speciation events. Two subfamilies (1 and 5) of SURL element reverse transcriptase sequences are recognized that diverged prior to the radiation of the Echinometridae. Comparisons of synonymous versus nonsynonymous substitutions indicate that SURL elements have been active in echinoid genomes and have evolved under purifying selection for millions of years. Rates of synonymous substitution for reverse transcriptase are similar to rates of single-copy DNA evolution and to rates of synonymous substitution for the H3 and H4 histone genes, contradicting the assumption that rates of evolution are accelerated in retrotransposons. Finally, codon usage in SURL elements is biased for codons ending in A or U relative to 42 sea urchin nuclear genes. Biased codon usage is sometimes cited as evidence for horizontal transfer, but in the case of SURL elements this bias occurs in spite of a long history of vertical transmission rather than because of horizontal transfer.
authors.affiliation: Department of Biology, University of California at Riverside 92521.
authors.forename: M S
authors.initials: MS
authors.lastname: Springer
authors.forename: N A
authors.initials: NA
authors.lastname: Tusneem
authors.forename: E H
authors.initials: EH
authors.lastname: Davidson
authors.forename: R J
authors.initials: RJ
authors.lastname: Britten
mesh_terms: D000818:Animals; D001483:Base Sequence; D005075:Biological Evolution; D002467:Cell Nucleus / Q000235:genetics; D022761:Gene Transfer, Horizontal; D005815:Genetic Code; D014644:Genetic Variation / Q000235:genetics; D006657:Histones / Q000235:genetics; D008969:Molecular Sequence Data; D012335:RNA, Ribosomal / Q000235:genetics; D012194:RNA-Directed DNA Polymerase / Q000235:genetics; D018626:Retroelements / Q000235:genetics*; D012617:Sea Urchins / Q000235:genetics*; D013997:Time Factors
chemical_list: D006657:Histones; D012335:RNA, Ribosomal; C075526:RNA, ribosomal, 12S; D018626:Retroelements; D012194:RNA-Directed DNA Polymerase