Molecular Biology and Evolution, Vol 12, 219-230, Copyright © 1995 by Society for Molecular Biology and Evolution
MS Springer, NA Tusneem, EH Davidson and RJ Britten
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.
ORIGINAL ARTICLE
Phylogeny, rates of evolution, and patterns of codon usage among sea urchin retroviral-like elements, with implications for the recognition of horizontal transfer
Department of Biology, University of California at Riverside 92521.
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