Springer, Mark S. and Tusneem, Nadeem A. and Davidson, Eric H. and Britten, Roy J. (1995) Phylogeny, rates of evolution, and patterns of codon usage among sea urchin retroviral-like elements, with implications for the recognition of horizontal transfer. Molecular Biology and Evolution, 12 (2). pp. 219-230. ISSN 0737-4038. https://resolver.caltech.edu/CaltechAUTHORS:20151223-111751365
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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.
Item Type: | Article | ||||||
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Additional Information: | © 1995 by The University of Chicago. Received May 26 1994; Accepted September 23 1994. We would like to thank Angela Burk, Laura Hollar, Anthony Metcalf, two anonymous reviewers, and Dr. Mitiko Go for helpful comments on earlier drafts of the manuscript. | ||||||
Subject Keywords: | retrotransposon; reverse transcriptase; codon usage, horizontal transfer | ||||||
Issue or Number: | 2 | ||||||
Record Number: | CaltechAUTHORS:20151223-111751365 | ||||||
Persistent URL: | https://resolver.caltech.edu/CaltechAUTHORS:20151223-111751365 | ||||||
Official Citation: | M S Springer, N A Tusneem, E H Davidson, and R J Britten Phylogeny, rates of evolution, and patterns of codon usage among sea urchin retroviral-like elements, with implications for the recognition of horizontal transfer. Mol Biol Evol (1995) 12 (2): 219-230 | ||||||
Usage Policy: | No commercial reproduction, distribution, display or performance rights in this work are provided. | ||||||
ID Code: | 63185 | ||||||
Collection: | CaltechAUTHORS | ||||||
Deposited By: | Tony Diaz | ||||||
Deposited On: | 23 Dec 2015 19:22 | ||||||
Last Modified: | 03 Oct 2019 09:26 |
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