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MBE Advance Access published online on October 20, 2004
Molecular Biology and Evolution, doi:10.1093/molbev/msi022
Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2004; all rights reserved
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Accepted October 4, 2004

Research Article

Isolation and Molecular Evolution of the Selenocysteine tRNA (Cf TRSP) and RNase P RNA (Cf RPPH1) Genes in the Dog Family, Canidae

Carolyne Bardeleben 1*, Rachael L. Moore 1, and Robert K. Wayne 1

1 Department of Ecology and Evolutionary Biology, University of California, Los Angeles 621 Charles E. Young Drive South, Los Angeles, California 90095-1606

* To whom correspondence should be addressed.
Carolyne Bardeleben, E-mail: carolyne_bard{at}yahoo.com


  Abstract

In an effort to identify rapidly evolving nuclear sequences useful for phylogenetic analyses of closely related species, we isolated two genes transcribed by RNA polymerase III (pol III), the selenocysteine tRNA gene (TRSP) and an RNase P RNA (RPPH1) gene from the domestic dog (Canis familiaris). We focus on genes transcribed by pol III because their coding regions are small (generally 100-300 basepairs (bp)) and their essential promoter elements are located within a couple hundred bps upstream of the coding region. Therefore, we predicted that regions flanking the coding region and outside of the promoter elements would be free of constraint and evolve rapidly. We amplified TRSP from 23 canids and RPPH1 from twelve canids and analyzed the molecular evolution of these genes and their utility as phylogenetic markers for resolving relationships among species in Canidae. We compared the rate of evolution of the gene flanking regions to other non-coding regions of nuclear DNA (introns) and to the mitochondrial encoded COII gene. Alignment of TRSP from 23 canids revealed that regions directly adjacent to the coding region display high sequence variability. We discuss this pattern in terms of functional mechanisms of transcription. Although the flanking regions evolve no faster than introns, both genes were found to be useful phylogenetic markers, in part, due to the synapomorphic indels found in the flanking regions. Gene trees generated from the TRSP and RPPH1 loci were generally in agreement with the published mtDNA phylogeny and are the first phylogeny of Canidae based on nuclear sequences.

Keywords: Selenocysteine tRNA; Canidae; molecular evolution; phylogeny; transcriptional start site; polymorphism.
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