MBE Advance Access originally published online on April 2, 2003
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Mol. Biol. Evol. 20(4):633-643. 2003
DOI: 10.1093/molbev/msg065
© 2003 by the Society for Molecular Biology and Evolution. ISSN: 0737-4038
Rate Variation Among Nuclear Genes and the Age of Polyploidy in Gossypium
* Department of Botany, Iowa State University
Pacific Northwest Research Station, USDA Forest Service
Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
Plant Genome Mapping Laboratory, University of Georgia, Riverbend Research Center
|| Department of EPO Biology, University of Colorado
¶ Department of Plant Sciences, University of Arizona
# Department of Agronomy and Range Science, University of California-Davis
Molecular evolutionary rate variation in Gossypium (cotton) was characterized using sequence data for 48 nuclear genes from both genomes of allotetraploid cotton, models of its diploid progenitors, and an outgroup. Substitution rates varied widely among the 48 genes, with silent and replacement substitution levels varying from 0.018 to 0.162 and from 0.000 to 0.073, respectively, in comparisons between orthologous Gossypium and outgroup sequences. However, about 90% of the genes had silent substitution rates spanning a more narrow threefold range. Because there was no evidence of rate heterogeneity among lineages for any gene and because rates were highly correlated in independent tests, evolutionary rate is inferred to be a property of each gene or its genetic milieu rather than the clade to which it belongs. Evidence from approximately 200,000 nucleotides (40,000 per genome) suggests that polyploidy in Gossypium led to a modest enhancement in rates of nucleotide substitution. Phylogenetic analysis for each gene yielded the topology expected from organismal history, indicating an absence of gene conversion or recombination among homoeologs subsequent to allopolyploid formation. Using the mean synonymous substitution rate calculated across the 48 genes, allopolyploid cotton is estimated to have formed circa 1.5 million years ago (MYA), after divergence of the diploid progenitors about 6.7 MYA.
Key Words: Gossypium • cotton • polyploidy • molecular clock • substitution rates • evolution
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