MBE Advance Access published online on April 2, 2003
Molecular Biology and Evolution, doi:10.1093/molbev/msg065
Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2003; all rights reserved
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1 Department of Botany, Iowa State University, Iowa 50011
* To whom correspondence should be addressed. E-mail: jfw{at}iastate.edu.
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 0.018-0.162 and 0.000-0.073, respectively, in comparisons between orthologous Gossypium and outgroup sequences. However, about 90% of the genes had silent substitution rates spanning a more narrow three-fold 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 homoeologues 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), following divergence of the diploid progenitors about 6.7 mya. Key Words:
Gossypium, cotton, polyploidy, molecular clock, substitution rates, evolution
© 2003 Society for Molecular Biology and Evolution
Original Articles
Rate Variation among Nuclear Genes and the Age of Polyploidy in Gossypium
2 Pacific Northwest Research Station, USDA Forest Service, 3200 SW Jefferson Way, Corvallis, OR 97331
3 Institute of Genetics and Cytology, Northeast Normal University, Changchun 130024, China
4 Plant Genome Mapping Laboratory, University of Georgia, Riverbend Research Center, Athens, GA 30602
5 Department of EPO Biology, University of Colorado, Boulder, CO 80309
6 Department of Plant Sciences, University of Arizona, 303 Forbes, Tucson, AZ 85721
7 Department of Agronomy & Range Science, University of California-Davis, Davis, CA 95616
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