MBE Advance Access originally published online on February 9, 2005
Molecular Biology and Evolution 2005 22(5):1193-1207; doi:10.1093/molbev/msi104
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Research Article |
Evolution of RAG-1 in Polyploid Clawed Frogs
* Department of Biology, McMaster University, Hamilton, Ontario, Canada; Department of Biological Sciences, Columbia University; Center for Environmental Research and Conservation and Department of Ecology, Evolution and Environmental Biology, Columbia University; and Section of Integrative Biology and Texas Memorial Museum, The University of Texas
E-mail: evansb{at}mcmaster.ca.
Possible genetic fates of a gene duplicate are silencing, redundancy, subfunctionalization, or novel function. These different fates can be realized at the DNA, RNA, or protein level, and their genetic determinants are poorly understood. We explored molecular evolution of duplicated RAG-1 genes in African clawed frogs (Xenopus and Silurana) (1) to examine the fate of paralogs of this gene at the DNA level in terms of recombination, positive selection, and gene degeneration and in the absence of extensive recombination among alleles at different paralogs, (2) to test phylogenetic hypotheses about the origins of polyploid species. We found that recombination between different RAG-1 paralogs is infrequent, that degeneration of some paralogs has occurred via stop codons and frameshift mutations, and that this degeneration occurred in paralogs inherited from only one diploid progenitor species. Simulations and phylogenetic analyses of RAG-1 and mitochondrial DNA support one origin of extant tetraploids in Xenopus and at least one origin in Silurana, five allopolyploid origins of extant octoploids, and two allopolyploid origins of extant dodecaploids. In allopolyploid species, which inherit a complete genome from two different ancestors, genes inherited from the same ancestor have a longer period of coevolution than genes inherited from different ancestors. Because of this, gene ancestry could potentially influence gene fate: interacting paralogs derived from the same lower ploidy ancestor might have similar genetic destinies.
Key Words: reticulate evolution • genome duplication • polyploidization • ortholog • paralog • Xenopus • Silurana • Pipidae
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