Despite the fact that the legume genus Glycine includes the cultivated soybean (G. max), much remains to be learned about its evolutionary history and taxonomic relationships. These include the origin of the entire genus associated with an ancient genome duplication event, relationships among the reproductively isolated "genome groups" to which the approximately 25 diploid perennial species of the genus belong, and the complex history of genetic differentiation among closely related species within these genome groups. All of these issues have in common the possibility that hybridization has played a role in producing the patterns observed in DNA variation from nuclear, chloroplast, and mitochondrial genes. Polyploidy (multiple sets of chromosomes) and hybridization separately, or together in allopolyploidy, are two of the most important processes that shape the genomes of plants, including cultivated plants such as wheat, maize, cotton, and soybean. In the case of Glycine it is unknown whether hybridization was involved in polyploid formation, as hypothesized to have occurred 15 million years ago, and if so, what species were the donors of the two genomes. This and other questions at progressively more recent stages in the history of Glycine that involve the role of polyploidy and hybridization can be addressed by studying a large number of genes on the different chromosomes or in different genomic compartments (mitochondrion, chloroplast). The largest source of such genes is the nuclear genome, and this project taps genomic projects in soybean and other legumes (e.g., Medicago truncatula) to provide many candidate genes for study. Around 100 nuclear genes will be assessed for their utility in addressing phylogenetic questions, taking into account such additional criteria as position on the soybean genetic map. Analytical methods will include phylogeny reconstruction using various approaches, assessment of incongruence, testing for polytomies and hybridity, network construction, and admixture assessment. The work will address general issues of dealing with incongruence, identifying and using low copy nuclear genes, and studying polyploidy. Achieving a better understanding of polyploidy and hybridization in general, and particularly in Glycine, is of broad relevance and significance for plant biology and genetics because of the prevalence of these phenomena. The project will have an impact on the infrastructure of science by training undergraduate and graduate students and a postdoctoral fellow, including minority undergraduate students who will participate in summer research internships. Collaboration with the Cornell Institute for Biology Teachers will lead to the development of phylogeny laboratories for high school and middle school students. The project is international in its scope, with researchers from the United States and Australia, and involves the use and enhancement of germplasm resources in the form of Glycine seed collections in both countries.
