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Title: A phylogenetic analysis of the grape genus (Vitis L.) reveals broad reticulation and concurrent diversification during neogene and quaternary climate change

Author
item WAN, YIZHEN - Northwest Agricultural & Forestry University
item Schwaninger, Heidi
item Baldo, Angela
item Labate, Joanne
item Zhong, Gan-Yuan
item SIMON, CHARLES - Former ARS Employee

Submitted to: BMC Evolutionary Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/7/2013
Publication Date: 5/10/2013
Citation: Wan, Y., Schwaninger, H.R., Baldo, A.M., Labate, J.A., Zhong, G., Simon, C. 2013. A phylogenetic analysis of the grape genus (Vitis L.) reveals broad reticulation and concurrent diversification during neogene and quaternary climate change. BMC Evolutionary Biology. 13:141.

Interpretive Summary:

Technical Abstract: There are about 60 interbreeding species in the genus Vitis. Phylogenetic relationships among these species are of keen interest for conservation and use of this germplasm. We selected 309 accessions from 48 Vitis species, varieties, and outgroups, examined ~11 kb (~3.4 Mb total) of aligned nuclear DNA sequences from 27 unlinked genes in a phylogenetic context, and estimated divergence times based on fossil calibrations. There was substantial support for species and less for higher-level groupings. As estimated from extant taxa, the crown age of Vitis was 28 Ma and divergence of subgenera (Vitis and Muscadinia) occurred at ~18 Ma. Higher clades in subgenus Vitisdiverged 16 – 5 Ma with overlapping confidence intervals, and ongoing divergence formed extant species at 12 – 1.3 Ma. Network analysis showed extensive reticulation at the core of subgenus Vitis representing the deeper nodes, with extensive reticulation radiating outward. Parsimony identified North America as the origin of the most recent common ancestor of extant Vitis species, fragmentation of an ancestral range during the Miocene, formation of extant species in the late Miocene-Pleistocene, and differentiation of species in the context of Pliocene-Quaternary tectonic and climatic change. Nuclear SNPs effectively resolved relationships at and below the species level in grapes and rectified misclassification of accessions in the USDA grape germplasm repositories. Our results challenge current higher-level classifications, reveal the abundance of genetic diversity in the genus that is potentially available for crop improvement, and provide a valuable resource for species delineation, germplasm conservation and use. http://www.biomedcentral.com/1471-2148/13/141