Multiple Nuclear Ortholog (COSII) Phylogeny of Wild Potatoes and Tomatoes.

Phylogenies reconstructed with only one or a few independently inherited loci may be unresolved or incongruent due to taxon and gene sampling, horizontal gene transfer, or differential selection and lineage sorting at individual loci. In an effort to remedy this situation, we examined more than 80 conserved orthologous set (COSII) nuclear loci to elucidate the phylogenetic relationships among Solanum species and 24 were chosen based on the presence of a single band amplification, intron content more than 60% and PCR-product more than 600 bp. These 24 COSII are being sequenced in a total of 73 diploid Solanum species; 69 are species in the sister clades tomato (17) and potato (52), four are other Solanum species (S. aviculare, S. caripense, S. dulcamara, S. melogena), and the remaining six are further outgroups in the genera Arabidopsis, Capsicum, Convolvulus, Datura, and Ipomoea. This study is a considerable expansion of a recently published study using 11 COSII in common for 30 species. Phylogenetic analyses are being conducted with each individual COSII and with the concatenated data set to determine the predominant history and to detect which mechanism most likely shaped the discordance.