Phylogenetic relationships of Capsicum (Solanaceae) using DNA sequences from two noncoding regions: The chloroplast atpB-rbcL spacer region and nuclear waxy introns

This study focuses on three phylogenetic problems related to Capsicum (Sola naceae): (1) the monophyly of the genus, (2) species delimitation within th e genus, and (3) phylogenetic relationships of species within Capsicum. The chloroplast atpB-rbcL noncoding spacer region was used to derive a phyloge ny for seven outgroup genera and 11 species of Capsicum. Data derived from five introns within the nuclear gene waxy were used, both separately and in combination with the atpB-rbcL spacer data, to resolve further questions o f species delimitation and phylogenetic relationships within Capsicum. Caps icum is monophyletic, with moderate support. Capsicum ciliatum, which is bo th molecularly and morphologically distinctive, is sister to a highly suppo rted clade consisting of all other Capsicum species studied. Capsicum carde nasii and C. eximium are sister species and are, in turn, sisters to a mode rately supported clade consisting of C. tovarii, C. pubescens, C. chacoense , C. baccatum, C. galapagoense, C. chinense, C. frutescens, and C. annuum. Capsicum galapagoense, whose taxonomic affinities have been largely unstudi ed, is included in a weakly supported clade consisting of C. annuum, C. chi nensis, and C. frutescens. Many species of Capsicum have sufficient molecul ar markers in the waxy data set (both nucleotide substitutions and insertio ns/deletions) to be useful in species delimitation. An informal classificat ion of the genus is proposed.