Phylogenetic Relationships of Capsicum (Solanaceae) Using DNA Sequences from Two Noncoding Regions: The Chloroplast atpB‐rbcL Spacer Region and Nuclear waxy Introns

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Abstract
This study focuses on three phylogenetic problems related to Capsicum (Solanaceae): (1) the monophyly of the genus, (2) species delimitation within the genus, and (3) phylogenetic relationships of species within Capsicum. The chloroplast atpB‐rbcL noncoding spacer region was used to derive a phylogeny 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 of species delimitation and phylogenetic relationships within Capsicum. Capsicum is monophyletic, with moderate support. Capsicum ciliatum, which is both molecularly and morphologically distinctive, is sister to a highly supported clade consisting of all other Capsicum species studied. Capsicum cardenasii and C. eximium are sister species and are, in turn, sisters to a moderately 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 unstudied, is included in a weakly supported clade consisting of C. annuum, C. chinensis, and C. frutescens. Many species of Capsicum have sufficient molecular markers in the waxy data set (both nucleotide substitutions and insertions/deletions) to be useful in species delimitation. An informal classification of the genus is proposed.