Phylogenetic utility of nuclear nitrate reductase: A multi-locus comparison of nuclear and chloroplast sequence data for inference of relationships among American Lycieae (Solanaceae)

There has been considerable interest and research into the benefits of multiple low-copy nuclear regions for phylogenetic studies at low taxonomic levels. In this study, the phylogenetic utility of DNA sequence data from two low-copy nuclear genes, nitrate reductase (NIA) and granule-bound starch synthase I (GBSSI), was compared with data from nuclear ribosomal ITS and the cpDNA spacers trnT–trnF and trnD–trnT across 33 closely related taxa in tribe Lycieae (Solanaceae). The NIA data (introns 1–2) had the most parsimony-informative characters, with over twice the number provided by GBSSI, but NIA also had greater homoplasy. Although gene trees were generally concordant across the four regions, there were some notable areas of incongruence, suggesting both incomplete lineage sorting as well as possible reticulate origins.