Phylogenetics

Phylogenetic relationships within Iochrominae (Solanaceae)

We used three nuclear regions (ITS, LFY intron II and waxy) to estimate the phylogeny of Iochrominae, a clade of around 34 species traditionally divided among 6 genera (Smith and Baum 2006, AJB). Five of these genera did not appear to be natural (monophyletic) groups, suggesting that taxonomic revision is needed. Also, comparison of the individual nuclear data sets revealed two interspecific hybrid taxa and a third possible case. Future work in Iochrominae will focus on using the concordance approach (see below) along with additional nuclear markers to resolve key nodes and quantify reticulate evolution.

Pictured on left: Combined three-gene phylogeny for Iochrominae from Smith and Baum (2006). Colored boxes indicate geographic distribution. Bold branches are strongly supported (>95%PP). Gray curved lines connect hybrids to putative parents. Click here for high resolution version.

Bayesian Concordance Analysis

Collaborating with Cécile Ané, Bret Larget and David Baum, I worked to develop a Bayesian approach for estimating the amount of concordance (topological agreement) among genes in multi-gene datasets (Ané et al. 2007, MBE). This method allows us to identify clades that are strongly supported across genes as well as areas of discordance, e.g. due horizontal transfer or incomplete lineage sorting. Concordance analysis is implemented by the program BUCKy.

Pictured at right: A examples of a gene-to-tree maps, the "currency" of concordance analysis