Our paper on phylogenetics of the asterid family Goodeniaceae has just been published in Molecular Phylogenetics and Evolution. This paper used Sanger and NGS sequence data to resolve the backbone of the phylogeny for this angiosperm family. The work was a collaboration with Drs. Rachel Jabaily and Andy Gardner of Rhodes College in Memphis, TN. It was great fun to work with them on this, especially thanks to Andy’s skills at creating beautiful figures!
Gardner AG*, Sessa EB*, Michener P, Johnson E, Shepherd KA, Howarth DG, Jabaily RS. Utilizing next-generation sequencing to resolve the backbone and inform taxonomy of the Core Goodeniaceae. Molecular Phylogenetics and Evolution, in press. PDF
*These authors contributed equally.
Abstract: Though considerable progress has been made in inferring phylogenetic relationships of many plant lineages, deep unresolved nodes remain a common problem that can impact downstream efforts, including taxonomic decision-making and character reconstruction. The Core Goodeniaceae is a group affected by this issue: data from the plastid regions trnL-trnF and matK have been insufficient to generate adequate support at key nodes along the backbone of the phylogeny. We performed genome skimming for 24 taxa representing major clades within Core Goodeniaceae. The plastome coding regions (CDS) and nuclear ribosomal repeats (NRR) were assembled and complemented with additional accessions sequenced for nuclear G3PDH and plastid trnL-trnF and matk. The CDS, NRR, and G3PDH alignments were analyzed independently and topology tests were used to detect the alignments’ ability to reject alternative topologies. The CDS, NRR, and G3PDH alignments independently supported a Brunonia (Scaevola s.l. (Coopernookia (Goodenia s.l.))) backbone topology, but within Goodenia s.l., the strongly-supported plas- tome topology (Goodenia A (Goodenia B (Velleia + Goodenia C))) contrasts with the poorly supported nuclear topology ((Goodenia A + Goodenia B) (Velleia + Goodenia C)). A fully resolved and maximally supported topology for Core Goodeniaceae was recovered from the plastome CDS, and there is excellent support for most of the major clades and relationships among them in all alignments. The composition of these seven major clades renders many of the current taxonomic divisions non-monophyletic, prompting us to suggest that Goodenia may be split into several segregate genera.