A framework phylogeny of the American oak clade based on sequenced RAD data

Publication Type:Journal Article
Year of Publication:2014
Authors:A. L. Hipp, Eaton, D. A. R., Cavender-Bares, J., Fitzek, E., Nipper, R., Manos, P. S.
Keywords:Expressed sequence tags (EST), Fagaceae, next-generation sequencing, phylogenomics, plant systematics, Quercus, restriction-site associated DNA

Oaks (Quercus, Fagaceae) are notorious in plant systematics for the problems they pose at the species level and for higher-level phylogenetics. Previous studies based on nuclear and chloroplast DNA sequences have failed to resolve the backbone phylogeny of the genus with strong support. In this study, we utilize next-generation sequencing of restriction-site associated DNA (RAD-Seq) to resolve a framework phylogeny of a predominantly American clade of oaks whose crown age is estimated at 23–33 million years old. Using a recently developed analytical pipeline for RAD-Seq phylogenetics, we created a concatenated matrix of 1.39E06 aligned nucleotides, constituting 27,727 sequence clusters or ‘loci.’ We reran a subset of seven individuals as technical replicates and found that RAD-Seq data are readily combined across runs, with no difference in phylogenetic placement between replicates, despite the fact that a change in sequencing platforms between replicate runs resulted in data overlap between technical replicates of only 43–64%. 17% (4,715) of the loci we analyzed could be matched with high confidence (BLASTN E-value < 1E–15) to one or more expressed sequence tags (ESTs) in NCBI Genbank. A concatenated matrix of the loci that BLAST to at least one EST sequence provides approximately half as many variable or parsimony-informative characters as same-sized datasets from the non-EST loci. The EST-associated matrix is more complete (fewer missing loci) and has slightly lower homoplasy than non-EST subsampled matrices of the same size, but there is no difference in phylogenetic support or relative attribution of base substitutions to internal versus terminal branches of the phylogeny. The phylogeny we recover provides a robust estimate of the framework phylogeny for the American oak clade and demonstrates the utility of RAD-Seq data for inferring phylogeny in a 23–33 million year-old vascular plant clade.

Short Title:PLoS ONE
Scratchpads developed and conceived by (alphabetical): Ed Baker, Katherine Bouton Alice Heaton Dimitris Koureas, Laurence Livermore, Dave Roberts, Simon Rycroft, Ben Scott, Vince Smith