Exploring the utility of "next-generation" sequence data on inferring the phylogeny of the South American Valeriana (Valerianaceae)

Molecular Phylogenetics and Evolution
Charles D Bell, Lauren A Gonzalez

Abstract

This study aimed to investigate the phylogenetic utility of genotyping-by-sequencing (GBS) data in the southern South American subclade of Valerianaceae (Dipsacales). The variety of forms that has arisen in this clade, presumably over the past 5-10 million years, has all the signatures of an adaptive and rapid radiation. While the phylogeny of Valerianaceae has received a great deal of attention in the last decade, species relationships have been hard to resolve using traditional phylogenetic markers. Here, we collected high-throughput genomic sequence data from reduced-representation libraries obtained through GBS protocols. Putative orthologs were identified using within- and among-sample clustering using the computer software pyRAD. We recovered over 3000 loci for 14 species of southern South AmericanValeriana,with 140 loci present across all samples.We analyzed a set of phylogenetic trees generated from each locus using maximum likelihood methods, as well as multispecies coalescent (∗BEAST) methods. For comparative purposes, we also used a supermatrix approach to infer the phylogeny for these taxa. Across different methods and data sets, we recovered consistent relationships for the southern South American valerians that we...Continue Reading

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