Abstract
Previous phylogenetic studies in oaks (Quercus, Fagaceae) have failed to resolve the backbone topology of the genus with strong support. Here, 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 1.40 E06 aligned nucleotides, constituting 27,727 sequence clusters. RAD-Seq data were readily combined across runs, with no difference in phylogenetic placement between technical replicates, which overlapped by only 43–64% in locus coverage. 17% (4,715) of the loci we analyzed could be mapped with high confidence to one or more expressed sequence tags 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 equal-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. We introduce a partitioned RAD visualization method (implemented in the R package RADami; http://cran.r-project.org/web/packages/RADami) to investigate the possibility that suboptimal topologies supported by large numbers of loci—due, for example, to reticulate evolution or lineage sorting—are masked by the globally optimal tree. We find no evidence for strongly-supported alternative topologies in our study, suggesting that the phylogeny we recover is a robust estimate of large-scale phylogenetic patterns in the American oak clade. Our study is one of the first to demonstrate the utility of RAD-Seq data for inferring phylogeny in a 23–33 million year-old clade.
Highlights
For organisms in which ecological and morphological differences persist even in the face of interspecific gene flow [1], phylogeny estimation can be problematic [2,3,4]
Our study demonstrates the utility of Restriction-site associated DNA (RAD) data for reconstructing phylogenetic relationships in a problematic group that spans a 23– 33 million-year-old divergence
Sequenced RAD markers for phylogenetic inference The pattern of locus-sharing among individuals loosely reflects phylogenetic history, as evidenced by the fact that, for example, accessions of sections Lobatae and Quercus sequenced in 2010 cluster together in an ordination based on the locus presence-absence matrix (Fig. 3), and clustering within those sections (Fig. 3) largely follows the geographic subclades identified in the phylogeny (Fig. 2)
Summary
For organisms in which ecological and morphological differences persist even in the face of interspecific gene flow [1], phylogeny estimation can be problematic [2,3,4]. Previous published studies utilizing chloroplast DNA (cpDNA) and low-copy nuclear gene (LCNG) data have recovered a provisional framework phylogeny for the genus Quercus and identified the relative position of Quercus within the Fagaceae [24,25,26]. This body of work identifies a predominantly American clade within Quercus, comprising sections Quercus (the white oaks sensu stricto, including the Virentes of the Americas and roburoids of Eurasia), Lobatae Loudon (the red or black oaks), and Protobalanus (Trelease) A.Camus (the intermediate or golden oaks). The Eurasian white oaks of section Quercus are embedded in this predominantly American clade, we refer to it hereafter in the paper as the ‘‘American clade.’’ The monophyly of each section is strongly supported in all analyses
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
