@article{TEXTUAL,
      recid = {10703},
      author = {Hipp, Andrew L. and Eaton, Deren A. R. and Cavender-Bares,  Jeannine and Fitzek, Elisabeth and Nipper, Rick and Manos,  Paul S.},
      title = {A Framework Phylogeny of the American Oak Clade Based on  Sequenced RAD Data},
      journal = {PLOS ONE},
      address = {2014-04-04},
      number = {TEXTUAL},
      abstract = {<p>Previous phylogenetic studies in oaks  (<em>Quercus</em>, 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; <a  href="http://cran.r-project.org/web/packages/RADami">http://cran.r-project.org/web/packages/RADami</a>)  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.</p>},
      url = {http://knowledge.uchicago.edu/record/10703},
}