title: Utilizing RADseq data for phylogenetic analysis of challenging taxonomic groups: A case study in Carex sect. Racemosae.
abstract: OBJECTIVE
  Relationships among closely related and recently diverged taxa can be especially difficult to resolve. Here we use both Sanger sequencing and next-generation RADseq data sets to estimate phylogenetic relationships among species of Carex section Racemosae (Cyperaceae), a clade largely restricted to high latitudes and elevations. Interest in relationships among these taxa derives from questions about the species' biogeographic histories and possible links between diversification and Pleistocene glaciations.
  
  
  METHODS
  A combination of approaches and molecular markers were used to estimate relationships among Carex species within sect. Racemosae and taxa from closely related sections. Nuclear and chloroplast loci generated by Sanger sequencing were analyzed with *BEAST, and SNP data from RADseq loci were analyzed as a concatenated data set using maximum likelihood and as independent loci using SVDquartets.
  
  
  RESULTS
  Sanger sequencing data sets resolved relationships among taxa at intermediate phylogenetic depths (albeit with low levels of support). Only the RADseq data resolved relationships with strong support at all phylogenetic depths. Moreover, different methods and data partitions of the RADseq data resulted in nearly identical topologies. Carex sect. Racemosae is a strongly supported clade, although a handful of species were found to group with closely related sections. Herbarium specimens up to 35 yr old successfully produced informative RADseq data.
  
  
  CONCLUSIONS
  Despite the short read lengths of RADseq data, they nevertheless resolved relationships that Sanger sequencing data did not. Resolution of the phylogenetic relationships among recently and rapidly diversifying taxa within sect. Racemosae clades suggest a role for the Pleistocene glaciations in clade diversification.
authors: Department of Ecology and Evolutionary Biology, The University of Michigan, Ann Arbor, Michigan, 41809-1079 USA massatti@umich.edu.
authors: Rob
authors: R
authors: Massatti
authors: Department of Ecology and Evolutionary Biology, The University of Michigan, Ann Arbor, Michigan, 41809-1079 USA.
authors: Anton A
authors: AA
authors: Reznicek
authors: Department of Ecology and Evolutionary Biology, The University of Michigan, Ann Arbor, Michigan, 41809-1079 USA.
authors: L Lacey
authors: LL
authors: Knowles
mesh_terms: D031255:Carex Plant / Q000235:genetics*; D002467:Cell Nucleus / Q000235:genetics; D002736:Chloroplasts / Q000235:genetics; D021901:DNA, Intergenic / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics; D019143:Evolution, Molecular; D008969:Molecular Sequence Data; D010802:Phylogeny; D017422:Sequence Analysis, DNA
chemical_list: D021901:DNA, Intergenic; D018744:DNA, Plant
keywords: Carex; Cyperaceae; Pleistocene; SVDquartets; glaciation; next-generation sequencing; section Racemosae