title: A protocol for targeted enrichment of intron-containing sequence markers for recent radiations: A phylogenomic example from Heuchera (Saxifragaceae).
abstract: OBJECTIVE
  Phylogenetic inference is moving to large multilocus data sets, yet there remains uncertainty in the choice of marker and sequencing method at low taxonomic levels. To address this gap, we present a method for enriching long loci spanning intron-exon boundaries in the genus Heuchera.
  
  
  METHODS
  Two hundred seventy-eight loci were designed using a splice-site prediction method combining transcriptomic and genomic data. Biotinylated probes were designed for enrichment of these loci. Reference-based assembly was performed using genomic references; additionally, chloroplast and mitochondrial genomes were used as references for off-target reads. The data were aligned and subjected to coalescent and concatenated phylogenetic analyses to demonstrate support for major relationships.
  
  
  RESULTS
  Complete or nearly complete (>99%) sequences were assembled from essentially all loci from all taxa. Aligned introns showed a fourfold increase in divergence as opposed to exons. Concatenated analysis gave decisive support to all nodes, and support was also high and relationships mostly similar in the coalescent analysis. Organellar phylogenies were also well-supported and conflicted with the nuclear signal.
  
  
  CONCLUSIONS
  Our approach shows promise for resolving a recent radiation. Enrichment for introns is highly successful with little or no sequencing dropout at low taxonomic levels despite higher substitution and indel frequencies, and should be exploited in studies of species complexes.
authors: Herbarium, The Ohio State University, Columbus, Ohio 43212 USA.
authors: Ryan A
authors: RA
authors: Folk
authors: Department of Biology, University of Memphis, Memphis, Tennessee 38152 USA.
authors: Jennifer R
authors: JR
authors: Mandel
authors: Herbarium, The Ohio State University, Columbus, Ohio 43212 USA.
authors: John V
authors: JV
authors: Freudenstein
keywords: COS marker; Heuchera; Saxifragaceae; intron enrichment; targeted enrichment