DOI: 10.5061/dryad.4cn66
title: Data from: A protocol for targeted enrichment of intron-containing sequence markers for recent radiations: a phylogenomic example from Heuchera (Saxifragaceae)

description: Premise of the study: 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
 (&gt;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. Discussion: 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.
description: Concatenated low-copy
 nuclear matrixConcatenated data matrix
 of all 277 successfully enriched loci, assembled by BWA and aligned by
 MAFFT.nuclearmatrix.phyConcatenated nuclear matrix, exons onlyConcatenated nuclear matrix, trimmed of introns.exononlymatrix.phy.txtConcatenated nuclear matrix, introns onlyThe concatenated nuclear matrix, with exonic regions deleted. The resultant matrix was shortened to match the exon-only alignment exactly in length, in order to fairly compare phylogenetic signal between the two regions.intrononlyreducedmatrix.phy.txtChloroplast genome matrixChloroplast genome alignment, assembled by BWA and aligned by MAFFT.chloroplastmatrix.phyMitochondrial genome matrixMitochondrial genome alignment, assembled in BWA and aligned with Mauve. Tree labels refer to specimen voucher numbers.mitochondrialmatrix.phyConcatenated nuclear ML treeMaximum likelihood tree inferred on the concatenated low-copy nuclear data using RAxML. Tree labels refer to specimen voucher numbers.RAxMLnucleartree.treChloroplast ML treeMaximum likelihood tree inferred on the chloroplast data using RAxML. Tree labels refer to specimen voucher numbers.RAxMLchloroplasttree.treMitochondrial ML treeMaximum likelihood tree inferred on the mitochondrial data using RAxML. Tree labels refer to specimen voucher numbers.RAxMLmitochondrialtree.treAnnotated target lociThe 278 loci for which probes were developed, with exonic and intronic regions annotated, in GenBank flatfile format. The loci are numbered in descending order of length, so that "Locus 1" is the longest and "Locus 278" the shortest. One locus was not consistently enriched and was dropped from analyses; this is labeled "Locus 4".AnnotatedTargetLoci.gbIndividual nuclear locus alignmentsIndividual locus alignments for the 277 successfully enriched loci. Labeling matches other files; hence loci are labeled by descending target length.Alignments.zipGene treesML gene trees (inferred in RAxML) for each of the 277 enriched loci. The gene trees are unlabeled, but they are in precisely the same order as other files (descending locus length), hence line 1 contains the tree for Locus 1, and line 277 contains the tree for Locus 278 (Locus 4 is again omitted, hence the numbering discrepancy). Gene tree labels refer to specimen voucher numbers.Genetrees.treMP-EST treeTree inferred in MP-EST; the STAR tree was topologically identical. Branch labels are coalescent branch lengths. Given the lack of infraspecific sampling, it is impossible to estimate tip branch lengths; coalescent programs generally plot these as the maximum possible value (here, 9) but these should be ignored. Internal branch estimates are correct assuming gene tree discord is solely due to the coalescent. Tree labels refer to specimen voucher numbers.MP_EST.tre