DOI: 10.5061/dryad.jm78g
title: Data from: Phylogenomic analyses of Sabal (Arecaceae) species relationships using targeted sequence capture

description: With the increasing availability of high-throughput sequencing,
 phylogenetic analyses are no longer constrained by the limited
 availability of a few loci. Here, we describe a sequence capture
 methodology, which we used to collect data for analyses of diversification
 within Sabal (Arecaceae), a palm genus native to the south-eastern USA,
 Caribbean, Bermuda and Central America. RNA probes were developed and used
 to enrich DNA samples for putatively low copy nuclear genes and the
 plastomes for all Sabal species and two outgroup species. Sequence data
 were generated on an Illumina MiSeq sequencer and target sequences were
 assembled using custom workflows. Both coalescence and supermatrix
 analyses of 133 nuclear genes were used to estimate species trees
 relationships. Plastid genomes were also analysed, yielding generally poor
 resolution with regard to species relationships. Species relationships
 described in both nuclear gene and plastome sequences largely reflect the
 biogeography of the group and, to a lesser extent, previous
 morphology-based hypotheses. Beyond the biological implications, this
 research validates a high-throughput methodology for generating a large
 number of genes for coalescence-based phylogenetic analyses in plant
 lineages.
description: Data files for Heyduk et
 al 2015 "Estimating species relationships within Sabal (Arecaceae)
 through multilocus analyses of sequence capture
 data."README for data related
 to Heyduk et al 2015 "Estimating species relationships within Sabal
 (Arecaceae) through multilocus analyses of sequence capture data." A
 note about gene alignment/tree naming: File names refer to the geneID from
 which baits were designed from. For example, "Elaeis_1007"
 indicates that this gene matches the exons "Elaeis_1007_*" which
 we submitted to MySelect for bait design. Some genes are named
 "Sabal" or "Nypa" because sequences from those species
 were submitted for the initial bait design. Files in this repository: 1)
 alignments.zip - folder containing alignments for all 133 nuclear genes
 used in phylogenetic analyses. Naming as described above. 2)
 bootstraps.zip - folder containing bootstrap replicates, 500 per each of
 133 genes, output from RAxML. Gene names are the same as described above.
 3) genetrees.zip - bipartition tree for the 133 nuclear gene trees, output
 from RAxML. Naming as described above. 4) concat.align.fasta - supermatrix
 alignment from concatenation of the 133 nuclear genes for all 17 species.
 5) plastid.align.fasta - alignment of 89kb of chloroplast sequence for all
 17 species. 6) mpest.tre, star.tre, concat.tre, and plastid.tre - newick
 tree files for each respective phylogenetic analysis (MP-EST, STAR,
 supermatrix, and plastome). MP-EST and STAR trees are the output of the
 respective programs, whereas the supermatrix tree and the plastid tree are
 output of RAxML. 7) binaligns.zip - folder containing alignments (nexus
 formatted for BEAST) of each of 27 bins. 8) starBEAST.xml - xml run file
 for *BEASTHeyduk_Sabal.tar.gz