DOI: 10.5061/dryad.fn2nt
title: Data from: Species level phylogeny and polyploid relationships in Hordeum (Poaceae) inferred by next-generation sequencing and in-silico cloning of multiple nuclear loci

description: Polyploidization is an important speciation mechanism in the barley genus
 Hordeum. To analyze evolutionary changes after allopolyploidization,
 knowledge of parental relationships is essential. One chloroplast and 12
 nuclear single-copy loci were amplified by polymerase chain reaction (PCR)
 in all Hordeum plus six out-group species. Amplicons from each of 96
 individuals were pooled, sheared, labeled with individual-specific
 barcodes and sequenced in a single run on a 454 platform. Reference
 sequences were obtained by cloning and Sanger sequencing of all loci for
 nine supplementary individuals. The 454 reads were assembled into contigs
 representing the 13 loci and, for polyploids, also homoeologues.
 Phylogenetic analyses were conducted for all loci separately and for a
 concatenated data matrix of all loci. For diploid taxa, a Bayesian
 concordance analysis and a coalescent-based dated species tree was
 inferred from all gene trees. Chloroplast matK was used to determine the
 maternal parent in allopolyploid taxa. The relative performance of
 different multilocus analyses in the presence of incomplete lineage
 sorting and hybridization was also assessed. The resulting multilocus
 phylogeny reveals for the first time species phylogeny and
 progenitor-derivative relationships of all di- and polyploid Hordeum taxa
 within a single analysis. Our study proves that it is possible to obtain a
 multilocus species-level phylogeny for di- and polyploid taxa by combining
 PCR with next-generation sequencing, without cloning and without creating
 a heavy load of sequence data.
description: Table S1 Individuals
 included in the study and number of reads per locusTableS1.xlsTable S2 Primers used in the PCR amplification of each locusTableS2.xls*BEAST input file 12 loci random local clockxml file for Figure 212_loci_MatK_RLC.xml*BEAST species tree*BEAST output (TreeAnnotator) from three identical analyses combined with LogCombiner (raw tree Fig. 2)12_loci_MatK_RLC_combined.species.treeBCA output from BUCKyConcordance file obtained from BUCKy on 12 loci (raw data Fig. S15)12_loci.concordanceHordeum diploids Supermatrix12 loci concatenated matrix, only diploids (data Fig. 1)Diploids_concat_MatK.nexHordeum diploids Supermatrix TreeBayesian Inference of Hordeum diploids Supermatrix (raw tree Fig. 1)Diploids_concat_MatK.nex.con.trematK all individuals MatrixMatrix locus matK (data for Fig. S14)MatK_diploids_corrected_Dvi.nexmatK all individuals TreeTree locus matK (raw tree for Fig. S14)MatK_diploids_corrected.nex.con.tre26 loci supermatrixMatrix including all loci from this study and Petersen et al. 2011 for one individual per diploid species (data for Fig. S17)26_loci.nex26 loci supermatrix TreeTree inferred from all loci from this study and Petersen et al. 2011 with one individual per diploid species (raw tree Fig. S17)26_loci.nex.con.treSupplementary InformationSupplementary Information containing annotated trees (Figs. S2-S17, S19), figures S1 and S18, tables S1 and S2 and references.Supplementary_Information_SysBio.pdf