DOI: 10.5061/dryad.25743
title: Data from: Dated tribe-wide whole chloroplast genome phylogeny indicates recurrent hybridizations within Triticeae

description: Background: Triticeae, the tribe of wheat grasses, harbours the cereals
 barley, rye and wheat and their wild relatives. Although economically
 important, relationships within the tribe are still not understood. We
 analysed the phylogeny of chloroplast lineages among nearly all
 monogenomic Triticeae taxa and polyploid wheat species aiming at a deeper
 understanding of the tribe’s evolution. We used on- and off-target reads
 of a target-enrichment experiment followed by Illumina sequencing.
 Results: The read data was used to assemble the plastid locus ndhF for 194
 individuals and the whole chloroplast genome for 183 individuals,
 representing 53 Triticeae species and 15 genera. We conducted Bayesian and
 multispecies coalescent analyses to infer relationships and estimate
 divergence times of the taxa. We present the most comprehensive dated
 Triticeae chloroplast phylogeny and review previous hypotheses in the
 framework of our results. Monophyly of Triticeae chloroplasts could not be
 confirmed, as either Bromus or Psathyrostachys captured a chloroplast from
 a lineage closely related to a Bromus-Triticeae ancestor. The most recent
 common ancestor of Triticeae occurred approximately between ten and 19
 million years ago. Conclusions: The comparison of the chloroplast
 phylogeny with available nuclear data in several cases revealed
 incongruences indicating past hybridizations. Recent events of chloroplast
 capture were detected as individuals grouped apart from con-specific
 accessions in otherwise monopyhletic groups.
description: Calibrated species trees
 based on trnK-matK, rbcL, and ndhF including
 Psathyrostachys.Calibrated multispecies
 coalescent derived from three chloroplast loci trnK-matK, rbcL and ndhF of
 all Triticeae accessions (excluding polyploid wheats). Sequences of
 Brachypodium distachyon, Oryza sativa and Zea mays were included as
 outgroups. Posterior probability values are given for all nodes.
 Divergence time estimates were inferred using the secondary calibration
 points from Marcussen et al. [20] for the Brachypodium-Triticeae split
 (mean 44.44 million years ago). Node bars indicate the age range with 95%
 interval of the highest probability density. For the analysis Triticum
 monococcum and T. boeoticum, Secale cereale and S. vavilovii,
 Pseudoroegneria tauri and Ps. libanotica, Taeniatherum caput-medusae and
 Tae. crinitum, Agropyron cristatum and Agr. cimmericum were each subsumed
 under a single species name (Additional file 1: Table
 S1).Additional_file_5_Figure_S2.jpgCalibrated species trees based on trnK-matK, rbcL, and ndhF omitting Psathyrostachys.Calibrated multispecies coalescent derived from three chloroplast loci trnK-matK, rbcL and ndhF considering all genomic Triticeae groups covered in the study but omitting Psathyrostachys and polyploid wheats. Sequences of Brachypodium distachyon, Oryza sativa and Zea mays were included as outgroups. Posterior probability values are given for all nodes. Divergence time estimates were inferred using the secondary calibration points from Marcussen et al. [20] for the Brachypodium-Triticeae split (mean 44.44 million years ago). Node bars indicate the age range with 95% interval of the highest probability density. For the analysis Triticum monococcum and T. boeoticum, Secale cereale and S. vavilovii, Pseudoroegneria tauri and Ps. libanotica, Taeniatherum caput-medusae and Tae. crinitum, Agropyron cristatum and Agr. cimmericum were each subsumed under a single species name (Additional file 1: Table S1).Additional_file_6_Figure_S3.jpgFull representation of the Bayesian phylogenetic tree based on whole chloroplast genome sequences.Phylogenetic tree derived from an alignment of whole genome chloroplast sequences via Bayesian phylogenetic inference (BI). The multiple sequence alignment comprised 183 genomes assembled in the present study and 39 genomes that were downloaded from GenBank. Brachypodium distachyon was used as outgroup taxon. The tree shown corresponds to an analysis based on the complete alignment of 123,531 base pairs (bp). Posterior probabilities (pp) for the main clades are depicted next to the nodes if they were higher then 0.75. Support values of a second BI analysis based on 114,788 bp of whole chloroplast genomes were alignment positions with more than 50% of missing data were masked are shown below the values of the corresponding nodes in the complete chloroplast analysis if the values differed between analyses. For clades comprising multiple taxa, the taxon affiliation of single accession is indicated by the same symbols behind accession and taxon name (e.g. ‘;“, *). The ploidy level is provided in brackets after the taxon label. Single accessions grouping apart from other accessions of their taxon are shown in bold. To the right the genomic groups are indicated. The red circle represents the secondary calibration point from Marcussen et al. [20] used for node calibrations in multispecies coalescent analyses (MSC). Major nodes are shown in blue and their estimated ages in million years are given in the box. Two age values for the same node correspond to the analysis with (first value) and without the inclusion of Psathyrostachys (second value). For more information on the results of the MSC analyses see Additional file 5: Fig. S2 and Additional file 6: Fig. S3. For the full representation of the tree showing the grouping of all single accessions see Additional file 4: Fig. S1. For species synonyms see Additional file 1: Table S1. Arrows with support values indicate the nodes they refer to.Additional_file_4_Figure_S1.pdfMarginal likelihoods and Bayes factor evaluation of Triticeae chloroplast relationships.Stepping-stone estimates of marginal likelihoods calculated with MRBAYES 3.2.6 on the ndhF dataset and Bayes factor estimated as 2(H1-H2), where H1 enforces monophyly and H2 enforces polyphyly of Triticeae chloroplasts. BF12 &lt;-10 indicates strong support for model 2.Additional_file_3_Table S3.docRead numbers mapping to the complete chloroplast sequences and ndhF.Number of reads mapping and mean coverage for the entire chloroplast genome and ndhF after the removal of duplicated reads. Also the proportions of all reads mapping to the chloroplast that mapped to ndhF are given.Additional_file_2_Table_S2.xlsAccessions considered in the study.Overview of the material considered in this study. For all materials, the GenBank identifier, the accession and species name as used in this study (Species) as well as their species synonyms used in the donor seed banks or in the NCBI GenBank (Material source/Reference) are provided. The genome symbol, and the country of origin, where the material was originally collected are given. The ploidy level measured in the scope of this study and the information if a herbarium voucher could be deposited in the herbarium of IPK Gatersleben (GAT) is given. Genomic formulas of tetraploids and hexploids are given as "female x male parent". The genomes of Aegilops taxa follow Kilian et al. [74] and Li et al. [84]. Genome denominations for Hordeum follow Blattner [107] and Bernhardt [12] for the remaining taxa.Additional_file_1_Table_S1.xls