Data from: Dated tribe-wide whole chloroplast genome phylogeny indicates recurrent hybridizations within Triticeae

Bernhardt N, Brassac J, Kilian B, Blattner FR, Bernhardt N

Date Published: June 14, 2017

DOI: http://dx.doi.org/10.5061/dryad.25743

 

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Title Calibrated species trees based on trnK-matK, rbcL, and ndhF including Psathyrostachys.
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Description 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).
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Title Calibrated species trees based on trnK-matK, rbcL, and ndhF omitting Psathyrostachys.
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Description 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).
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Title Full representation of the Bayesian phylogenetic tree based on whole chloroplast genome sequences.
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Description 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.
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Title Marginal likelihoods and Bayes factor evaluation of Triticeae chloroplast relationships.
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Description 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 <-10 indicates strong support for model 2.
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Title Read numbers mapping to the complete chloroplast sequences and ndhF.
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Description 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.
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Title Accessions considered in the study.
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Description 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.
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When using this data, please cite the original publication:

Bernhardt N, Brassac J, Kilian B, Blattner FR (2017) Dated tribe-wide whole chloroplast genome phylogeny indicates recurrent hybridizations within Triticeae. BMC Evolutionary Biology 17: 141. http://dx.doi.org/10.1186/s12862-017-0989-9

Additionally, please cite the Dryad data package:

Bernhardt N, Brassac J, Kilian B, Blattner FR, Bernhardt N (2017) Data from: Dated tribe-wide whole chloroplast genome phylogeny indicates recurrent hybridizations within Triticeae. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.25743
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