BCdatabaser - trnl.quercus.none.2019-12-14.zip

Parameters: --marker-search-string trnl --taxonomic-range Quercus --sequence-length-filter 100:2000 --sequences-per-taxon 9 </ul

Seed set in the studied Trollius europaeus populations

Data on the number of produced seeds from Trollius europaeus populations. Number of ovules (column ovules_sum) and developing seeds (column seed_sum) were counted in five carpels per fruit

Additional file 3: of Contrasting evolutionary origins of two mountain endemics: Saxifraga wahlenbergii (Western Carpathians) and S. styriaca (Eastern Alps)

Figure S1. Maximum likelihood phylogram of Saxifraga (arrow) and representative genera of Saxifragaceae based on nuclear ribosomal ITS DNA Sanger sequence data. Pterostemon rotundifolius and Itea virginica (Iteaceae) were chosen as outgroups. Maximum likelihood and maximum parsimony bootstrap support values as well as posterior probabilities of Bayesian inference ≥50% are indicated on the branches. The sections of Saxifraga are labelled on the right-hand side. (PDF 2680 kb

Additional file 1: of Contrasting evolutionary origins of two mountain endemics: Saxifraga wahlenbergii (Western Carpathians) and S. styriaca (Eastern Alps)

Table S1. Taxa included in the phylogenetic analysis. ENA/GenBank accession numbers are given for all ITS, trnL–trnF and rpl32–trnL Sanger sequences used in this study, followed by available ITS2 sequences obtained from NGS (without ENA/GenBank entry). They are denoted as “ITS2 variants A–D”. Missing sequence data are indicated by “NA” (not available). Voucher data (country and region, collector and collection number, herbarium code according to Thiers et al. [97]) are provided for newly generated sequences, which are in bold print. MR: herbarium of G. & S. Miehe deposited at the Institute of Geography, University Marburg, Germany. (PDF 502 kb

Additional file 4: of Contrasting evolutionary origins of two mountain endemics: Saxifraga wahlenbergii (Western Carpathians) and S. styriaca (Eastern Alps)

Figure S2. Maximum likelihood phylogram of Saxifraga (arrow) and representative genera of Saxifragaceae based on plastid trnL–trnF and rpl32–trnL Sanger sequence data. Pterostemon rotundifolius and Itea virginica (Iteaceae) were chosen as outgroups. Maximum likelihood and maximum parsimony bootstrap support values as well posterior probabilities of Bayesian inference ≥50% are indicated on the branches. The sections of Saxifraga are labelled on the right-hand side. (PDF 793 kb

Data for: Assessing the potential of RAD-sequencing to resolve phylogenetic relationships within species radiations: the fly genus Chiastocheta (Diptera: Anthomyiidae) as a case study

Data files used for the phylogenetic and phylogenomic analysis of the genus Chiastocheta (Diptera: Anthomyiidae) for the paper: Suchan T, Espíndola A, Rutschmann S, Emerson BC, Gori K, Dessimoz C, Arrigo N, Ronikier M, Alvarez N (2017) Data from: Assessing the potential of RAD-sequencing to resolve phylogenetic relationships within species radiations: the fly genus Chiastocheta (Diptera: Anthomyiidae) as a case study. Molecular Phylogenetics and Evolution Details on the methods can be found in the main paper. Description of the data files: Chiastocheta_c75d6m20p10-blk-bad.alleles - pyRAD alleles file of the RAD-seq data Chiastocheta_c75d6m20p10-blk-bad.phy - Phylip file of the concatenated RAD-seq data Chiastocheta_COI_COII_dloop.phy - Phylip file of the concatenated mtDNA regions: COI, COII, D-loop (with gaps occuring in more than 50% of individuals removed) Chiastocheta_COI_COII_dloop.partitions - partitions file for the Phylip file of the concatenated mtDNA regions: COI, COII, and D-loop (with gaps occuring in more than 50% of individuals removed) Chiastocheta_COI_COII.phy - Phylip file of the concatenated mtDNA regions: COI and COII Chiastocheta_COI_COII.partitions - partitions file for the Phylip file of the concatenated mtDNA regions: COI and COI

Data for: Assessing the potential of RAD-sequencing to resolve phylogenetic relationships within species radiations: the fly genus Chiastocheta (Diptera: Anthomyiidae) as a case study

Data files used for the phylogenetic and phylogenomic analysis of the genus Chiastocheta (Diptera: Anthomyiidae) for the paper: Suchan T, Espíndola A, Rutschmann S, Emerson BC, Gori K, Dessimoz C, Arrigo N, Ronikier M, Alvarez N (2017) Data from: Assessing the potential of RAD-sequencing to resolve phylogenetic relationships within species radiations: the fly genus Chiastocheta (Diptera: Anthomyiidae) as a case study. Molecular Phylogenetics and Evolution Details on the methods can be found in the main paper. Description of the data files: Chiastocheta_c75d6m20p10-blk-bad.alleles - pyRAD alleles file of the RAD-seq data Chiastocheta_c75d6m20p10-blk-bad.phy - Phylip file of the concatenated RAD-seq data Chiastocheta_COI_COII_dloop.phy - Phylip file of the concatenated mtDNA regions: COI, COII, D-loop (with gaps occuring in more than 50% of individuals removed) Chiastocheta_COI_COII_dloop.partitions - partitions file for the Phylip file of the concatenated mtDNA regions: COI, COII, and D-loop (with gaps occuring in more than 50% of individuals removed) Chiastocheta_COI_COII.phy - Phylip file of the concatenated mtDNA regions: COI and COII Chiastocheta_COI_COII.partitions - partitions file for the Phylip file of the concatenated mtDNA regions: COI and COI

Lab-work procedure used for hyRAD development.

Homologous reads from shotgun genomic libraries are captured through hybridization on random RAD-based probes. These fragments are then separated using streptavidin-coated beads and sequenced.</p

Summary of <i>Oedaleus decorus</i> samples used in the study.

<p>Summary of <i>Oedaleus decorus</i> samples used in the study.</p

Mean number of SNPs per sample obtained for different types of DNA preparations and bioinformatic pipelines.

<p>Mean number of SNPs per sample obtained for different types of DNA preparations and bioinformatic pipelines.</p