DOI: 10.5061/dryad.60vb576
title: Data from: An empirical assessment of a single family-wide hybrid capture locus set at multiple evolutionary timescales in Asteraceae

description: Premise of the study: Hybrid capture with high-throughput sequencing
 (Hyb-Seq) is a powerful tool for evolutionary studies. The applicability
 of an Asteraceae family-specific Hyb-Seq method and the outcomes of
 different phylogenetic analyses are assessed. Methods: Hyb-Seq data from
 112 Asteraceae samples were organized into groups at different taxonomic
 levels (tribe, genus, and species). For each group, datasets of
 non-paralogous loci were built and proportions of parsimony informative
 characters estimated. The impacts of the analyzing alternative datasets,
 removing long branches and type of analysis on tree resolution and
 inferred topologies were investigated in tribe Cichorieae. Results:
 Alignments of the Asteraceae-wide Hyb-Seq locus set were parsimony
 informative at all taxonomic levels. Each genus contained uniquely
 non-paralogous loci within their respective tribes. Levels of resolution
 and topologies inferred at shallower nodes differed depending on the locus
 dataset and the type of analysis, and were affected by the presence of
 long branches. Discussion: The approach used to build a Hyb-Seq locus
 dataset and methodological artefacts, such as long branch attraction,
 influence resolution and topologies inferred in phylogenetic analyses. The
 Astereaceae Hyb-Seq probe set is applicable at multiple taxonomic depths
 and therefore probe sets do not necessarily need to be lineage specific.
description: Trimming approach
 testing of supercontig (exon + flanking intron region)
 alignmentsTwo trimming approaches
 were assessed for two datasets: Cichorieae wide and Picris hieracioides
 species complex in order to select an approach for all other datasets (see
 Tables 1 and 2 Jones et al. 2019 APPS). Trimal v. 1.4 (Capella-Gutiérrez
 et al., 2009) was used to remove spurious sequences from each alignment in
 all datasets. The following two trimming approaches were assessed: 1,
 “strict” - resoverlap and -seqoverlap were set to 0.75 and 0.80
 respectively and 2, “less-strict” - resoverlap and -seqoverlap were set to
 0.65 and 70, respectively. In addition, we used the -gappyout parameter,
 which efficiently removes poorly aligned regions (Capella-Gutiérrez et
 al., 2009). We manually checked ~30 alignments from each dataset and found
 that the “less-strict” approach described above generated reliable
 alignments and minimized numbers of samples that needed to be removed.
 Therefore, all other sample groups were subject to the following
 parameters in trimal: -resoverlap and –seqoverlap = 0.65 and 70. We
 provide the alignments and summary statistics from both approaches for the
 two sample groups.1_Alignments_preliminary_supercontig_splashzones_Appendix_S4_APPS_Jonesetal.zipAsteraceae exon alignments after removing long branches in TreeShrink ("shrunken" datasets)Alignments of exon "shrunken" datasets were built for the Cichorieae wide and Picris hieracioides species complex datasets according to the following steps: gene trees were estimated for locus exon alignments (see dryad data file "Asteraceae exon alignments of non paralogous loci after trimming") using RAxML (see Table 2 in Jones et al. 2019 APPS) with the GTR+GAMMA model and 100 rapid BS replicates. Subsequently, we used TreeShrink to detect samples that had unexpectedly long branches in gene trees (false-positive tolerance level 0.10); we then removed those samples from alignments (Table 2).All_alignments_shrunken_APPS_Jonesetal.zipAsteraceae exon alignments of non paralogous loci after trimmingExon alignments of COS loci for all Asteraceae sample groups in Table 1 in Jones et al 2019 APPS. HybPhyloMaker steps 1-3 were used for raw read quality filtering, mapping to targets and contig assembly. Alignments were built according to the following steps: 1. aligning with MAFFT, 2. removing samples with &gt;70% missing length from the particular locus alignment and 3. a 100% sample presence criterion was applied and loci that were not present in all samples were removed from each sample group. See Table 1 attached for names of sample groups and numbers of loci. And Appendix S9 in Jones et al. 2019 APPS for exon alignment summary statistics.All_alignments_exons_nonparalogs_posttrimming.zipAsteraceae supercontig (exon + intron) alignmentsSupercontig matrices built using HybPiper (intronerate.py) for all sample groups in Table 1 (Jones et al. 2019 APPS). All matrices were aligned using MAFFT and cleaned using the following trimal settings: resoverlap and -seqoverlap were 0.65 and 70, respectively with the -gappyout parameter. Potentially paralagous loci flagged for each sample group (according to HybPiper) were then removed from all alignments. See Appendix S8 in Jones et al. APPS for details of numbers of samples in alignments per sample group and summary statistics for alignments for all samples groups.All_alignments_supercontigs_APPS_Jonesetal_2019.zipCichorieae and Picris species complex supercontig alignments analysedSupercontig alignments analysed for the Cichorieae wide and the Picris hieracioides species complex sample groups (see table 2 Jones et al. 2019 APPS). See Fig. 2 for pipeline and analyses conducted for the two datasets.Supercontig_alignments_analysed_Cichorieae_and_Picris_spcomple_APPS_Jonesetal.zip