Abstract
PremiseHybrid capture with high‐throughput sequencing (Hyb‐Seq) is a powerful tool for evolutionary studies. The applicability of an Asteraceae family‐specific Hyb‐Seq probe set and the outcomes of different phylogenetic analyses are investigated here.MethodsHyb‐Seq data from 112 Asteraceae samples were organized into groups at different taxonomic levels (tribe, genus, and species). For each group, data sets of non‐paralogous loci were built and proportions of parsimony informative characters estimated. The impacts of analyzing alternative data sets, removing long branches, and type of analysis on tree resolution and inferred topologies were investigated in tribe Cichorieae.ResultsAlignments of the Asteraceae family‐wide Hyb‐Seq locus set were parsimony informative at all taxonomic levels. Levels of resolution and topologies inferred at shallower nodes differed depending on the locus data set and the type of analysis, and were affected by the presence of long branches.DiscussionThe approach used to build a Hyb‐Seq locus data set influenced resolution and topologies inferred in phylogenetic analyses. Removal of long branches improved the reliability of topological inferences in maximum likelihood analyses. The Astereaceae Hyb‐Seq probe set is applicable at multiple taxonomic depths, which demonstrates that probe sets do not necessarily need to be lineage‐specific.
Highlights
Levels of resolution and topologies inferred at shallower nodes differed depending on the locus data set and the type of analysis, and were affected by the presence of long branches
We investigate the impact of using different approaches (e.g., maximum likelihood (ML), ASTRAL, and networks), as well as the influence of removing long branches, on resolution and topologies inferred within Cichorieae
Because the same COS locus set is used for Hyb-Seq in this study across a wide range of taxa within the Asteraceae family, we explore the influence of combinations of lab steps on the number of reads mapped to targets and off-target regions
Summary
Hyb-Seq data from 112 Asteraceae samples were organized into groups at different taxonomic levels (tribe, genus, and species). To test the suitability of the COS locus set at a range of taxonomic depths and to demonstrate the power of the COS locus set at multiple taxonomic levels in greater depth, the samples were grouped according to monophyletic taxa at different taxonomic levels (i.e., tribe, genus, species complex, species; Table 1). The number of PCR cycles during library preparation ranged from eight to 15 (Appendix S2). Incubation temperature was always 65°C, as per the manufacturer’s protocol; incubation times were 26, 27, or 36 h; and the number of cycles for amplification of the capture reactions to yield enriched libraries was either 12 or 16. Spiked or unspiked enriched libraries were pooled (equimolar) and the following sequencing platforms were used: HiSeq 2000 (200 cycles), HiSeq 2500 (high-output mode; 300 cycles), HiSeq 3000 (200 cycles), NextSeq (mid-output mode; 300 cycles) or MiSeq v. 2 (300 cycles) (Illumina)
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