An empirical assessment of a single family-wide hybrid capture locus set at multiple evolutionary timescales in Asteraceae

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.