An Empirical Assessment of a Single Family‐Wide Hybrid Capture Locus
APPLICATION ARTICLE An empirical assessment of a single family-wide hybrid capture locus set at multiple evolutionary timescales in Asteraceae Katy E. Jones1,14 , Tomáš Fér2 , Roswitha E. Schmickl2,3 , Rebecca B. Dikow4 , Vicki A. Funk5 , Sonia Herrando-Moraira6 , Paul R. Johnston7,8,9, Norbert Kilian1 , Carolina M. Siniscalchi10,11 , Alfonso Susanna6 , Marek Slovák2,12 , Ramhari Thapa10,11, Linda E. Watson13 , and Jennifer R. Mandel10,11 Manuscript received 27 February 2019; revision accepted PREMISE: Hybrid capture with high-throughput sequencing (Hyb-Seq) is a powerful tool for 5 September 2019. evolutionary studies. The applicability of an Asteraceae family-specific Hyb-Seq probe set and 1 Botanischer Garten und Botanisches Museum Berlin, Freie the outcomes of different phylogenetic analyses are investigated here. Universität Berlin, Königin-Luise-Str. 6–8, 14195 Berlin, Germany 2 Department of Botany, Faculty of Science, Charles University, METHODS: Hyb-Seq data from 112 Asteraceae samples were organized into groups at differ- Benátská 2, CZ 12800 Prague, Czech Republic ent taxonomic levels (tribe, genus, and species). For each group, data sets of non-paralogous 3 Institute of Botany, The Czech Academy of Sciences, Zámek 1, CZ loci were built and proportions of parsimony informative characters estimated. The impacts 25243 Průhonice, Czech Republic of analyzing alternative data sets, removing long branches, and type of analysis on tree reso- 4 Data Science Lab, Office of the Chief Information lution and inferred topologies were investigated in tribe Cichorieae. Officer, Smithsonian Institution, Washington, D.C. 20013-7012, USA RESULTS: Alignments of the Asteraceae family-wide Hyb-Seq locus set were parsimony infor- 5 Department of Botany, National Museum of Natural mative at all taxonomic levels.
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