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

Jones, Katy E.; Fér, Tomáš; Schmickl, Roswitha E.; Dikow, Rebecca B.; Funk, Vicki A.; Herrando‐Moraira, Sonia; Johnston, Paul R.; Kilian, Norbert; Siniscalchi, Carolina M.; Susanna, Alfonso; Slovák, Marek; Thapa, Ramhari; Watson, Linda E.; Mandel, Jennifer R.

doi:10.1002/aps3.11295

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

Journal Article · Fri Oct 25 00:00:00 EDT 2019 · Applications in Plant Science

DOI:https://doi.org/10.1002/aps3.11295· OSTI ID:1572101

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Botanischer Garten und Botanisches Museum Berlin Freie Universität Berlin Königin‐Luise‐Str. 6–8 14195 Berlin Germany
Department of Botany Faculty of Science Charles University Benátská 2 CZ 12800 Prague Czech Republic
Department of Botany Faculty of Science Charles University Benátská 2 CZ 12800 Prague Czech Republic, Institute of Botany The Czech Academy of Sciences Zámek 1 CZ 25243 Průhonice Czech Republic
Data Science Lab Office of the Chief Information Officer Smithsonian Institution Washington D.C. 20013‐7012 USA
Department of Botany National Museum of Natural History Smithsonian Institution Washington D.C. 20013‐7012 USA
Botanic Institute of Barcelona (IBB‐CSIC‐ICUB) Pg. del Migdia s.n. ES 08038 Barcelona Spain
Freie Universität Berlin Evolutionary Biology Berlin Germany, Berlin Center for Genomics in Biodiversity Research Berlin Germany, Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Berlin Germany
Department of Biological Sciences University of Memphis Memphis Tennessee 38152 USA, Center for Biodiversity University of Memphis Memphis Tennessee 38152 USA
Department of Botany Faculty of Science Charles University Benátská 2 CZ 12800 Prague Czech Republic, Plant Science and Biodiversity Centre Slovak Academy of Sciences SK‐84523 Bratislava Slovakia
Department of Plant Biology, Ecology, and Evolution Oklahoma State University Stillwater Oklahoma 74078 USA

Premise Hybrid 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. Methods Hyb‐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. Results Alignments 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. Discussion The 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.

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Sponsoring Organization:: USDOE

OSTI ID:: 1572101

Alternate ID(s):: OSTI ID: 1572102

Journal Information:: Applications in Plant Science, Journal Name: Applications in Plant Science Vol. 7 Journal Issue: 10; ISSN 2168-0450

Publisher:: Wiley Blackwell (John Wiley & Sons)Copyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 18 works

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