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

Abstract

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.

Authors:
ORCiD logo [1]; ORCiD logo [2]; ORCiD logo [3]; ORCiD logo [4]; ORCiD logo [5]; ORCiD logo [6];  [7]; ORCiD logo [1]; ORCiD logo [8]; ORCiD logo [6]; ORCiD logo [9];  [8]; ORCiD logo [10]; ORCiD logo [8]
  1. Botanischer Garten und Botanisches Museum Berlin Freie Universität Berlin Königin‐Luise‐Str. 6–8 14195 Berlin Germany
  2. Department of Botany Faculty of Science Charles University Benátská 2 CZ 12800 Prague Czech Republic
  3. 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
  4. Data Science Lab Office of the Chief Information Officer Smithsonian Institution Washington D.C. 20013‐7012 USA
  5. Department of Botany National Museum of Natural History Smithsonian Institution Washington D.C. 20013‐7012 USA
  6. Botanic Institute of Barcelona (IBB‐CSIC‐ICUB) Pg. del Migdia s.n. ES 08038 Barcelona Spain
  7. 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
  8. Department of Biological Sciences University of Memphis Memphis Tennessee 38152 USA, Center for Biodiversity University of Memphis Memphis Tennessee 38152 USA
  9. 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
  10. Department of Plant Biology, Ecology, and Evolution Oklahoma State University Stillwater Oklahoma 74078 USA
Publication Date:
Sponsoring Org.:
USDOE
OSTI Identifier:
1572101
Alternate Identifier(s):
OSTI ID: 1572102
Resource Type:
Published Article
Journal Name:
Applications in Plant Science
Additional Journal Information:
Journal Name: Applications in Plant Science Journal Volume: 7 Journal Issue: 10; Journal ID: ISSN 2168-0450
Publisher:
Wiley Blackwell (John Wiley & Sons)
Country of Publication:
United States
Language:
English

Citation Formats

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., and Mandel, Jennifer R. An empirical assessment of a single family‐wide hybrid capture locus set at multiple evolutionary timescales in Asteraceae. United States: N. p., 2019. Web. doi:10.1002/aps3.11295.
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. An empirical assessment of a single family‐wide hybrid capture locus set at multiple evolutionary timescales in Asteraceae. United States. https://doi.org/10.1002/aps3.11295
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., and Mandel, Jennifer R. Fri . "An empirical assessment of a single family‐wide hybrid capture locus set at multiple evolutionary timescales in Asteraceae". United States. https://doi.org/10.1002/aps3.11295.
@article{osti_1572101,
title = {An empirical assessment of a single family‐wide hybrid capture locus set at multiple evolutionary timescales in Asteraceae},
author = {Jones, Katy E. and Fér, Tomáš and Schmickl, Roswitha E. and Dikow, Rebecca B. and Funk, Vicki A. and Herrando‐Moraira, Sonia and Johnston, Paul R. and Kilian, Norbert and Siniscalchi, Carolina M. and Susanna, Alfonso and Slovák, Marek and Thapa, Ramhari and Watson, Linda E. and Mandel, Jennifer R.},
abstractNote = {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.},
doi = {10.1002/aps3.11295},
journal = {Applications in Plant Science},
number = 10,
volume = 7,
place = {United States},
year = {Fri Oct 25 00:00:00 EDT 2019},
month = {Fri Oct 25 00:00:00 EDT 2019}
}

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Resolving phylogenetic relationships of the recently radiated carnivorous plant genus Sarracenia using target enrichment
journal, April 2015

  • Stephens, Jessica D.; Rogers, Willie L.; Heyduk, Karolina
  • Molecular Phylogenetics and Evolution, Vol. 85
  • DOI: 10.1016/j.ympev.2015.01.015

A comparative study of SVDquartets and other coalescent-based species tree estimation methods
journal, January 2015


Selecting optimal partitioning schemes for phylogenomic datasets
journal, January 2014

  • Lanfear, Robert; Calcott, Brett; Kainer, David
  • BMC Evolutionary Biology, Vol. 14, Issue 1
  • DOI: 10.1186/1471-2148-14-82

Patterns and causes of incongruence between plastid and nuclear Senecioneae (Asteraceae) phylogenies
journal, May 2010

  • Pelser, Pieter B.; Kennedy, Aaron H.; Tepe, Eric J.
  • American Journal of Botany, Vol. 97, Issue 5
  • DOI: 10.3732/ajb.0900287

Bayesian Inference of Species Trees from Multilocus Data
journal, November 2009

  • Heled, J.; Drummond, A. J.
  • Molecular Biology and Evolution, Vol. 27, Issue 3
  • DOI: 10.1093/molbev/msp274