From cacti to carnivores: Improved phylotranscriptomic sampling and hierarchical homology inference provide further insight into the evolution of Caryophyllales
Por:
Walker, Joseph F., Yang, Ya, Feng, Tao, Timoneda, Alfonso, Mikenas, Jessica, Hutchison, Vera, Edwards, Caroline, Wang, Ning, Ahluwalia, Sonia, Olivieri, Julia, Walker-Hale, Nathanael, Majure, Lucas C., Puente, Raul, Kadereit, Gudrun, Lauterbach, Maximilian, Eggli, Urs, Flores-Olvera, Hilda, Ochoterena, Helga, Brockington, Samuel F., Moore, Michael J., Smith, Stephen A.
Publicada:
1 mar 2018
Resumen:
Premise of the Study: The Caryophyllales contain ~12,500 species and are known for their cosmopolitan distribution, convergence of trait evolution, and extreme adaptations. Some relationships within the Caryophyllales, like those of many large plant clades, remain unclear, and phylogenetic studies often recover alternative hypotheses. We explore the utility of broad and dense transcriptome sampling across the order for resolving evolutionary relationships in Caryophyllales. Methods: We generated 84 transcriptomes and combined these with 224 publicly available transcriptomes to perform a phylogenomic analysis of Caryophyllales. To overcome the computational challenge of ortholog detection in such a large data set, we developed an approach for clustering gene families that allowed us to analyze >300 transcriptomes and genomes. We then inferred the species relationships using multiple methods and performed gene-tree conflict analyses. Key Results: Our phylogenetic analyses resolved many clades with strong support, but also showed significant gene-tree discordance. This discordance is not only a common feature of phylogenomic studies, but also represents an opportunity to understand processes that have structured phylogenies. We also found taxon sampling influences species-tree inference, highlighting the importance of more focused studies with additional taxon sampling. Conclusions: Transcriptomes are useful both for species-tree inference and for uncovering evolutionary complexity within lineages. Through analyses of gene-tree conflict and multiple methods of species-tree inference, we demonstrate that phylogenomic data can provide unparalleled insight into the evolutionary history of Caryophyllales. We also discuss a method for overcoming computational challenges associated with homolog clustering in large data sets. © 2018 The Authors. American Journal of Botany is published by Wiley Periodicals, Inc. on behalf of the Botanical Society of America.
Filiaciones:
Walker, Joseph F.:
Department of Ecology & Evolutionary Biology, University of Michigan, 830 North University Avenue, Ann Arbor, MI, United States
Univ Michigan, Dept Ecol & Evolutionary Biol, 830 North Univ Ave, Ann Arbor, MI 48109 USA
Yang, Ya:
Department of Plant and Microbial Biology, University of Minnesota-Twin Cities, 1445 Gortner Avenue, St. Paul, MN, United States
Univ Minnesota Twin Cities, Dept Plant & Microbial Biol, 1445 Gortner Ave, St Paul, MN 55108 USA
Feng, Tao:
Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
Univ Cambridge, Dept Plant Sci, Cambridge CB2 3EA, England
Timoneda, Alfonso:
Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
Univ Cambridge, Dept Plant Sci, Cambridge CB2 3EA, England
Mikenas, Jessica:
Department of Biology, Oberlin College, Science Center K111, 119 Woodland Street, Oberlin, OH, United States
USGS Canyonlands Research Station, Southwest Biological Science Center, 2290 S West Resource Blvd, Moab, UT, United States
Oberlin Coll, Dept Biol, Sci Ctr K111,119 Woodland St, Oberlin, OH 44074 USA
USGS Canyonlands Res Stn, Southwest Biol Sci Ctr, 2290 S West Resource Blvd, Moab, UT 84532 USA
Hutchison, Vera:
Department of Biology, Oberlin College, Science Center K111, 119 Woodland Street, Oberlin, OH, United States
Oberlin Coll, Dept Biol, Sci Ctr K111,119 Woodland St, Oberlin, OH 44074 USA
Edwards, Caroline:
Department of Biology, Oberlin College, Science Center K111, 119 Woodland Street, Oberlin, OH, United States
Oberlin Coll, Dept Biol, Sci Ctr K111,119 Woodland St, Oberlin, OH 44074 USA
Wang, Ning:
Department of Ecology & Evolutionary Biology, University of Michigan, 830 North University Avenue, Ann Arbor, MI, United States
Univ Michigan, Dept Ecol & Evolutionary Biol, 830 North Univ Ave, Ann Arbor, MI 48109 USA
Ahluwalia, Sonia:
Department of Ecology & Evolutionary Biology, University of Michigan, 830 North University Avenue, Ann Arbor, MI, United States
Univ Michigan, Dept Ecol & Evolutionary Biol, 830 North Univ Ave, Ann Arbor, MI 48109 USA
Olivieri, Julia:
Department of Biology, Oberlin College, Science Center K111, 119 Woodland Street, Oberlin, OH, United States
Institute of Computational and Mathematical Engineering (ICME), Stanford University, 475 Via Ortega, Suite B060, Stanford, CA, United States
Oberlin Coll, Dept Biol, Sci Ctr K111,119 Woodland St, Oberlin, OH 44074 USA
Stanford Univ, ICME, 475 Via Ortega,Suite B060, Stanford, CA 94305 USA
Walker-Hale, Nathanael:
School of Biological Sciences, Victoria University of Wellington, Kelburn Parade, Kelburn, Wellington, New Zealand
Victoria Univ Wellington, Sch Biol Sci, Wellington 6012, New Zealand
Majure, Lucas C.:
Department of Research, Conservation and Collections, Desert Botanical Garden, 1201 N. Galvin Pkwy, Phoenix, AZ, United States
Desert Bot Garden, Dept Res Conservat & Collect, 1201 N Galvin Pkwy, Phoenix, AZ 85008 USA
Puente, Raul:
Department of Research, Conservation and Collections, Desert Botanical Garden, 1201 N. Galvin Pkwy, Phoenix, AZ, United States
Desert Bot Garden, Dept Res Conservat & Collect, 1201 N Galvin Pkwy, Phoenix, AZ 85008 USA
Kadereit, Gudrun:
Institut für Molekulare Physiologie, Johannes Gutenberg-Universität Mainz, Mainz, Germany
Institut für Molekulare und Organismische Evolutionsbiologie, Johannes Gutenberg-Universität Mainz, Mainz, Germany
Johannes Gutenberg Univ Mainz, Inst Mol Physiol, D-55099 Mainz, Germany
Johannes Gutenberg Univ Mainz, Inst MOl & Organism Evolut Biol, D-55099 Mainz, Germany
Lauterbach, Maximilian:
Institut für Molekulare Physiologie, Johannes Gutenberg-Universität Mainz, Mainz, Germany
Institut für Molekulare und Organismische Evolutionsbiologie, Johannes Gutenberg-Universität Mainz, Mainz, Germany
Johannes Gutenberg Univ Mainz, Inst Mol Physiol, D-55099 Mainz, Germany
Johannes Gutenberg Univ Mainz, Inst MOl & Organism Evolut Biol, D-55099 Mainz, Germany
Eggli, Urs:
Sukkulenten-Sammlung Zürich / Grün Stadt Zürich, Mythenquai 88, Zürich, Switzerland
Grun Stadt Zurich, Sukkulenten Sammlung Zurich, Mythenquai 88, CH-8002 Zurich, Switzerland
Flores-Olvera, Hilda:
Departamento de Botánica, Universidad Nacional Autónoma de México, Apartado, Postal 70-367, Mexico City, Mexico
Univ Nacl Autonoma Mexico, Dept Bot, Apartado Postal 70-367, Mexico City 04510, DF, Mexico
Ochoterena, Helga:
Departamento de Botánica, Universidad Nacional Autónoma de México, Apartado, Postal 70-367, Mexico City, Mexico
Univ Nacl Autonoma Mexico, Dept Bot, Apartado Postal 70-367, Mexico City 04510, DF, Mexico
Brockington, Samuel F.:
Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
Univ Cambridge, Dept Plant Sci, Cambridge CB2 3EA, England
Moore, Michael J.:
Department of Biology, Oberlin College, Science Center K111, 119 Woodland Street, Oberlin, OH, United States
Oberlin Coll, Dept Biol, Sci Ctr K111,119 Woodland St, Oberlin, OH 44074 USA
Smith, Stephen A.:
Department of Ecology & Evolutionary Biology, University of Michigan, 830 North University Avenue, Ann Arbor, MI, United States
Univ Michigan, Dept Ecol & Evolutionary Biol, 830 North Univ Ave, Ann Arbor, MI 48109 USA
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