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Front Plant Sci. 2019 Jul 12;10:864. doi: 10.3389/fpls.2019.00864. eCollection 2019.

Targeted Capture of Hundreds of Nuclear Genes Unravels Phylogenetic Relationships of the Diverse Neotropical Palm Tribe Geonomateae.

Author information

1
Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.
2
Department for Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland.
3
Centre for Biodiversity and Environment Research, University College London, London, United Kingdom.
4
Department of Biology, Unit Ecology and Evolution, University of Fribourg, Fribourg, Switzerland.
5
Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria.
6
Natural History Museum of Geneva, Geneva, Switzerland.
7
Department of Zoology, University of British Columbia, Vancouver, BC, Canada.
8
Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden.
9
Gothenburg Global Biodiversity Centre, Gothenburg, Sweden.
10
Department of Bioscience, Biodiversity and Ecoinformatics, Aarhus University, Aarhus, Denmark.
11
Science Museums, Aarhus University, Aarhus, Denmark.
12
Cambridge University Botanic Garden, Cambridge, United Kingdom.
13
IRD, DIADE, University of Montpellier, Montpellier, France.
14
National Forestry Office, Fort-de-France, France.
15
Parc National de la Guadeloupe, Guadeloupe, France.
16
National Forestry Office, Guadeloupe, France.
17
Facultad de Ciencias y Biotecnología, Universidad CES, Medellin, Colombia.
18
Programa de Pós-Graduação em Biologia Vegetal, Departamento de Botânica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
19
Department of Botany and Plant Biology, Conservatory and Botanical Garden of the City of Geneva, University of Geneva, Geneva, Switzerland.
20
Department of Biology, Memorial University of Newfoundland, St. John's, NL, Canada.

Abstract

The tribe Geonomateae is a widely distributed group of 103 species of Neotropical palms which contains six ecologically important understory or subcanopy genera. Although it has been the focus of many studies, our understanding of the evolutionary history of this group, and in particular of the taxonomically complex genus Geonoma, is far from complete due to a lack of molecular data. Specifically, the previous Sanger sequencing-based studies used a few informative characters and partial sampling. To overcome these limitations, we used a recently developed Arecaceae-specific target capture bait set to undertake a phylogenomic analysis of the tribe Geonomateae. We sequenced 3,988 genomic regions for 85% of the species of the tribe, including 84% of the species of the largest genus, Geonoma. Phylogenetic relationships were inferred using both concatenation and coalescent methods. Overall, our phylogenetic tree is highly supported and congruent with taxonomic delimitations although several morphological taxa were revealed to be non-monophyletic. It is the first time that such a large genomic dataset is provided for an entire tribe within the Arecaceae. Our study lays the groundwork not only for detailed macro- and micro-evolutionary studies within the group, but also sets a workflow for understanding other species complexes across the tree of life.

KEYWORDS:

Arecaceae; Geonoma; Neotropics; phylogenetic informativeness; phylogenomics; species complexes

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