Department of Biology

Aarhus University Seal / Aarhus Universitets segl

Henrik Balslev

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

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaperJournal articleResearchpeer-review

Standard

Targeted Capture of Hundreds of Nuclear Genes Unravels Phylogenetic Relationships of the Diverse Neotropical Palm Tribe Geonomateae. / Loiseau, Oriane; Oliyares, Ingrid; Paris, Margot et al.

In: Frontiers in Plant Science, Vol. 10, 864, 07.2019.

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaperJournal articleResearchpeer-review

Harvard

Loiseau, O, Oliyares, I, Paris, M, de La Harpe, M, Weigand, A, Koubinova, D, Rolland, J, Bacon, CD, Balslev, H, Borchsenius, F, Cano, A, Couvreur, TLP, Delnatte, C, Fardin, F, Gayot, M, Mejia, F, Mota-Machado, T, Ferret, M, Roncal, J, Sanin, MJ, Stauffer, F, Lexer, C, Kessler, M & Salamin, N 2019, 'Targeted Capture of Hundreds of Nuclear Genes Unravels Phylogenetic Relationships of the Diverse Neotropical Palm Tribe Geonomateae', Frontiers in Plant Science, vol. 10, 864. https://doi.org/10.3389/fpls.2019.00864

APA

Loiseau, O., Oliyares, I., Paris, M., de La Harpe, M., Weigand, A., Koubinova, D., Rolland, J., Bacon, C. D., Balslev, H., Borchsenius, F., Cano, A., Couvreur, T. L. P., Delnatte, C., Fardin, F., Gayot, M., Mejia, F., Mota-Machado, T., Ferret, M., Roncal, J., ... Salamin, N. (2019). Targeted Capture of Hundreds of Nuclear Genes Unravels Phylogenetic Relationships of the Diverse Neotropical Palm Tribe Geonomateae. Frontiers in Plant Science, 10, [864]. https://doi.org/10.3389/fpls.2019.00864

CBE

Loiseau O, Oliyares I, Paris M, de La Harpe M, Weigand A, Koubinova D, Rolland J, Bacon CD, Balslev H, Borchsenius F, et al. 2019. Targeted Capture of Hundreds of Nuclear Genes Unravels Phylogenetic Relationships of the Diverse Neotropical Palm Tribe Geonomateae. Frontiers in Plant Science. 10:Article 864. https://doi.org/10.3389/fpls.2019.00864

MLA

Vancouver

Loiseau O, Oliyares I, Paris M, de La Harpe M, Weigand A, Koubinova D et al. Targeted Capture of Hundreds of Nuclear Genes Unravels Phylogenetic Relationships of the Diverse Neotropical Palm Tribe Geonomateae. Frontiers in Plant Science. 2019 Jul;10. 864. https://doi.org/10.3389/fpls.2019.00864

Author

Loiseau, Oriane ; Oliyares, Ingrid ; Paris, Margot et al. / Targeted Capture of Hundreds of Nuclear Genes Unravels Phylogenetic Relationships of the Diverse Neotropical Palm Tribe Geonomateae. In: Frontiers in Plant Science. 2019 ; Vol. 10.

Bibtex

@article{0a47e6b9787b4c5eb002a1a6a689940d,
title = "Targeted Capture of Hundreds of Nuclear Genes Unravels Phylogenetic Relationships of the Diverse Neotropical Palm Tribe Geonomateae",
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, MACROSTACHYS ARECACEAE VARIETIES, GENOME SEQUENCE, DATED PHYLOGENY, DNA-SEQUENCES, GENIC VIEW, REVISION, FOREST, TREE, ARECOIDEAE, BIOGEOGRAPHY",
author = "Oriane Loiseau and Ingrid Oliyares and Margot Paris and {de La Harpe}, Marylaure and Anna Weigand and Darina Koubinova and Jonathan Rolland and Bacon, {Christine D.} and Henrik Balslev and Finn Borchsenius and Angela Cano and Couvreur, {Thomas L. P.} and Cesar Delnatte and Frederique Fardin and Marc Gayot and Fabian Mejia and Talita Mota-Machado and Mathieu Ferret and Julissa Roncal and Sanin, {Maria Jose} and Fred Stauffer and Christian Lexer and Michael Kessler and Nicolas Salamin",
year = "2019",
month = jul,
doi = "10.3389/fpls.2019.00864",
language = "English",
volume = "10",
journal = "Frontiers in Plant Science",
issn = "1664-462X",
publisher = "Frontiers Media S.A",

}

RIS

TY - JOUR

T1 - Targeted Capture of Hundreds of Nuclear Genes Unravels Phylogenetic Relationships of the Diverse Neotropical Palm Tribe Geonomateae

AU - Loiseau, Oriane

AU - Oliyares, Ingrid

AU - Paris, Margot

AU - de La Harpe, Marylaure

AU - Weigand, Anna

AU - Koubinova, Darina

AU - Rolland, Jonathan

AU - Bacon, Christine D.

AU - Balslev, Henrik

AU - Borchsenius, Finn

AU - Cano, Angela

AU - Couvreur, Thomas L. P.

AU - Delnatte, Cesar

AU - Fardin, Frederique

AU - Gayot, Marc

AU - Mejia, Fabian

AU - Mota-Machado, Talita

AU - Ferret, Mathieu

AU - Roncal, Julissa

AU - Sanin, Maria Jose

AU - Stauffer, Fred

AU - Lexer, Christian

AU - Kessler, Michael

AU - Salamin, Nicolas

PY - 2019/7

Y1 - 2019/7

N2 - 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.

AB - 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.

KW - Arecaceae

KW - Geonoma

KW - Neotropics

KW - phylogenetic informativeness

KW - phylogenomics

KW - species complexes

KW - MACROSTACHYS ARECACEAE VARIETIES

KW - GENOME SEQUENCE

KW - DATED PHYLOGENY

KW - DNA-SEQUENCES

KW - GENIC VIEW

KW - REVISION

KW - FOREST

KW - TREE

KW - ARECOIDEAE

KW - BIOGEOGRAPHY

U2 - 10.3389/fpls.2019.00864

DO - 10.3389/fpls.2019.00864

M3 - Journal article

C2 - 31396244

VL - 10

JO - Frontiers in Plant Science

JF - Frontiers in Plant Science

SN - 1664-462X

M1 - 864

ER -