DrosoPhyla: resources for drosophilid phylogeny and systematics

Cédric Finet; Victoria A Kassner; Antonio B Carvalho; Henry Chung; Jonathan P Day; Stephanie Day; Emily K Delaney; Francine C De Ré; Héloïse D Dufour; Eduardo Dupim; Hiroyuki F Izumitani; Thaísa B Gautério; Jessa Justen; Toru Katoh; Artyom Kopp; Shigeyuki Koshikawa; Ben Longdon; Elgion L Loreto; Maria D S Nunes; Komal K B Raja; Mark Rebeiz; Michael G Ritchie; Gayane Saakyan; Tanya Sneddon; Machiko Teramoto; Venera Tyukmaeva; Thyago Vanderlinde; Emily E Wey; Thomas Werner; Thomas M Williams; Lizandra J Robe; Masanori J Toda; Ferdinand Marlétaz

doi:10.1093/gbe/evab179

DrosoPhyla: resources for drosophilid phylogeny and systematics

Cédric Finet, Victoria A Kassner, Antonio B Carvalho, Henry Chung, Jonathan P Day, Stephanie Day, Emily K Delaney, Francine C De Ré, Héloïse D Dufour, Eduardo Dupim, Hiroyuki F Izumitani, Thaísa B Gautério, Jessa Justen, Toru Katoh, Artyom Kopp, Shigeyuki Koshikawa, Ben Longdon, Elgion L Loreto, Maria D S Nunes, Komal K B RajaMark Rebeiz, Michael G Ritchie, Gayane Saakyan, Tanya Sneddon, Machiko Teramoto, Venera Tyukmaeva, Thyago Vanderlinde, Emily E Wey, Thomas Werner, Thomas M Williams, Lizandra J Robe, Masanori J Toda, Ferdinand Marlétaz

Research output: Contribution to journal › Article › peer-review

Abstract

The vinegar fly Drosophila melanogaster is a pivotal model for invertebrate development, genetics, physiology, neuroscience, and disease. The whole family Drosophilidae, which contains over 4,400 species, offers a plethora of cases for comparative and evolutionary studies. Despite a long history of phylogenetic inference, many relationships remain unresolved among the genera, subgenera, and species groups in the Drosophilidae. To clarify these relationships, we first developed a set of new genomic markers and assembled a multilocus data set of 17 genes from 704 species of Drosophilidae. We then inferred a species tree with highly supported groups for this family. Additionally, we were able to determine the phylogenetic position of some previously unplaced species. These results establish a new framework for investigating the evolution of traits in fruit flies, as well as valuable resources for systematics.

Original language	English
Article number	evab179
Number of pages	13
Journal	Genome Biology and Evolution
Volume	13
Issue number	8
Early online date	3 Aug 2021
DOIs	https://doi.org/10.1093/gbe/evab179
Publication status	Published - Aug 2021

Keywords

Drosophilidae
Phylogenomics
Systematics

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10.1093/gbe/evab179Licence: CC BY

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Copyright © The Author(s) 2021. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
Final published version, 848 KBLicence: CC BY

DrosoPhyla
Finet, C. (Contributor), Zenodo, 12 Jul 2021
DOI: 10.5281/zenodo.5091961
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Finet, C., Kassner, V. A., Carvalho, A. B., Chung, H., Day, J. P., Day, S., Delaney, E. K., De Ré, F. C., Dufour, H. D., Dupim, E., Izumitani, H. F., Gautério, T. B., Justen, J., Katoh, T., Kopp, A., Koshikawa, S., Longdon, B., Loreto, E. L., Nunes, M. D. S., ... Marlétaz, F. (2021). DrosoPhyla: resources for drosophilid phylogeny and systematics. Genome Biology and Evolution, 13(8), Article evab179. https://doi.org/10.1093/gbe/evab179

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abstract = "The vinegar fly Drosophila melanogaster is a pivotal model for invertebrate development, genetics, physiology, neuroscience, and disease. The whole family Drosophilidae, which contains over 4,400 species, offers a plethora of cases for comparative and evolutionary studies. Despite a long history of phylogenetic inference, many relationships remain unresolved among the genera, subgenera, and species groups in the Drosophilidae. To clarify these relationships, we first developed a set of new genomic markers and assembled a multilocus data set of 17 genes from 704 species of Drosophilidae. We then inferred a species tree with highly supported groups for this family. Additionally, we were able to determine the phylogenetic position of some previously unplaced species. These results establish a new framework for investigating the evolution of traits in fruit flies, as well as valuable resources for systematics.",

keywords = "Drosophilidae, Phylogenomics, Systematics",

author = "C{\'e}dric Finet and Kassner, {Victoria A} and Carvalho, {Antonio B} and Henry Chung and Day, {Jonathan P} and Stephanie Day and Delaney, {Emily K} and {De R{\'e}}, {Francine C} and Dufour, {H{\'e}lo{\"i}se D} and Eduardo Dupim and Izumitani, {Hiroyuki F} and Gaut{\'e}rio, {Tha{\'i}sa B} and Jessa Justen and Toru Katoh and Artyom Kopp and Shigeyuki Koshikawa and Ben Longdon and Loreto, {Elgion L} and Nunes, {Maria D S} and Raja, {Komal K B} and Mark Rebeiz and Ritchie, {Michael G} and Gayane Saakyan and Tanya Sneddon and Machiko Teramoto and Venera Tyukmaeva and Thyago Vanderlinde and Wey, {Emily E} and Thomas Werner and Williams, {Thomas M} and Robe, {Lizandra J} and Toda, {Masanori J} and Ferdinand Marl{\'e}taz",

year = "2021",

month = aug,

doi = "10.1093/gbe/evab179",

language = "English",

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Finet, C, Kassner, VA, Carvalho, AB, Chung, H, Day, JP, Day, S, Delaney, EK, De Ré, FC, Dufour, HD, Dupim, E, Izumitani, HF, Gautério, TB, Justen, J, Katoh, T, Kopp, A, Koshikawa, S, Longdon, B, Loreto, EL, Nunes, MDS, Raja, KKB, Rebeiz, M, Ritchie, MG, Saakyan, G, Sneddon, T, Teramoto, M, Tyukmaeva, V, Vanderlinde, T, Wey, EE, Werner, T, Williams, TM, Robe, LJ, Toda, MJ & Marlétaz, F 2021, 'DrosoPhyla: resources for drosophilid phylogeny and systematics', Genome Biology and Evolution, vol. 13, no. 8, evab179. https://doi.org/10.1093/gbe/evab179

TY - JOUR

T1 - DrosoPhyla

T2 - resources for drosophilid phylogeny and systematics

AU - Finet, Cédric

AU - Kassner, Victoria A

AU - Carvalho, Antonio B

AU - Chung, Henry

AU - Day, Jonathan P

AU - Day, Stephanie

AU - Delaney, Emily K

AU - De Ré, Francine C

AU - Dufour, Héloïse D

AU - Dupim, Eduardo

AU - Izumitani, Hiroyuki F

AU - Gautério, Thaísa B

AU - Justen, Jessa

AU - Katoh, Toru

AU - Kopp, Artyom

AU - Koshikawa, Shigeyuki

AU - Longdon, Ben

AU - Loreto, Elgion L

AU - Nunes, Maria D S

AU - Raja, Komal K B

AU - Rebeiz, Mark

AU - Ritchie, Michael G

AU - Saakyan, Gayane

AU - Sneddon, Tanya

AU - Teramoto, Machiko

AU - Tyukmaeva, Venera

AU - Vanderlinde, Thyago

AU - Wey, Emily E

AU - Werner, Thomas

AU - Williams, Thomas M

AU - Robe, Lizandra J

AU - Toda, Masanori J

AU - Marlétaz, Ferdinand

PY - 2021/8

Y1 - 2021/8

N2 - The vinegar fly Drosophila melanogaster is a pivotal model for invertebrate development, genetics, physiology, neuroscience, and disease. The whole family Drosophilidae, which contains over 4,400 species, offers a plethora of cases for comparative and evolutionary studies. Despite a long history of phylogenetic inference, many relationships remain unresolved among the genera, subgenera, and species groups in the Drosophilidae. To clarify these relationships, we first developed a set of new genomic markers and assembled a multilocus data set of 17 genes from 704 species of Drosophilidae. We then inferred a species tree with highly supported groups for this family. Additionally, we were able to determine the phylogenetic position of some previously unplaced species. These results establish a new framework for investigating the evolution of traits in fruit flies, as well as valuable resources for systematics.

AB - The vinegar fly Drosophila melanogaster is a pivotal model for invertebrate development, genetics, physiology, neuroscience, and disease. The whole family Drosophilidae, which contains over 4,400 species, offers a plethora of cases for comparative and evolutionary studies. Despite a long history of phylogenetic inference, many relationships remain unresolved among the genera, subgenera, and species groups in the Drosophilidae. To clarify these relationships, we first developed a set of new genomic markers and assembled a multilocus data set of 17 genes from 704 species of Drosophilidae. We then inferred a species tree with highly supported groups for this family. Additionally, we were able to determine the phylogenetic position of some previously unplaced species. These results establish a new framework for investigating the evolution of traits in fruit flies, as well as valuable resources for systematics.

KW - Drosophilidae

KW - Phylogenomics

KW - Systematics

U2 - 10.1093/gbe/evab179

DO - 10.1093/gbe/evab179

M3 - Article

SN - 1759-6653

VL - 13

JO - Genome Biology and Evolution

JF - Genome Biology and Evolution

IS - 8

M1 - evab179

ER -

DrosoPhyla: resources for drosophilid phylogeny and systematics

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DrosoPhyla

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