Darwin's Fancy Revised: An Updated Understanding of the Genomic Constitution of Pigeon Breeds

Research output: Contribution to journal › Journal article › Research › peer-review

Standard

Darwin's Fancy Revised: An Updated Understanding of the Genomic Constitution of Pigeon Breeds. / Pacheco, George; van Grouw, Hein; Shapiro, Michael D.; Gilbert, Tom; Vieira, Filipe Garrett.

In: Genome Biology and Evolution, Vol. 12, No. 3, 2020, p. 136-150.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Pacheco, G, van Grouw, H, Shapiro, MD, Gilbert, T & Vieira, FG 2020, 'Darwin's Fancy Revised: An Updated Understanding of the Genomic Constitution of Pigeon Breeds', Genome Biology and Evolution, vol. 12, no. 3, pp. 136-150. https://doi.org/10.1093/gbe/evaa027

APA

Pacheco, G., van Grouw, H., Shapiro, M. D., Gilbert, T., & Vieira, F. G. (2020). Darwin's Fancy Revised: An Updated Understanding of the Genomic Constitution of Pigeon Breeds. Genome Biology and Evolution, 12(3), 136-150. https://doi.org/10.1093/gbe/evaa027

Vancouver

Pacheco G, van Grouw H, Shapiro MD, Gilbert T, Vieira FG. Darwin's Fancy Revised: An Updated Understanding of the Genomic Constitution of Pigeon Breeds. Genome Biology and Evolution. 2020;12(3):136-150. https://doi.org/10.1093/gbe/evaa027

Author

Pacheco, George ; van Grouw, Hein ; Shapiro, Michael D. ; Gilbert, Tom ; Vieira, Filipe Garrett. / Darwin's Fancy Revised: An Updated Understanding of the Genomic Constitution of Pigeon Breeds. In: Genome Biology and Evolution. 2020 ; Vol. 12, No. 3. pp. 136-150.

Bibtex

@article{3476e7d1e3f54333879aecb6f6dddbb9,
title = "Darwin's Fancy Revised: An Updated Understanding of the Genomic Constitution of Pigeon Breeds",
abstract = "{\textcopyright} The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. Through its long history of artificial selection, the rock pigeon (Columba livia Gmelin 1789) was forged into a large number of domestic breeds. The incredible amount of phenotypic diversity exhibited in these breeds has long held the fascination of scholars, particularly those interested in biological inheritance and evolution. However, exploiting them as a model system is challenging, as unlike with many other domestic species, few reliable records exist about the origins of, and relationships between, each of the breeds. Therefore, in order to broaden our understanding of the complex evolutionary relationships among pigeon breeds, we generated genome-wide data by performing the genotyping-by-sequencing (GBS) method on close to 200 domestic individuals representing over 60 breeds. We analyzed these GBS data alongside previously published whole-genome sequencing data, and this combined analysis allowed us to conduct the most extensive phylogenetic analysis of the group, including two feral pigeons and one outgroup. We improve previous phylogenies, find considerable population structure across the different breeds, and identify unreported interbreed admixture events. Despite the reduced number of loci relative to whole-genome sequencing, we demonstrate that GBS data provide sufficient analytical power to investigate intertwined evolutionary relationships, such as those that are characteristic of animal domestic breeds. Thus, we argue that future studies should consider sequencing methods akin to the GBS approach as an optimal cost-effective approach for addressing complex phylogenies.",
keywords = "animal breeding, genotyping-by-sequencing, pigeon breeds, population genomics",
author = "George Pacheco and {van Grouw}, Hein and Shapiro, {Michael D.} and Tom Gilbert and Vieira, {Filipe Garrett}",
year = "2020",
doi = "10.1093/gbe/evaa027",
language = "English",
volume = "12",
pages = "136--150",
journal = "Genome Biology and Evolution",
issn = "1759-6653",
publisher = "Oxford University Press",
number = "3",

}

RIS

TY - JOUR

T1 - Darwin's Fancy Revised: An Updated Understanding of the Genomic Constitution of Pigeon Breeds

AU - Pacheco, George

AU - van Grouw, Hein

AU - Shapiro, Michael D.

AU - Gilbert, Tom

AU - Vieira, Filipe Garrett

PY - 2020

Y1 - 2020

N2 - © The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. Through its long history of artificial selection, the rock pigeon (Columba livia Gmelin 1789) was forged into a large number of domestic breeds. The incredible amount of phenotypic diversity exhibited in these breeds has long held the fascination of scholars, particularly those interested in biological inheritance and evolution. However, exploiting them as a model system is challenging, as unlike with many other domestic species, few reliable records exist about the origins of, and relationships between, each of the breeds. Therefore, in order to broaden our understanding of the complex evolutionary relationships among pigeon breeds, we generated genome-wide data by performing the genotyping-by-sequencing (GBS) method on close to 200 domestic individuals representing over 60 breeds. We analyzed these GBS data alongside previously published whole-genome sequencing data, and this combined analysis allowed us to conduct the most extensive phylogenetic analysis of the group, including two feral pigeons and one outgroup. We improve previous phylogenies, find considerable population structure across the different breeds, and identify unreported interbreed admixture events. Despite the reduced number of loci relative to whole-genome sequencing, we demonstrate that GBS data provide sufficient analytical power to investigate intertwined evolutionary relationships, such as those that are characteristic of animal domestic breeds. Thus, we argue that future studies should consider sequencing methods akin to the GBS approach as an optimal cost-effective approach for addressing complex phylogenies.

AB - © The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. Through its long history of artificial selection, the rock pigeon (Columba livia Gmelin 1789) was forged into a large number of domestic breeds. The incredible amount of phenotypic diversity exhibited in these breeds has long held the fascination of scholars, particularly those interested in biological inheritance and evolution. However, exploiting them as a model system is challenging, as unlike with many other domestic species, few reliable records exist about the origins of, and relationships between, each of the breeds. Therefore, in order to broaden our understanding of the complex evolutionary relationships among pigeon breeds, we generated genome-wide data by performing the genotyping-by-sequencing (GBS) method on close to 200 domestic individuals representing over 60 breeds. We analyzed these GBS data alongside previously published whole-genome sequencing data, and this combined analysis allowed us to conduct the most extensive phylogenetic analysis of the group, including two feral pigeons and one outgroup. We improve previous phylogenies, find considerable population structure across the different breeds, and identify unreported interbreed admixture events. Despite the reduced number of loci relative to whole-genome sequencing, we demonstrate that GBS data provide sufficient analytical power to investigate intertwined evolutionary relationships, such as those that are characteristic of animal domestic breeds. Thus, we argue that future studies should consider sequencing methods akin to the GBS approach as an optimal cost-effective approach for addressing complex phylogenies.

KW - animal breeding

KW - genotyping-by-sequencing

KW - pigeon breeds

KW - population genomics

UR - http://www.scopus.com/inward/record.url?scp=85083537841&partnerID=8YFLogxK

U2 - 10.1093/gbe/evaa027

DO - 10.1093/gbe/evaa027

M3 - Journal article

C2 - 32053199

VL - 12

SP - 136

EP - 150

JO - Genome Biology and Evolution

JF - Genome Biology and Evolution

SN - 1759-6653

IS - 3

ER -

ID: 240314546