Darwin's Fancy Revised: An Updated Understanding of the Genomic Constitution of Pigeon Breeds
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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.
I: Genome Biology and Evolution, Bind 12, Nr. 3, 2020, s. 136-150.Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › fagfællebedømt
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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