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

Abstract

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.

A Pilot Study Investigating the Dynamics of Pigeon Circovirus Recombination in Domesticated Pigeons Housed in a Single Loft

“…Similar behavior of living in groups is also observed in the feral domestic pigeon population inhabiting cities around the world, which are referred to as urban pigeons [ 2 ]. Nowadays, numerous pigeon breeds are known, and some are used for either meat production, such as ornamental birds, or for pigeon sports (carrier pigeons) [ 3 ]. The carrier pigeons are used extensively for racing, and various studies have explored the influence of genetics and dietary parameters as well as infections on race performance [ 4 , 5 , 6 , 7 ].…”

A ROR2 coding variant is associated with craniofacial variation in domestic pigeons

“…In addition, because the mapping population was derived from just two birds that represent a fraction of the morphological diversity across pigeon breeds, we have no way of knowing if the beak length QTL we identified is relevant beyond the RH x OGO cross. Short beaks are characteristic of numerous related pigeon breeds that belong to the Owl family, but have also been selected for in a variety of unrelated non-Owl breeds 26–28 . Pigeon breeders might have repeatedly selected the same standing variant in different breeds, independent variants of the same gene in different breeds, or different genes altogether in different breeds.…”

A ROR2 coding variant is associated with craniofacial variation in domestic pigeons

“…Short beaks are characteristic of numerous closely related pigeon breeds that belong to the owl family, but are also part of the breed standard, and thus under positive selection, in a variety of unrelated non-owl breeds. [26][27][28] Pigeon breeders might have repeatedly selected the same standing variant in different breeds, independent variants of the same gene in different breeds, or different genes altogether in different breeds.…”