Darwin’s Fancy Revised: An Updated Understanding of the Genomic Constitution of Pigeon Breeds
George Pacheco, Hein van Grouw, Michael D Shapiro, Marcus Thomas P Gilbert, Filipe Garrett Vieira, Darwin’s Fancy Revised: An Updated Understanding of the Genomic Constitution of Pigeon Breeds, Genome Biology and Evolution, Volume 12, Issue 3, March 2020, Pages 136–150, https://doi.org/10.1093/gbe/evaa027
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.
Domestic animal lineages have long been appreciated for their value as model systems with which to identify the genomic mechanisms underlying their often remarkable phenotypic variation ( Andersson and Georges 2004), thus contributing to our understanding of fundamental evolutionary processes ( Andersson et al. 2012; Imsland et al. 2012; Rubin et al. 2012). In this regard, domestic pigeons exhibit some of the most extraordinary biological variations, and as such attracted the interest of Charles Darwin himself. Not only did he, on November 4, 1855, end a letter to his friend and colleague Charles Lyell, with the following words: “I will show you my pigeons! which is the greatest treat, in my opinion, which can be offered to human being” [sic] ( Darwin 1855), but he also opted to introduce his theory of natural selection by discussing the role of artificial selection in the development of pigeon breeds ( Darwin 1859). Furthermore, in his later book that focused specifically on describing the products of both animal and plant domestication ( Darwin 1968), two whole chapters were dedicated to pigeons, where he expanded his rationale behind his claim that despite the immense biological diversity seen in pigeon breeds, they all descended from a single species—the rock pigeon (Columba livia Gmelin 1789) ( Darwin 1968). It is unsurprising, therefore, that pigeons have also been of interest to geneticists since the field’s earliest days ( Staples-Browne 1908; Bonhote and Smalley 1911), due to not only their astonishing phenotypic diversity but also the ease with which samples can be obtained from domestic stocks and cross-breeding experiments undertaken.
