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

Hein Van Grouw,Michael D Shapiro,George Pacheco,Marcus Thomas P Gilbert,Filipe Garrett Vieira,Jay Storz

doi:10.1093/gbe/evaa027

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.

Highlights

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), contributing to our understanding of fundamental evolutionary processes (Andersson et al 2012; Imsland et al 2012; Rubin et al 2012)
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
In his later book that focused 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)

Summary

Introduction

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), contributing to our understanding of fundamental evolutionary processes (Andersson et al 2012; Imsland et al 2012; Rubin et al 2012). Which is the greatest treat, in my opinion, which can be offered to human being” [sic] (Darwin 1855), but he opted to introduce his theory of natural selection by discussing the role of artificial selection in the development of pigeon breeds (Darwin 1859) In his later book that focused 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).

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Conclusion