George Pacheco:
Flying Rats Shall No Longer Be. A Population Genomic Analysis of Fancy and Feral Pigeons

Date: 01-04-2019    Supervisor: Thomas Gilbert




It has been supported by archaeological evidences that the rock pigeon (Columba livia Gmelin, 1789) was first domesticated during the Neolithic period in the Middle East, being initially used as a source of both food and fertiliser as well as in religious rituals. Later on, not only was the extent of its service to humankind spun into a wider variety of practical roles, but during the eighteenth century a great interest arose in the development and maintenance of so-called fancy pigeon breeds. As a result, over 230 pigeon breeds are officially recognised at the present, which encompass a well-known and truly fabulous range of phenotypic diversity. Furthermore, the long history of the pigeon’s domestication has also been tightly coupled with a long-standing process of feralisation, as domestic pigeons escaping from captive stocks successfully populated surrounding urban areas. In this way, populations of feral pigeons are found today to inhabit a great portion of the modern urban landscapes worldwide, leading many to view the feral pigeon as a pest species that requires active management. Moreover, as has been reported for wild ancestors of other domestic species, it is reasonable to suspect that the preservation of the gene pools of potential remaining wild rock pigeon colonies might be at risk due to admixture with feral pigeons. Although some studies have investigated the question concerning the complex phylogenetic relationships amongst the purebred pigeon breeds, these studies either included few breeds and few individuals per breed, or few genetic markers. On the other hand, no previous genomic work has properly addressed the natural history of feral pigeons so far.

During the last few years, reduced-representation library sequencing methods have been successfully established, which have facilitated the ready genotyping of thousands of genomic markers covering different regions of a species’ genome. Both the studies presented in this PhD thesis take advantage of this sequencing method, which allowed us to conduct the largest genomic studies to date on both purebred and free-living pigeon individuals:

In Chapter I, based on a genomic dataset including over 200 purebred pigeon individuals representing 67 breeds, we perform analyses of phylogenomics, MDS, Admixture, as well as we estimate several population genetic parameters. We report considerable genetic structure across the different pigeon breeds as well as substantial variation in their levels of genetic diversity. Importantly, we identify previously unreported interbreed admixture events. Moreover, we also investigate the suitability of genomic data generated through reduced-representation library protocols for studies aiming to correlate phenotypic variation with genomic modification.

In Chapter II, based on a genomic dataset including 450 free-living pigeons from 41 worldwide localities, we conduct phylogenomic, MDS and Admixture analyses as well as estimate several population genetic parameters aiming to shed first light on the pigeon feralisation question. Our results show that there is strong population structure across global populations of feral pigeons, and that most populations present signs of admixture with domestic lineages in considerably different degrees. Nonetheless, our results also indicate that some remote localities might still harbour wild colonies of rock pigeons that have been virtually free of contamination with domestic genotypes.