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Canine genomics and the evolution of phenotypic diversity

Final Activity Report Summary - CANINE GENOMICS (Canine genomics and the evolution of phenotypic diversity)

The amount of biodiversity we see in the natural world is overwhelming. Species are big and small, have none, two or more legs, some have wings to fly and others do not, some swim, some crawl, some leap and so on. Moreover there are the ones that photosynthesise, those that live in dry conditions and the ones that thrive in wet environments, and we could continue endlessly in this manner. Organisms appear and disappear, and they evolve. When Darwin, in 1859, in his book ‘On the origin of species’, developed his ‘theory of evolution by means of natural selection’, he did so basing his observations not only on wild species, but also on domestic animals and how they responded to selection. Domestic animals represent the largest experiment ever done in evolutionary biology, since a group of animals has been removed from natural selective pressures and, during thousands of generations, has been subjected to extreme selective forces imposed by breeders. As Darwin noted, understanding the origin of diversity in domestic animals can illustrate how diversity appears in nature.

The domestication process started about 10 000 years ago or less for most domestic animals, which is an extremely short time from the evolutionary point of view. Despite this we see enormous differences in, for example, milk, fat and meat yield or body size, shape and colour in cattle, sheep or pig breeds. Among all domestic animals the diversity found in dogs is unparalleled. Breeds started to be reproductively isolated from each other about 200 years ago, and the International Canine Federation recognises today about 350 breeds, with morphologies as different as the size of a chihuahua and a St. Bernard, or the face shape of a bulldog and a greyhound, or the coat of the shaggy puli and the naked Mexican hairless. In such a short time, the morphological, physiological and behavioural differences fixed between dog breeds are greater than those accumulated in 15 million years of evolution by all members of the same family, the so-called canidae, which includes wolves, coyotes, jackals and foxes. The question is where all the diversity seen in dogs comes from.

Another important feature that makes the dog an interesting study subject is that its wild ancestor, the wolf, is still extant, and therefore both species can be compared. This is not the case for other domestic mammals, such as horses, sheep or cows, for which their wild ancestors are unknown, extinct, almost extinct or deeply affected by human activities.

In this project, we compared the genome of the dog, canis familiaris, with that of its wild ancestor, the wolf, canis lupus. We also compared different dog breeds with each other. In this case we evaluated whether domestication affected the rapid production of variation in dogs. The study of deoxyribonucleic acid (DNA) and the recent advances in genomic techniques brought about this possibility. We looked at two genetic mechanisms. One involved the process in which the DNA of the father and the mother was reshuffled to create new combinations in the genes of the offspring, i.e. recombination. We investigated if this process was accelerated in dogs compared to wolves. The other genetic mechanism we studied had to do with the actual sequence of DNA. Variations in the sequence of a gene, for example, shorter or longer or with some nucleotide differences, could have effects on the appearance of individuals. We studied the presence of fragments of DNA that might be involved in the expression of genes. If there were changes in those areas, the phenotype of the individual could be affected. Furthermore, we looked at differences across dog breeds and between dogs and wolves. In this way, we took advantage of this ‘long domestication experiment’ and tried to understand if any of these two mechanisms could be involved in the genesis of the huge diversity observed in dogs. The results of this study could help us understand the formation of species and the processes involved in generation of diversity in nature.