Using whole-genome sequencing data for demographic and functional evaluations of small managed populations

Genetic diversity is the foundation for selection to act upon a population: without diversity, evolution can not occur and species can not adapt to changing environments. In this thesis, I provide an in-depth analysis of the genome-wide patterns of diversity in local chicken breeds of small effective population size. Since their domestication in Southeast Asia around 9,500 years ago, domestic chickens have undergone human-driven selection resulting in the creation of hundreds of breeds, each described by a precise set of morphological features. Domesticated chicken breeds are therefore an excellent study system to investigate the effects of demography on genomic variation. Using a combination of the latest genomics tools, I show that, besides signs of recent inbreeding and declined diversity, changes in breeding preferences generated novel and identifiable variation. Interestingly, the genetic basis of some of this variation has evolved in other bird species through parallel evolution despite their divergence from chicken millions of years ago. However, as I emphasize, the outstanding diversity harboured by local chicken breeds can only be preserved in the near future if conservation programmes become genomics-informed. The rationale is the ability of genomic data to provide additional infor- mation on the functional relevance of such variation, which has important implications for conservation. Therefore, by means of genomic data, we can better control for deleterious alleles, while increasing genetic diversity. The identification of functionally important mutations have for a long time been limited to protein-coding genes. In this thesis, I demonstrate through the development of the ch(icken)CADD model that sub regions within conserved non-coding elements also harbour variants with a negative fitness effect, as their association with known disease genes in other vertebrate species demonstrate. Overall, the findings of this thesis show that genetic diversity should