Project title: Evolutionary Genomics of Domestication: Characterizing the genetic architecture of fast evolving traits in dogs
Summary: The domestication of plants and animals had a dramatic influence on human history by promoting the transition from a nomadic to sedentary. The agricultural revolution significantly altered the landscape around human settlements creating different ecological niches. These new niches induced different selective pressure on some species and promoted their domestication. Over millennium of artificial selection, following animal domestication, humans have explored the phenotypic landscape of domestic species very rapidly to differentiate them from their wild progenitors.
Our understanding of the process of domestication, however, is still rudimentary. Compelling evidence of gene flow between wild and domestic lineages have also been reported suggesting that animal domestication has been a reticulate process analogous to parapatric speciation characterised by a population bottleneck followed by an expansion. Gene-flow is particularly interesting given that it is expected to reduce the phenotypic differentiation between populations. On the other hand, introgression also represents a potential source of new variants that can become beneficial in a new environment or simply provide standing genetic variation for selection to act on. Population bottlenecks instead have the opposite effects: they reduce diversity and can lead to relaxed selection. Random genetic drift could therefore have increased the frequency of rare, previously deleterious, variants. If these variations were mostly recessive this might have increased additive genetic variance in domestic taxa, which could have accelerated the exploration of phenotypic landscape through artificial selection. As such, bottlenecks may have been primordial for the rapid morphological differentiation between wild and domestic populations.
My project aims to address these questions using genomics and geometric morphometrics. More specifically, I will compare ancient genomes obtained from archaeological remains with modern samples of wild/domestic populations to quantify admixture and test whether this process was adaptive. Furthermore, by using forward simulations, I will attempt to characterize the selective response of a population following a bottleneck, especially when a shift in the selection coefficient is applied. This will allow me to assess whether the specific demographic history of domestic species might have facilitated their morphological evolution.
Finally, I intend to analyze a combination of geometric morphometrics (GMM) and genetic data (SNPs) from modern/ancient wolves and dogs. These time series data will allow me to perform GWAS like analyses using time as information to infer the genetic architecture of traits such as skull shape and body size and assess whether these traits (and their underlying genetic markers) were under selection in the past. This will allow me to address multiple questions 1) whether the same markers that determine size in modern dog breeds are also informative about size in ancient dogs and wolves 2) whether these markers were under selection in the past.