Speciation and domestication in Suiformes: a genomic perspective

<strong>Abstract</strong> Frantz, L.A.F. (2015). Speciation and Domestication in <em>Suiformes</em>: a genomic perspective. PhD thesis, Wageningen University, the Netherlands The diversity of life on earth owes its existence to the process of speciation. The concept of speciation is primordial for evolutionary biologists because it provides a framework to understand how contemporary biodiversity came to be. Moreover, not only natural phenomena can result in the differentiation of life forms. Indeed, biodiversity can also be the result of direct and indirect human influence such as domestication. In this thesis, I investigate these evolutionary processes (speciation and domestication) in the <em>Suiformes</em> superfamily (pigs and related species). I use complete genome sequences to illuminate many specific aspects of the speciation and domestication in <em>Suiformes</em> as well as to draw general conclusions on these crucial processes. In chapter 2 I show how genomes provide an essential source of information to retrieve deep taxonomic relationships among <em>Suiformes</em>. This allows me to describe multiple novel aspects of their early evolutionary history such as the fact that <em>Suiformes</em> colonised North America at least twice. In this chapter, I further highlight and discuss novel methodological limitations that are inherent to phylogenomics. In chapters 3, 4 and 5 I use genome sequences to resolve the evolutionary history of the genus <em>Sus</em> (domestic pigs and wild boars species). More precisely, I show that, contrary to the expectation of simple models of speciation, the evolutionary history of these species involved alternating periods of gene-flow and genetic differentiation that are tightly linked to past climatic fluctuations that took place over the last 4 million years. In addition, these chapters also provide novel insights into the process of speciation by demonstrating that genetic differentiation between species can be achieved, even when gene-flow is strong. Lastly, in chapter 6 I tested multiple models of domestication for <em>S. scrofa</em>. In this chapter I show that models involving reproductive isolation between wild and domestic forms are incompatible with genomic data. Moreover, this chapter demonstrates that, while domestic pigs are morphologically homogenous, they are not genetically homogenous. Together, these findings have important implications for our understanding of the process of domestication because it shows that this process was not solely the result of captivity. Together, the results of this work not only provide a comprehensive evolutionary history for the <em>Suiformes</em>, but also novel insights into the complex processes (speciation and domestication) that are responsible for the diversity of life on earth.