Sequencing the genomes of the pig and related Suids reveals extensive intra- and inter-specific gene flow during speciation

M.A.M. Groenen, O. Madsen, L. Frantz, M. Bosse, Y. Paudel, A.L. Archibald, L.B. Schook, R. Crooijmans, H.J. Megens
Plant and Animal Genome XXI Conference, January 11-13, 2013, San Diego, CA


During evolution genomes have been shaped by speciation events and selection. Recent developments in genome sequencing have opened up unprecedented possibilities to study these changes and events. Within the ERC funded project SelSweep we have started to address these questions in detail at the molecular level in the pig and other Suids. Domestication and selection has resulted in a large number of distinct breeds worldwide with very distinct characteristics. Furthermore, the Suidea family is extremely well suited to study speciation due to the availability of at least 12 different species that have diverged over a time span of 1 to 10 million years. Within the SelSweep project we study the genes and genomic regions that have been under strong selection during speciation, early domestication and during subsequent development of specific breeds in the pig. In this presentation I will focus on the speciation of the genus Sus in SouthEast Asia and the divergence between the European and Asian wild boar.

The genus Sus, which provides an excellent proxy to study speciation influenced by past glaciation. consists of around 7 different species, found in island (ISEA) and mainland (MSEA) Southeast Asia (figure 1), an area comprised of five biodiversity hotspots with the largest pig diversity in the world.  To investigate speciation, selection and admixture within the genus Sus, we have sequenced the complete genome of multiple individuals from a variety of breeds from Sus scrofa as well as several individuals from four other members of this genus (Sus celebensis, Sus verrucosus, Sus barbatus and Sus cebifrons). As an outgroup we sequenced the more distantly related African Warthog (Phacochoerus africanus). We applied several different phylogenomics methods, all resulting in the same topology. We were able to estimate the time of divergence from the common ancestors for all Sus species sequenced and our sequence results also reveal a deep phylogenetic split between European and Asian wild boars that occurred ~1 million years ago.

Each speciation event could be traced back to a precise geological stage, highlighting the importance of cyclical climatic fluctuations during the Plio-Pleistocene on diversification in ISEA. Moreover, admixture analysis revealed extensive intra- and inter-specific gene flow. Together, our results show that glacial intervals which created land-bridges between islands and mainland directly influenced dispersal and gene flow. In addition, we show that human translocation of pigs also played a role in their repartition across ISEA and MSEA. Our results show that genomes of closely related (sub)species are shaped by a myriad of past evolutionary events.