Genome sequencing reveals fine scale diversification and reticulation history during speciation in Sus

Frantz et al. Genome Biology Genome sequencing reveals fine scale diversification and reticulation history during speciation in Sus Laurent AF Frantz 0 1 Joshua G Schraiber 1 Ole Madsen 0 1 Hendrik-Jan Megens 0 1 Mirte Bosse 0 1 Yogesh Paudel 0 1 Gono Semiadi 1 Erik Meijaard 1 Ning Li 1 Richard PMA Crooijmans 0 1 Alan L Archibald 1 Montgomery Slatkin 1 Lawrence B Schook 1 Greger Larson 1 2 Martien AM Groenen 0 1 0 Animal Breeding and Genomics Group, Wageningen University , De Elst 1, Wageningen, WD 6708 , The Netherlands 1 of Illinois , Urbana-Champaign, Illinois 61801 , USA 2 Durham Evolution and Ancient DNA, Department of Archaeology, Durham University , Durham DH1 3LE , UK Background: Elucidating the process of speciation requires an in-depth understanding of the evolutionary history of the species in question. Studies that rely upon a limited number of genetic loci do not always reveal actual evolutionary history, and often confuse inferences related to phylogeny and speciation. Whole-genome data, however, can overcome this issue by providing a nearly unbiased window into the patterns and processes of speciation. In order to reveal the complexity of the speciation process, we sequenced and analyzed the genomes of 10 wild pigs, representing morphologically or geographically well-defined species and subspecies of the genus Sus from insular and mainland Southeast Asia, and one African common warthog. Results: Our data highlight the importance of past cyclical climatic fluctuations in facilitating the dispersal and isolation of populations, thus leading to the diversification of suids in one of the most species-rich regions of the world. Moreover, admixture analyses revealed extensive, intra- and inter-specific gene-flow that explains previous conflicting results obtained from a limited number of loci. We show that these multiple episodes of gene-flow resulted from both natural and human-mediated dispersal. Conclusions: Our results demonstrate the importance of past climatic fluctuations and human mediated translocations in driving and complicating the process of speciation in island Southeast Asia. This case study demonstrates that genomics is a powerful tool to decipher the evolutionary history of a genus, and reveals the complexity of the process of speciation. - Background The diversity of life on Earth owes its existence to the process of speciation. The emergence of genetic techniques has allowed the relationships amongst hundreds of species to be investigated, and DNA studies have been invaluable in resolving long-standing taxonomic and phylogenetic questions (for example, [1,2]. The use of limited numbers of genomic markers, however, can result in misleading impressions of the phylogenetic relationships between organisms [3]. In addition, traditional bifurcating trees are constructed on the presumption that little or no gene-flow occurs following a split between two species, though gene-flow has been shown to occur during the splits between species [4,5]. The recent advent of high-throughput sequencing allows inferences to be drawn from near-complete genomes, in turn offering an unprecedented understanding of organismal evolutionary history. The commensurate increase in resolving power has allowed numerous questions to be addressed, including those related to genomic structure, deep phylogenetic relationships, the genetic variation responsible for specific phenotypes, and hybridization patterns between ancient hominids [6,7]. Few studies, however, have taken advantage of complete genomes to investigate the process of speciation. Wallace [8] first recognized that Island Southeast Asia (ISEA) is an ideal natural laboratory to study speciation. Over the past 50 million years (My) tectonic activity has considerably altered the geography of this region. In addition, large-scale climatic fluctuations beginning in the early Pliocene [9] affected the regions biogeography [10]. Successive glacial and interglacial periods lowered and raised sea levels, thus alternately separating and connecting large landmasses. During cold periods, the Malay Peninsula, Borneo, Sumatra and Java formed the contiguous landmass known as Sundaland (Figure 1A), while in warmer periods these islands were isolated from each other. These alternating climatic conditions required frequent adaptation and induced intermittent allopatric and parapatric speciation processes. The fluctuations also created an ideal environment for diversification that has resulted in a complex and species-rich assemblage [10]. The development of models that explain the process of speciation in ISEA has been further complicated by anthropogenic factors that have influenced the dispersal and distribution of numerous species in the region [11]. The five biodiversity hotspots found in ISEA and Mainland Southeast Asia (MSEA) [12] are host to at least seven morphologically defined species of pig in the genus Sus [13]. Aside from Sus scrofa (Eurasian wild boar and domestic pigs), which is distributed across most of Eurasia and parts of northern Africa, all other species of the genus Sus are restricted to MSEA and ISEA (Figure 1A). Because these species are still capable of interbreeding and producing fertile offspring [14], the genus Sus presents an excellent model to study ongoing speciation. Moreover, previous studies have found discrepancies between and among the phylogenies inferred from morphological and mitochondrial DNA (mtDNA) markers [13,15,16]. Thus, the phylogeny of these species remains controversial. These discrepancies could be explained by either gene-flow between sympatric populations of different species or a rapid radiation that would have left little power to resolve the phylogeny. The lack of a post-zygotic reproductive barrier in pigs is not an isolated case. Indeed, many vertebrate taxa, recognized as different species, can still interbreed and produce fertile offspring. For example, it has been claimed that approximately 6% of European mammalian species can interbreed with at least one other species [17]. Additionally, while most of these species are young, there are examples of interbreeding species of birds that diverged over 55 million years ago (Mya) [18]. Given the ease with which numerous closely related (and some distantly related) species can interbreed, it is important to develop and test methods that are not only robust to inter-specific gene-flow, but can also identify it. Speciation with geneflow is expected to result in a richer phylogenetic history including periods of divergence (bifurcations) and periods of secondary contact (reticulations), and thus should leave genomic signatures. In order to investigate the speciation history of these suids, and to assess the usefulness of whole-genome sequences to infer complex evolutionary histories, we sequenced and analyzed the complete genomes of 11 individual pigs representing five Sus species and an African common warthog (Phacochoeru (...truncated)