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

Abstract

BackgroundElucidating 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.ResultsOur 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.ConclusionsOur 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.

A tree of geese: A phylogenomic perspective on the evolutionary history of True Geese

“…Previous research indicated that SMALT is appropriate for mapping paired end reads when the reference genome is distantly related to the sampled species (Frantz et al, 2013 ). Furthermore, preliminary analyses showed that this soft ware produces the best results compared to other mapping soft ware (Fig.…”

Mining the pig genome to investigate the domestication process

“…As we will discuss later, the spatial and temporal coexistence of these suid species involved frequent hybridization events . This circumstance complicates the reconstruction of the evolutionary history of the genus Sus and calls into question whether species such as Sus celebensis, which currently live in the wild but may have been domesticated in the past, could have contributed to the gene pool of Asian pigs (Albarella et al, 2006;Larson et al, 2011;Frantz et al, 2013).…”

“…There is a general consensus that the Eurasian wild boar (Sus scrofa) and other sister species, such as Sus celebensis (Celebes warty pig), Sus verrucosus (Java warty pig), Sus cebifrons (Visayan warty pig), Sus philippensis (Philippine warty pig) and Sus barbatus (Bornean bearded pig), emerged in Southeast Asia in the early Pliocene (Figure 1), approximately 5.3-3.5 Myr ago (Larson et al, 2007a(Larson et al, , 2011Frantz et al, 2013). As we will discuss later, the spatial and temporal coexistence of these suid species involved frequent hybridization events .…”

Crossing species boundaries : the hybrid histories of the true geese

“…The significant D-statistics varied from 0.07 to 0.17, which is slightly higher compared to analyses on recent radiations, such as Darwin's Finches (0.004 -0.092; Lamichhaney et al, 2015) and butterflies of the genera Heliconius (0.04; Dasmahapatra et al, 2012) and Papilio (0.04; Zhang et al, 2013). These values do fall within the range of studies on other hybridizing species, such as pigs (0.11 -0.23; Frantz et al, 2013), bears (0.04 -0.46; Liu et al, 2014, Cahill et al, 2015 and Xiphophorus fish (0.03 -0.56; Cui et al, 2013). A significant D-statistic does not necessarily indicate introgression between the species from which the genomes are being compared.…”

“…Previous research indicated that SMALT is appropriate for mapping paired-end reads when the reference genome is distantly related to the sampled species (Frantz et al, 2013). Furthermore, preliminary analyses showed that this software produces the best results compared to other mapping software ( Figure S7.1).…”