Testing models of speciation from genome sequences: divergence and asymmetric admixture in Island South‐East Asian Sus species during the Plio‐Pleistocene climatic fluctuations

Abstract

In many temperate regions, ice ages promoted range contractions into refugia resulting in divergence (and potentially speciation), while warmer periods led to range expansions and hybridization. However, the impact these climatic oscillations had in many parts of the tropics remains elusive. Here, we investigate this issue using genome sequences of three pig (Sus) species, two of which are found on islands of the Sundashelf shallow seas in Island South-East Asia (ISEA). A previous study revealed signatures of interspecific admixture between these Sus species (Genome biology, 14, 2013, R107). However, the timing, directionality and extent of this admixture remain unknown. Here, we use a likelihood-based model comparison to more finely resolve this admixture history and test whether it was mediated by humans or occurred naturally. Our analyses suggest that interspecific admixture between Sunda-shelf species was most likely asymmetric and occurred long before the arrival of humans in the region. More precisely, we show that these species diverged during the late Pliocene but around 23% of their genomes have been affected by admixture during the later Pleistocene climatic transition. In addition, we show that our method provides a significant improvement over D-statistics which are uninformative about the direction of admixture.

Population genetic structure of Oryza rufipogon and Oryza nivara: implications for the origin of O. nivara

“…; Frantz et al . ). Huang & Schaal () used SDM to investigate the past, present and future distribution of O. rufipogon and concluded that the historically disjunct distribution might contribute to the current genetic subdivision of this species.…”

“…; Frantz et al . ) when O. rufipogon was widespread and O. nivara originated (Zheng & Ge ). Therefore, the genetic structure of O. rufipogon populations can be explained by a metapopulation model (Slatkin ; Horne ), where the populations are not those in the conventional sense but rather networks of local populations connected by patterns of gene flow.…”

“…Evidence shows that climatic fluctuations accompanied by temperature and sea level changes during glacial ages in the Quaternary are the most important processes shaping the population genetic structure of species (Hewitt 2000;Davis & Shaw 2001;Zachos et al 2001;Miller et al 2005;Berg et al 2010). This process led to repeated cycles of land bridge formation, result-ing in multiple mergers and separations among islands or between islands and the mainland (Miller et al 2005;Bisconti et al 2011;Frantz et al 2014). Huang & Schaal (2012) used SDM to investigate the past, present and future distribution of O. rufipogon and concluded that the historically disjunct distribution might contribute to the current genetic subdivision of this species.…”

“…; Huang & Schaal ; Frantz et al . ). Population genetic studies incorporating approaches such as phylogeographic analysis and species distribution modelling (SDM) have contributed the understanding of the evolutionary history and dynamics of populations and species (Elith et al .…”

“…Climatic fluctuations during the Quaternary have been increasingly acknowledged to have possibly resulted in significant range shifts, population dispersals and extinction processes, thereby consequently playing vital roles in shaping population genetics and the local adaptation of both plant and animal species (Hewitt 2000;Davis & Shaw 2001;Zachos et al 2001;Miller et al 2005;Berg et al 2010;Bisconti et al 2011;Huang & Schaal 2012;Frantz et al 2014). Population genetic studies incorporating approaches such as phylogeographic analysis and species distribution modelling (SDM) have contributed the understanding of the evolutionary history and dynamics of populations and species (Elith et al 2006;Londo et al 2006;Li et al 2011;St Onge et al 2011;Huang & Schaal 2012;Huang et al 2012a;Grossenbacher et al 2014).…”