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

Comparative Study

. 2014 Nov;23(22):5566-74.

doi: 10.1111/mec.12958. Epub 2014 Nov 5.

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Free PMC article

Comparative Study

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

Laurent A F Frantz et al. Mol Ecol. 2014 Nov.

Free PMC article

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 Sunda-shelf 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.

Keywords: conservation genetics; genomics; hybridization; phylogeography; population genetics; speciation.

© 2014 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.

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Figures

Figure 1
Figure 1

Map of Island South-East Asia (upper part) with sea level fluctuations (lower part) over the last 4My (adapted from Miller. 2005). Dark grey and light grey areas on the map represent the exposure of the Sunda-shelf at 40 m and 75 m below current sea level, respectively.

Figure 2
Figure 2

Schematic representation of the five models tested in this study: a) Strict divergence (DIV without admixture or divergence with) b) with admixture from S. scrofa to S. verrucosus (IUA_SS), c) admixture from S. verrucosus to S. scrofa (IUA_SV), d) symmetrical admixture (ISA) and e) bidirectional admixture (IBA).

Figure 3
Figure 3

Expected (under IBA model with parameters fixed at their MLE) and observed mutational configuration. The X-axis represents the proportion of blocks with k mutations (Y axis) for different topologies. Blue bars = (S. scrofa, (S. verrucosus,S. cebifrons)), green bars = (S. verrucosus, (S. cebifrons,S. scrofa)) and orange = (S. cebifrons, (S. verrucosus,S. scrofa)).

Figure 4
Figure 4

Marginal support (Δ;lnL) for a) admixture fraction (f) and b) divergence and admixture times. Solid and dashed lines represent Δ;lnL curves under the IUA_SV and IBA models, respectively. The black dashed horizontal lines delimit the 95% confidence interval. a) admixture fraction from S. verrucosus into S. scrofa and from S. scrofa into S. verrucosus are shown in red and blue represent respectively b) T2, T1 and Tgf are shown in black, blue and red respectively.

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