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

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 Southeast Asia (ISEA). A previous study revealed signatures of inter-specific admixture between these Sus species (Frantz et al. (2013) Genome sequencing reveals fine scale diversification and reticulation history during speciation in Sus. Genome biology, 14, 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 inter-specific 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.

在多数温带区域，冰期驱动物种分布范围收缩至避难所，进而引发种群分化（甚至潜在的物种形成），而温暖期则促使分布范围扩张并发生杂交渐渗。然而，这类气候振荡对热带多数地区的影响仍有待厘清。本研究以三种猪属（Sus）物种的基因组序列为研究材料，针对该问题开展探究，其中两个物种分布于东南亚岛屿地区（ISEA）的巽他陆架浅海岛屿之上。既往研究已揭示这些猪属物种间存在种间基因渗入的遗传印记（Frantz等，2013：《基因组测序揭示猪属物种形成过程中的精细尺度分化与网状演化历史》，《基因组生物学》，14卷，R107）。不过，该基因渗入事件的发生时间、方向与规模仍未明确。本研究采用基于似然的模型比较方法，以更精细地解析该基因渗入历史，并检验其究竟是由人类介导还是自然发生。分析结果显示，巽他陆架物种间的种间基因渗入极大概率是不对称的，且早在人类涉足该区域之前便已出现。更确切地说，我们证实这些物种于上新世晚期发生分化，但约23%的基因组在更新世晚期的气候转型阶段受到了基因渗入的影响。此外，本研究还表明，相较于无法提供基因渗入方向信息的D统计量，本研究采用的方法具备显著的改进优势。