Data from: A reassessment of explanations for discordant introgressions of mitochondrial and nuclear genomes

Hybridization is increasingly recognized as a significant evolutionary process, in particular because it can lead to introgression of genes from one species to another. A striking pattern of discordance in the amount of introgression between mitochondrial and nuclear markers exists such that substantial mitochondrial introgression is often found in combination with no or little nuclear introgression. Multiple mechanisms have been proposed to explain this discordance, including positive selection for introgressing mitochondrial variants, several types of sex-biases, drift, negative selection against introgression in the nuclear genome, and spatial expansion. Most of these hypotheses are verbal, and have not been quantitatively evaluated so far. We use individual-based, multi-locus, computer simulations of secondary contact under a wide range of demographic and genetic scenarios to evaluate the ability of the different mechanisms to produce discordant introgression. Sex-biases and spatial expansions fail to produce substantial mito-nuclear discordance. Drift and nuclear selection can produce strong discordance, but only under a limited range of conditions. In contrast, selection on the mitochondrial genome produces strong discordance, particularly when dispersal rates are low. However, commonly used statistical tests have little power to detect this selection. Altogether, these results dismiss several popular hypotheses, and provide support for adaptive mitochondrial introgression.杂交（Hybridization）日益被学界视为一类关键的进化进程，究其核心原因，其可介导基因跨物种的渐渗（introgression）。当前已观测到一类显著的线粒体与核标记（mitochondrial and nuclear markers）间渐渗量不一致的模式：大量线粒体基因渐渗现象，常伴随无或极微量的核基因渐渗。学界已提出多种机制以阐释该不一致现象，包括对渐渗线粒体变异的正向选择、多种类型的性别偏向、遗传漂变、核基因组针对基因渐渗的负选择，以及空间扩张过程。上述假说大多仅为定性描述，迄今尚未得到定量评估。本研究采用基于个体的多位点计算机模拟方法，在广泛的种群统计与遗传情景下模拟二次接触（secondary contact）过程，以评估不同机制引发渐渗不一致现象的能力。性别偏向与空间扩张过程均无法产生显著的线粒体-核渐渗不一致（mito-nuclear discordance）。遗传漂变与核选择仅能在有限的条件范围内，引发强烈的渐渗不一致现象。与之相对，线粒体基因组上的选择可引发强烈的渐渗不一致，尤其当物种扩散速率较低时。但当前常用的统计检验（statistical tests）几乎不具备检测这类选择的效力。综上，本研究结果驳斥了数种主流假说，并为适应性线粒体基因渐渗（adaptive mitochondrial introgression）提供了实证支持。