Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA.
Mol Ecol. 2011 Nov;20(22):4722-36. doi: 10.1111/j.1365-294X.2011.05285.x. Epub 2011 Oct 18.
In the early stages of reproductive isolation, genomic regions of reduced recombination are expected to show greater levels of differentiation, either because gene flow between species is reduced in these regions or because the effects of selection at linked sites within species are enhanced in these regions. Here, we study the patterns of DNA sequence variation at 27 autosomal loci among populations of Mus musculus musculus, M. m. domesticus, and M. m. castaneus, three subspecies of house mice with collinear genomes. We found that some loci exhibit considerable shared variation among subspecies, while others exhibit fixed differences. We used an isolation-with-gene-flow model to estimate divergence times and effective population sizes (N(e) ) and to disentangle ancestral variation from gene flow. Estimates of divergence time indicate that all three subspecies diverged from one another within a very short period of time approximately 350,000 years ago. Overall, N(e) for each subspecies was associated with the degree of genetic differentiation: M. m. musculus had the smallest N(e) and the greatest proportion of monophyletic gene genealogies, while M. m. castaneus had the largest N(e) and the smallest proportion of monophyletic gene genealogies. M. m. domesticus and M. m. musculus were more differentiated from each other than either were from M. m. castaneus, consistent with greater reproductive isolation between M. m. domesticus and M. m. musculus. F(ST) was significantly greater at loci experiencing low recombination rates compared to loci experiencing high recombination rates in comparisons between M. m. castaneus and M. m. musculus or M. m. domesticus. These results provide evidence that genomic regions with less recombination show greater differentiation, even in the absence of chromosomal rearrangements.
在生殖隔离的早期阶段，预计重组减少的基因组区域会表现出更高水平的分化，这要么是因为这些区域种间基因流动减少，要么是因为物种内连锁位点的选择效应在这些区域得到增强。在这里，我们研究了三个家鼠亚种——野生小家鼠（Mus musculus musculus）、家养小家鼠（M. m. domesticus）和坎氏小家鼠（M. m. castaneus）——的 27 个常染色体基因座的 DNA 序列变异模式。我们发现，一些基因座在亚种之间表现出相当大的共享变异，而其他基因座则表现出固定差异。我们使用带有基因流的隔离模型来估计分歧时间和有效种群大小（N(e)），并区分祖先变异和基因流。分歧时间的估计表明，所有三个亚种彼此之间在很短的时间内发生分歧，大约在 35 万年前。总体而言，每个亚种的 N(e)与遗传分化程度相关：野生小家鼠的 N(e)最小，单系基因谱系的比例最大，而坎氏小家鼠的 N(e)最大，单系基因谱系的比例最小。家养小家鼠和野生小家鼠彼此之间的分化程度大于它们与坎氏小家鼠之间的分化程度，这与家养小家鼠和野生小家鼠之间更大的生殖隔离一致。在坎氏小家鼠和野生小家鼠或家养小家鼠之间的比较中，经历低重组率的基因座的 F(ST)明显大于经历高重组率的基因座。这些结果提供了证据，表明即使没有染色体重排，重组较少的基因组区域也会表现出更大的分化。
