Data from: Perched at the mito-nuclear crossroads: divergent mitochondrial lineages correlate with environment in the face of ongoing nuclear gene flow in an Australian bird

Relationships among multi-locus genetic variation, geography and environment can reveal how evolutionary processes affect genomes. We examined the evolution of an Australian bird, the eastern yellow robin Eopsaltria australis, using mitochondrial (mtDNA) and nuclear (nDNA) genetic markers, and bioclimatic variables. In southeastern Australia, two divergent mtDNA lineages occur east and west of the Great Dividing Range, perpendicular to latitudinal nDNA structure. We evaluated alternative scenarios to explain this striking discordance in landscape genetic patterning. Stochastic mtDNA lineage sorting can be rejected because the mtDNA lineages are essentially distinct geographically for >1500 km. Vicariance is unlikely: the Great Dividing Range is neither a current barrier nor was it at the Last Glacial Maximum according to species distribution modeling; nuclear gene flow inferred from coalescent analysis affirms this. Female philopatry contradicts known female-biased dispersal. Contrasting mtDNA and nDNA demographies indicate their evolutionary histories are decoupled. Distance-based redundancy analysis, in which environmental temperatures explain mtDNA variance above that explained by geographic position and isolation-by-distance, favors a non-neutral explanation for mitochondrial phylogeographic patterning. Thus, observed mito-nuclear discordance accords with environmental selection on a female-linked trait, such as mtDNA, mtDNA-nDNA interactions or genes on W-chromosome, driving mitochondrial divergence in the presence of nuclear gene flow.

多位点遗传变异、地理因素与环境之间的关联，可揭示演化过程如何作用于基因组。本研究以澳大利亚特有鸟类东黄鸲（Eopsaltria australis）为研究对象，采用线粒体DNA（mtDNA）与核DNA（nDNA）遗传标记及生物气候变量，对其演化过程展开分析。
在澳大利亚东南部，两个分化的线粒体DNA支系分别分布于大分水岭（Great Dividing Range）东西两侧，其分布格局与沿纬度梯度分布的核DNA结构呈垂直关系。
本研究评估了多种假说，以解释该景观遗传格局中的显著不一致性。
随机线粒体DNA谱系分选可被排除，因为该线粒体DNA支系在超过1500公里的范围内地理分布完全分化。
异域分化假说亦不成立：根据物种分布模型，大分水岭既非当前的基因流屏障，在末次盛冰期也并非如此；基于溯祖分析推断的核基因流也证实了这一点。
雌性居留行为与已知的雌性偏向扩散现象相悖。
线粒体DNA与核DNA的种群历史特征存在显著差异，表明二者的演化史相互独立。
基于距离的冗余分析显示，环境温度对线粒体DNA变异的解释度高于地理位置和距离隔离（isolation-by-distance）的解释度，这支持线粒体系统地理格局的非中性演化解释。
因此，观测到的核质不一致性，与雌性相关性状（如线粒体DNA、线粒体-核DNA互作或W染色体上的基因）所受的环境选择相契合——这种选择在核基因流存在的情况下，推动了线粒体DNA的分化。