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、地理与环境之间的关联，可揭示进化过程如何作用于基因组。本研究以线粒体DNA（mtDNA）和核DNA（nDNA）遗传标记，结合生物气候变量，对澳大利亚鸟类东黄鸲（*Eopsaltria australis*）的演化展开探究。在澳大利亚东南部，大分水岭东西两侧存在两个分化的线粒体DNA谱系，其空间分布与呈纬度梯度的核DNA结构相互垂直。针对景观遗传格局中这一显著的不一致现象，我们评估了多种替代解释场景。随机线粒体DNA谱系分选可被排除，因为该线粒体DNA谱系在超过1500公里的范围内地理分布基本完全分化。地理隔离分化假说不成立：根据物种分布模型结果，大分水岭目前并非物种扩散障碍，在末次冰盛期也未成为屏障；溯祖分析推断的核基因流也印证了这一点。雌性栖居保守性与已知的雌性偏向扩散现象相悖。线粒体DNA与核DNA的种群历史动态特征存在显著差异，表明二者的演化历史相互解耦。基于距离的冗余分析（distance-based redundancy analysis）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，该结果支持线粒体系统地理格局存在非中性演化机制。综上，本研究观测到的线粒体-核基因组不一致现象，与雌性连锁性状（如线粒体DNA、线粒体DNA-核DNA互作或W染色体上的基因）所受的环境选择相符——在核基因流持续存在的背景下，这类选择驱动了线粒体DNA的分化。