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.

多基因座遗传变异、地理与环境之间的关系，能够揭示进化过程如何影响基因组。我们利用线粒体（mtDNA）和核（nDNA）遗传标记以及生物气候变量，研究了澳大利亚鸟类——东黄鸲鹟（Eopsaltria australis）的进化过程。在澳大利亚东南部，大分水岭东西两侧存在两个分化的mtDNA谱系，与核DNA的纬度结构呈垂直分布。我们评估了多种备选情景，以解释景观遗传模式中这一显著的不一致性。随机线粒体谱系分选（Stochastic mtDNA lineage sorting）的可能性可以被排除，因为这两个mtDNA谱系在地理上相距超过1500公里，本质上是不同的。地理隔离（Vicariance）的可能性也不大：根据物种分布模型，大分水岭既不是当前的屏障，在末次盛冰期也不是；通过溯祖分析推断的核基因流也证实了这一点。雌性恋巢性（Female philopatry）与已知的雌性偏向扩散相矛盾。线粒体DNA和核DNA的种群历史存在差异，表明它们的进化历史是解耦的。基于距离的冗余分析（Distance-based redundancy analysis）显示，环境温度对mtDNA变异的解释度高于地理位置和距离隔离；这一结果支持线粒体系统地理模式的非中性解释。因此，观察到的线粒体-核不一致性与雌性连锁性状（如mtDNA、mtDNA-nDNA互作或W染色体上的基因）受到环境选择的情况一致，这种选择在核基因流存在的情况下推动了线粒体的分化。