Data from: Positive and purifying selection in mitochondrial genomes of a bird with mitonuclear discordance

Diversifying selection on metabolic pathways can reduce intraspecific gene flow and promote population divergence. An opportunity to explore this arises from mitonuclear discordance observed in an Australian bird Eopsaltria australis. Across >1,500 Km, nuclear differentiation is low and latitudinally structured by isolation-by-distance, whereas two highly divergent, parapatric mitochondrial lineages (>6.6% in ND2) show a discordant longitudinal geographic pattern and experience different climates. Vicariance, incomplete lineage sorting and sex-biased dispersal were shown earlier to be unlikely drivers of the mitonuclear discordance; instead, natural selection on a female-linked trait was the preferred hypothesis. Accordingly, here we tested for signals of positive, divergent selection on mitochondrial genes in E. australis. We used codon models and physicochemical profiles of amino acid replacements to analyse complete mitochondrial genomes of the two mitochondrial lineages in E. australis, its sister species E. griseogularis, and outgroups. We found evidence of positive selection on at least five amino acids, encoded by genes of two oxidative phosphorylation pathway complexes, NADH dehydrogenase (ND4 and ND4L) and Cytochrome bc1 (cyt-b) against a background of widespread purifying selection on all mitochondrial genes. Three of these amino acid replacements were fixed in ND4 of the geographically most widespread E. australis lineage. The other two replacements were fixed in ND4L and cyt-b of the geographically more restricted E. australis lineage. We discuss whether this selection may reflect local environmental adaptation, a by-product of other selective processes, or genetic incompatibilities, and propose how these hypotheses can be tested in future.

代谢通路的多样化选择可降低种内基因流，促进种群分化。我们可通过观察澳大利亚鸟类澳洲黄鸲鹟（Eopsaltria australis）中的核质冲突（mitonuclear discordance）来探索这一现象。在超过1500公里的分布范围内，其核基因组分化程度较低，且通过距离隔离效应呈现纬度结构；而两个高度分化、邻域分布的线粒体谱系（ND2（烟酰胺腺嘌呤二核苷酸脱氢酶亚基2）基因序列差异达6.6%以上）却呈现不一致的纵向地理格局，并栖息于不同气候区域。此前研究表明，地理隔离、不完全谱系分选以及性别偏向扩散均不太可能是该核质冲突的成因，而与雌性相关性状的自然选择才是更受支持的假说。据此，本研究针对澳洲黄鸲鹟的线粒体基因检测了正向分化选择的信号。我们采用密码子模型与氨基酸替换的理化性质特征，对澳洲黄鸲鹟的两个线粒体谱系、其近缘姊妹种灰喉啸鹟（E. griseogularis）以及外类群的完整线粒体基因组进行了分析。在所有线粒体基因普遍经历纯化选择的背景下，我们发现氧化磷酸化通路两个复合物的基因（NADH脱氢酶（ND4与ND4L）以及细胞色素bc1复合物（cyt-b））中至少有5个氨基酸位点受到正向选择。其中3个氨基酸替换在地理分布最广的澳洲黄鸲鹟线粒体谱系的ND4基因中固定下来，另外2个替换则在分布范围更受限的澳洲黄鸲鹟线粒体谱系的ND4L与cyt-b基因中固定。本研究讨论了该选择信号可能反映局部环境适应、其他选择过程的副产物或是遗传不相容性，并提出了未来可用于验证这些假说的研究方向。