Abstract
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 E opsaltria australis . Across >1500 km, nuclear differentiation is low and latitudinally structured by isolation by distance, whereas two highly divergent, parapatric mitochondrial lineages (>6.6% in ND 2) 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 opsaltria 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 ( ND 4 and ND 4L) and cytochrome bc 1 (cyt‐ b ) against a background of widespread purifying selection on all mitochondrial genes. Three of these amino acid replacements were fixed in ND 4 of the geographically most widespread E . australis lineage. The other two replacements were fixed in ND 4L 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.