Biochemical and evolutionary interactions between mitochondrial and nuclear genomes (‘mitonuclear interactions’) are proposed evolutionary drivers of sexual reproduction, sexual selection, adaptation, and speciation. We investigated the role of pre-mating isolation in maintaining functional mitonuclear interactions in wild populations bearing diverged proposed co-adapted mitonuclear genotypes. Two lineages of eastern yellow robin Eopsaltria australis—putatively climate-adapted to ’inland’ and ‘coastal’ climates—differ by ~7% of mitochondrial DNA positions, whereas nuclear genome differences are concentrated into a sex-linked region enriched with genes with mitochondrial functions. This pattern can be explained by female-linked selection accompanied by male-mediated gene flow across the narrow hybrid zone where the two lineages coexist. It remains unknown whether lineage divergence is driven by intrinsic incompatibilities (particularly in females, under Haldane’s rule), extrinsic incompatibilities, both, or other drivers. We tested whether lineage divergence could be facilitated by non-random mate-pairing with respect to partners’ mitolineage or nuclear Z sex-chromosome DNA sequences, which differ between the lineages. We used field-, Z-linked-, and mitolineage data from two locations where the lineages hybridize, to test whether females mate disproportionately with (1) males of their own mitolineage and/or bearing similar Z-linked variation, as might be expected if hybrids experience intrinsic incompatibilities, or (2) putatively locally-adapted males, as expected under environmental selection. Comparing field observations with simulations provided no evidence of non-random mating, thus the observed patterns consistent with reduced female gene flow likely occur post-mating. Future tests of female-biased mortality at different life stages and habitat selection may clarify any mechanisms of selection.

Conservation of breeding seabirds typically requires detailed data on where they feed at sea. Ecological niche models (ENMs) can fill data gaps, but rarely perform well when transferred to new regions. Alternatively, the foraging radius approach simply encircles the sea surrounding a breeding seabird colony (a foraging circle), but overestimates foraging habitat. Here, we investigate whether ENMs can transfer (predict) foraging niches of breeding tropical seabirds between global colonies, and whether ENMs can refine foraging circles. We collate a large global dataset of tropical seabird tracks (12000 trips, 16 species, 60 colonies) to build a comprehensive summary of tropical seabird foraging ranges and to train ENMs. We interrogate ENM transferability and assess the confidence with which unsuitable habitat predicted by ENMs can be excluded from within foraging circles. We apply this refinement framework to the Great Barrier Reef (GBR), Australia to identify a network of candidate marine protected areas (MPAs) for seabirds. We found little ability to generalise and transfer breeding tropical seabird foraging niches across all colonies for any species (mean AUC: 0.56, range 0.4-0.82). Low global transferability was partially explained by colony clusters that predicted well internally but other colony clusters poorly. After refinement with ENMs, foraging circles still contained 89% of known foraging areas from tracking data, providing confidence that important foraging habitat was not erroneously excluded by greater refinement from high transferability ENMs nor minor refinement from low transferability ENMs. Foraging radii estimated the total foraging area of the GBR breeding seabird community as 2,941,000 km2, which was refined by excluding between 197,000 km2 and 1,826,000 km2 of unsuitable foraging habitat. ENMs trained on local GBR tracking achieved superior refinement over globally trained models, demonstrating the value of local tracking. Our framework demonstrates an effective method to delineate candidate MPAs for breeding seabirds in data-poor regions.