Re-sequenced genomes of 124 Melidectes birds to investigate speciation histories

Speciation is a fundamental concept in evolutionary biology and understanding the mechanisms driving speciation remains the foremost research topic within this field. Hybridisation is often involved in speciation and can influence its rates, potentially accelerating, decelerating, or even reversing the speciation process. In this study, we investigate the evolutionary history of the New Guinean bird genus Melidectes, consisting of six species that inhabit various montane regions at different elevations. While most species of Melidectes have allopatric distributions, two species' distributions overlap in the central mountain range. These two species hybridise, but plumage differences and adaptations to partly different elevations are assumed to maintain the species' boundaries. Utilising mainly specimens from natural history collections and comprehensive genomic analyses, including a de novo reference genome assembly, we characterise patterns of allopatric speciation within the genus and highlight potential areas of future speciation driven by climate change. Contrary to previous hypotheses, our findings suggest that plumage differences and adaptations to specific elevations do not form barriers to gene flow in the two species with distributional overlap. Furthermore, we find limited acoustic differentiation and extensive admixture patterns across most of their distributions. Admixture proportions conform poorly to the current taxonomy as levels of divergence and introgression follow a clear geographical pattern in which the most isolated populations at the ends of the overlapping distribution are most divergent and show least admixture. However, the investigated individuals' mitochondrial genomes are grouping more in accordance with their suggested species identity into two deeply divergent lineages. We propose that this system demonstrates the ephemeral nature of the speciation process, in which two incipient species have started mixing extensively as they came into secondary contact. This has resulted in nearly complete fusion into a single lineage.