The family Melampittidae is endemic to New Guinea and consists of two monotypic genera: Melampitta lugubris (Lesser Melampitta) and Megalampitta gigantea (Greater Melampitta). Both Melampitta species have scattered and disconnected distributions across New Guinea in the central mountain range and in some of the outlying ranges. While M. lugubris is common and found in most montane regions of the island, M. gigantaea is elusive and known from only six localities in isolated pockets on New Guinea with very specific habitats of limestone and sinkholes. In this project, we apply museomics to determine the population structure and demographic history of these two species. We re-sequenced the genomes of all seven known M. gigantaea samples housed in museum collections as well as 24 M. lugubris samples from across its distribution. By comparing population structure between the two species, we investigate to what extent habitat dependence, such as in M. gigantaea, may affect population connectivity. Phylogenetic and population genomic analyses, as well as acoustic variation revealed that M. gigantaea consists of a single population in contrast to M. lugubris that shows much stronger population structure across the island. We suggest a recent collapse of M. gigantaea into its fragmented habitats as an explanation to its unexpected low diversity and lack of population structure. The deep genetic divergences between the M. lugubris populations on the Vogelkop region, in the western central range and the eastern central range, respectively, suggests that these three populations should be elevated to full species level. This work sheds new light on the mechanisms that have shaped the intriguing distribution of the two species within this family and is a prime example of the importance of museum collections for genomic studies of poorly known and rare species.

Genomic studies have revealed introgressive hybridization as a common phenomenon across the tree of life, particularly among young radiations. As incipient speciation tends to be induced by vicariance events, it is assumed that introgressive hybridization is more frequent in young radiations in which allopatrically distributed species have a high probability of coming into secondary contact. In this study we utilize whole genomic data to investigate spatio-temporal introgression patterns in a songbird radiation that has colonized a highly dynamic island region in the Indo-Pacific. Some taxa within this radiation have colonized remote oceanic islands whereas others occur on landmasses and islands in the Sahul region that were periodically connected during Pleistocene periods of lower sea levels. Our results show that introgressive hybridization has been pervasive within this young radiation, despite prominent plumage differences between taxa. Geographical proximity has been an important factor for hybridization and we further find that species occupying islands in the environmentally unstable Sahul region exhibit particularly high signatures of introgressive hybridization. Yet, one species appears to have been shielded against hybridization, perhaps due to specific ecological specializations. Finally, we identify a hybrid species on an island where two oceanic radiations meet. Our results also caution against relying solely on analyses that only detect asymmetric introgression when examining systems with complex introgression histories. Collectively, our results support a growing body of literature that suggests that reticulate speciation is much more common than previously thought. This has implications for our understanding of species formation and their persistence through time.

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 process. This study investigates the evolutionary history of the New Guinean bird genus Melidectes, consisting of six species that inhabit various montane regions at different elevations. While most Melidectes species have allopatric distributions, two species overlap in the central mountain range and hybridise. However, plumage differences and elevational adaptations are assumed to maintain the species' boundaries. Utilising specimens from natural history collections and comprehensive genomic analyses, including a de novo genome assembly, we characterise allopatric speciation patterns within the genus and highlight how future speciation could potentially be driven by climate change. Contrary to previous hypotheses, our findings suggest that in the two distributionally overlapping species, phenotypic differences do not prevent gene flow. We find limited acoustic differentiation and extensive admixture across most of their distributions. Divergence and admixture levels conform poorly to the current taxonomy and follow a geographical pattern in which the most isolated populations at the ends of the distributions are most divergent and show least admixture. However, in contrast, their mitochondrial genomes do group in accordance with species identity, namely, into two deeply divergent lineages. We propose that this system demonstrates the ephemeral nature of speciation, in which two incipient species have started mixing extensively as they came into secondary contact, resulting in nearly complete fusion into a single lineage.

Speciation is a continuous process and understanding how incipient lineages evolve along this continuum remains a major challenge. Hybridisation and sexual selection play key roles in driving or constraining speciation, but their interaction can be complex. While strong mate choice should limit gene flow, interspecific hybridisation can lead to both lineage fusion or the introduction of genetic variants that can facilitate diversification. Birds-of-paradise provide a compelling system to explore these dynamics, as they exhibit some of the most elaborate forms of mate choice and sexually selected traits, and yet commonly hybridise. Using whole-genome sequencing of 108 historical specimens, we investigated phylogenetic relationships, gene flow, and genetic differentiation across the genus Paradisaea and its sister genus Paradisornis. Our results reveal species that vary in their relative position along the speciation continuum. While some allopatric species exhibit strong genetic differentiation, other species admix extensively even though they differ in plumage traits. The widespread mainland species complex (P. minor, P. apoda, and P. raggiana) in particular, follows a geographic gradient of genetic exchange, forming a pattern where geographically close populations show increasing admixture. Notwithstanding phenotypic variation in putatively sexually selected traits, the gradual shift in shared ancestry raises questions about the degree to which these taxa represent distinct species versus populations along a broader continuum of differentiation. Most strikingly, despite consistent signatures of genomic admixture between contiguous populations, P. minor and P. raggiana seem to be largely reproductively isolated in eastern New Guinea where the two lineages meet at the end of the central mountain range. The spatial distribution of divergence and hybridisation between P. minor, P. apoda, and P. raggiana, is therefore ring-like along the New Guinea highlands and presents a prime example of incipient lineages at different stages along the speciation continuum. Our findings illustrate how speciation can be simultaneously shaped by a complex interplay of geography, gene flow, and sexual selection, and how such processes in concert can lead to different stages of reproductive isolation across lineages and regions.