The overarching theme of this thesis was to investigate speciation histories and biogeographical patterns of New Guinean birds, by using whole genomes primarily extracted from natural history collections.

In Chapter I, I detected hidden diversity within the Lesser Melampitta, a species, which is widely distributed across different mountain ranges throughout New Guinea. In contrast, I found no strong differentiation between populations in the Greater Melampitta, a species characterised by a much more scattered distribution. I hypothesized that this unexpected pattern in the latter species may have been the result of a relatively recent collapse into its current fragmented distribution. Moreover, this chapter was instrumental in establishing and optimising bioinformatic workflows that I applied in the subsequent chapters. In Chapter II we investigated hybridisation patterns within a lineage of whistlers (Pachycephala). The study revealed a complex network of interactions between species that appears to be linked to geography. Species inhabiting islands and landmasses that were connected in the past during periods of lower sea levels were less differentiated and showed higher signals of introgression than species inhabiting more remote oceanic islands. Chapter III focussed on speciation dynamics within a genus of honeyeaters (Melidectes). The results support that most species within the genus have formed as a consequence of geographic isolation. However, two taxa with partially overlapping distributions in the central mountains of New Guinea, which are known to hybridise, exhibit a very complex genetic structure that does not follow the current species classification, as the hybridising taxa appear to be genetically indistinguishable. Yet, I recovered some genetic signals of past differentiation and consequently present this complex as a rare empirical example of ephemeral speciation. In addition, I investigated how future climate change may potentially result in new speciation events.  For Chapter IV, I investigated the extent of reproductive isolation and hybridisation patterns in the Birds-of-paradise genus Paradisaea and discuss the placement of various species along the speciation continuum. Unlike species with more isolated distributions, such as those found on islands surrounding New Guinea, three species on New Guinea’s mainland exhibit low genetic differentiation and a pattern of more or less unrestricted gene flow across much of the lowlands. An exception to this are the Lesser and Raggiana Birds-of-paradise that show marked genetic differentiation and the absence of ongoing gene flow. The population structure and differentiation of Paradisaea species on the New Guinean mainland thus closely resembles that of a ring species.

In the broader context, this thesis has demonstrated the value that historical DNA offers when studying speciation dynamics, especially for species and populations that are difficult to sample. Furthermore, it also highlights the impact of system-specific mechanisms which calls for caution when generalising conclusions within the field of speciation.