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The honeyeaters are the most species-rich clade of birds east of Wallace's Line. They occupy a wide range of habitats, from desert to rainforest, and occur throughout Australia, New Guinea, and oceanic islands across Wallacea and the Pacific. Honeyeater natural history is well characterised, but comparative studies of this group are hampered by the lack of a well-supported phylogeny. Here, we infer the first genome-scale, genus-level phylogeny of the honeyeaters using 4397 ultraconserved elements from 57 species. We analysed the data using concatenated and species-tree approaches, and we found support for novel clades previously undetected in analyses of single- or multi-locus datasets. Despite sequencing thousands of loci, phylogenetic relationships of the New Caledonian Crow Honeyeater (Gymnomyza aubryana) remain equivocal. This study provides a new phylogenetic framework from which to study the ecology and evolution of one of Australasia's most iconic avian clades. [ABSTRACT FROM AUTHOR]

[Display omitted] • We inferred a timetree of the whistlers (Aves: Pachycephalidae) with UCEs. • P. nudigula , P. rufogularis , P. soror , and P. schlegelii are placed confidently. • Ancestral range reconstruction supported an Australo-Papuan origin of the family. • Whistlers colonized oceanic archipelagos multiple times. • Biogeographic results were equivocal when regions were parsed more finely. The utility of islands as natural laboratories of evolution is exemplified in the patterns of differentiation in widespread, phenotypically variable lineages. The whistlers (Aves: Pachycephalidae) are one of the most complex avian radiations, with a combination of widespread and locally endemic taxa spanning the vast archipelagos of the Indo-Pacific, making them an ideal group to study patterns and processes of diversification on islands. Here, we present a robust, species-level phylogeny of all five genera and 85% of species within Pachycephalidae, based on thousands of ultraconserved elements (UCEs) generated with a target-capture approach and high-throughput sequencing. We clarify phylogenetic relationships within Pachycephala and report on divergence timing and ancestral range estimation. We explored multiple biogeographic coding schemes that incorporated geological uncertainty in this complex region. The biogeographic origin of this group was difficult to discern, likely owing to aspects of dynamic Earth history in the Indo-Pacific. The Australo-Papuan region was the likely origin of crown-group whistlers, but the specific ancestral area could not be identified more precisely than Australia or New Guinea, and Wallacea may have played a larger role than previously realized in the evolutionary history of whistlers. Multiple independent colonizations of island archipelagos across Melanesia, Wallacea, and the Philippines contributed to the relatively high species richness of extant whistlers. This work refines our understanding of one of the regions' most celebrated bird lineages and adds to our growing knowledge about the patterns and processes of diversification in the Indo-Pacific. [ABSTRACT FROM AUTHOR]

The complex island archipelagoes of Wallacea and Melanesia have provided empirical data behind integral theories in evolutionary biology, including allopatric speciation and island biogeography. Yet, questions regarding the relative impact of the layered biogeographic barriers, such as deep-water trenches and isolated island systems, on faunal diversification remain underexplored. One such barrier is Wallace's Line, a significant biogeographic boundary that largely separates Australian and Asian biodiversity. To assess the relative roles of biogeographic barriers-specifically isolated island systems and Wallace's Line-we investigated the tempo and mode of diversification in a diverse avian radiation, Corvides (Crows and Jays, Birds-of-paradise, Vangas, and allies). We combined a genus-level data set of thousands of ultraconserved elements (UCEs) and a species-level, 12-gene Sanger sequence matrix to produce a well-resolved supermatrix tree that we leveraged to explore the group's historical biogeography and the effects of the biogeographic barriers on their macroevolutionary dynamics. The tree is well resolved and differs substantially from what has been used extensively for past comparative analyses within this group. We confirmed that Corvides, and its major constituent clades, arose in Australia and that a burst of dispersals west across Wallace's Line occurred after the uplift of Wallacea during the mid-Miocene. We found that dispersal across this biogeographic barrier was generally rare, though westward dispersals were two times more frequent than eastward dispersals. Wallacea's central position between Sundaland and Sahul no doubt acted as a bridge for island-hopping dispersal out of Australia, across Wallace's Line, to colonize the rest of Earth. In addition, we found that the complex island archipelagoes east of Wallace's Line harbor the highest rates of net diversification and are a substantial source of colonists to continental systems on both sides of this biogeographic barrier. Our results support emerging evidence that island systems, particularly the geologically complex archipelagoes of the Indo-pacific, are drivers of species diversification. [Historical biogeography; island biogeography; Melanesia; molecular phylogenetics; state-dependent diversification and extinction.]., (© The Author(s) 2022. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

Avian diversification has been influenced by global climate change, plate tectonic movements, and mass extinction events. However, the impact of these factors on the diversification of the hyperdiverse perching birds (passerines) is unclear because family level relationships are unresolved and the timing of splitting events among lineages is uncertain. We analyzed DNA data from 4,060 nuclear loci and 137 passerine families using concatenation and coalescent approaches to infer a comprehensive phylogenetic hypothesis that clarifies relationships among all passerine families. Then, we calibrated this phylogeny using 13 fossils to examine the effects of different events in Earth history on the timing and rate of passerine diversification. Our analyses reconcile passerine diversification with the fossil and geological records; suggest that passerines originated on the Australian landmass ∼47 Ma; and show that subsequent dispersal and diversification of passerines was affected by a number of climatological and geological events, such as Oligocene glaciation and inundation of the New Zealand landmass. Although passerine diversification rates fluctuated throughout the Cenozoic, we find no link between the rate of passerine diversification and Cenozoic global temperature, and our analyses show that the increases in passerine diversification rate we observe are disconnected from the colonization of new continents. Taken together, these results suggest more complex mechanisms than temperature change or ecological opportunity have controlled macroscale patterns of passerine speciation., Competing Interests: The authors declare no conflict of interest., (Copyright © 2019 the Author(s). Published by PNAS.)

Phylogenetic analyses of nuclear and mitochondrial DNA sequences were used to test a recent phylogenetic hypothesis for the avian genus Gallicolumba that relied heavily on preserved museum study skins for DNA samples. Our comparisons show that several published gene sequences represent pseudogenes or chimeras of multiple taxa, and these sequences had an adverse influence on phylogeny estimation. A new phylogenetic hypothesis strongly supports the monophyly of Philippine bleeding-hearts, the monophyly of Gallicolumba sensu stricto, and places Leucosarcia as part of an Australasian radiation rather than sister to Alopecoenas. These findings clarify Gallicolumba biogeography and also highlight the need for greater caution in the use of suboptimal source material in molecular systematic studies., (Copyright © 2012 Elsevier Inc. All rights reserved.)