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  1. Abstract

    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 thatmore »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.]

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  2. 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. Takenmore »together, these results suggest more complex mechanisms than temperature change or ecological opportunity have controlled macroscale patterns of passerine speciation.

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  3. Abstract Aim

    To test the importance of alternative diversification drivers and biogeographical processes for the evolution of Amazonian upland forest birds through a densely sampled analysis of diversification of the endemic Amazonian genusRhegmatorhinaat multiple taxonomic and temporal scales.




    Antbirds (Thamnophilidae).


    We sequenced four mtDNAand nuclear gene regions of 120 individuals from 50 localities representing all recognized species and subspecies of the genus. We performed molecular phylogenetic analyses using both gene tree and species tree methods, molecular dating analysis and estimated population demographic history and gene flow.


    Dense sampling throughout the distribution ofRhegmatorhinarevealed that the main Amazonian rivers delimit the geographic distribution of taxa as inferred from mtDNAlineages. Molecular phylogenetic analyses resulted in a strongly supported phylogenetic hypothesis for the genus, with two main clades currently separated by the Madeira River. Molecular dating analysis indicated diversification during the Quaternary. Reconstruction of recent demographic history of populations revealed a trend for population expansion in eastern Amazonia and stability in the west. Estimates of gene flow corroborate the possibility that migration after divergence had some influence on the current patterns of diversity.

    Main Conclusions

    Based on broad‐scale sampling, a clarification of taxonomic boundaries, and strongly supported phylogenetic relationships, we confirm that, first,more »mitochondrial lineages within this upland forest Amazonian bird genus agree with spatial patterns known for decades based on phenotypes, and second, that most lineages are geographically delimited by the large Amazonian rivers. The association between past demographic changes related to palaeoclimatic cycles and the historically varying strength and size of rivers as barriers to dispersal may be the path to the answer to the long‐standing question of identifying the main drivers of Amazonian diversification.

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  4. Disjunct, pantropical distributions are a common pattern among avian lineages, but disentangling multiple scenarios that can produce them requires accurate estimates of historical relationships and timescales. Here, we clarify the biogeographical history of the pantropical avian family of trogons (Trogonidae) by re‐examining their phylogenetic relationships and divergence times with genome‐scale data. We estimated trogon phylogeny by analysing thousands of ultraconserved element (UCE) loci from all extant trogon genera with concatenation and coalescent approaches. We then estimated a time frame for trogon diversification using MCMCTree and fossil calibrations, after which we performed ancestral area estimation using BioGeoBEARS. We recovered the first well‐resolved hypothesis of relationships among trogon genera. Trogons comprise three clades, each confined to one of three biogeographical regions: Africa, Asia and the Neotropics, with the African clade sister to the others. These clades diverged rapidly during the Oligocene‐Miocene transition. Our biogeographical analyses identify a Eurasian origin for stem trogons and a crown clade arising from ancestors broadly distributed across Laurasia and Africa. The pantropical ranges of trogons are relicts of a broader Afro‐Laurasian distribution that was fragmented across Africa, Asia and the New World in near coincident fashion during the Oligocene‐Miocene transition by global cooling and changing habitatsmore »along the Beringian land bridge and North Africa.

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  5. The tropics are the source of most biodiversity yet inadequate sampling obscures answers to fundamental questions about how this diversity evolves. We leveraged samples assembled over decades of fieldwork to study diversification of the largest tropical bird radiation, the suboscine passerines. Our phylogeny, estimated using data from 2389 genomic regions in 1940 individuals of 1283 species, reveals that peak suboscine species diversity in the Neotropics is not associated with high recent speciation rates but rather with the gradual accumulation of species over time. Paradoxically, the highest speciation rates are in lineages from regions with low species diversity, which are generally cold, dry, unstable environments. Our results reveal a model in which species are forming faster in environmental extremes but have accumulated in moderate environments to form tropical biodiversity hotspots.