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Amazonia is a ‘source’ of biodiversity for other Neotropical ecosystems, but which conditions trigger in situ speciation and emigration is contentious. Three hypotheses for how communities have assembled include (1) a stochastic model wherein chance dispersal events lead to gradual emigration and species accumulation, (2) diversity-dependence wherein successful dispersal events decline through time due to ecological limits, and (3) barrier displacement wherein environmental change facilitates dispersal to other biomes via transient habitat corridors. We sequenced thousands of molecular markers for the Neotropical Tityrinae (Aves) and applied a novel filtering protocol to identify loci with high utility for dated phylogenomics. We used these loci to estimate divergence times and model Tityrinae's evolutionary history. We detected a prominent role for speciation driven by barriers including synchronous speciation across the Andes and found that dispersal increased toward the present. Because diversification was continuous but dispersal was non-random over time, we show that barrier displacement better explains Tityrinae's history than stochasticity or diversity-dependence. We propose that Amazonia is a source of biodiversity because (1) it is a relic of a biome that was once more extensive, (2) environmentally mediated corridors facilitated emigration and (3) constant diversification is attributed to a spatially heterogeneous landscape that is perpetually dynamic through time.

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Aim: Vertebrate diversity in the Guineo-Congolian forests (GCF) of Africa is high, yet mechanisms responsible for generating that diversity remain remarkably understudied. These forests have alternatively been viewed as centres of diversification ("cradles") or more recently, as the opposite ("museums"). Here, we use a comparative dataset of avian and mammalian species to examine genetic diversification patterns across these forests and use these results to explain observed patterns in light of Plio-Pleistocene climatic change and life-history.Location: Africa. Methods:We analysed patterns of diversification across the GCF using a dataset composed of 629 and 1,048 mitochondrial sequences from 60 avian and 36 mammalian species, respectively. Uncorrected pairwise genetic distances were compared at three distinct geographical levels: west versus east of the Dahomey Gap, among the three major forest blocks, and among seven historical refugial areas. The timing of diversification was assessed for passerines, Rodentia, and Chiroptera. Results:We found substantial signatures of diversification in all three levels of our geographical comparisons. We recovered substantial disparity in the amount and depth of structure of diversification patterns between low dispersers (understorey birds and rodents) and more capable dispersers (other bird species and bats). Additionally, our chronogram recovered recent speciation and intraspecific diversification across songbird and mammalian lineages. Main conclusions:The discrete, and often deep, structuring of genetic diversification for both birds and mammals across the GCF revealed strong correlations between historic landscape fragmentation and dispersal ability. Our results revealed a striking amount of unrecognized genetic diversity, which may be suggestive of cryptic species.Given the rate at which these forests are being negatively impacted by human intervention, our general lack of knowledge concerning vertebrate diversity across these forests may very well impact our ability to identify evolutionary processes underlying diversity and enact meaningful conservation efforts in the future.

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Large Amazonian rivers impede dispersal for many species, but lowland river networks frequently rearrange, thereby altering the location and effectiveness of river barriers through time. These rearrangements may promote biotic diversification by facilitating episodic allopatry and secondary contact among populations. We sequenced genome-wide markers to evaluate the histories of divergence and introgression in six Amazonian avian species complexes. We first tested the assumption that rivers are barriers for these taxa and found that even relatively small rivers facilitate divergence. We then tested whether species diverged with gene flow and recovered reticulate histories for all species, including one potential case of hybrid speciation. Our results support the hypothesis that river rearrangements promote speciation and reveal that many rainforest taxa are micro-endemic, unrecognized, and thus threatened with imminent extinction. We propose that Amazonian hyper-diversity originates partly from fine-scale barrier displacement processes—including river dynamics—which allow small populations to differentiate and disperse into secondary contact.

Current generation high-throughput sequencing technology has facilitated the generation of more genomic-scale data than ever before, thus greatly improving our understanding of avian biology across a range of disciplines. Recent developments in linked-read sequencing (Chromium 10×) and reference-based whole-genome assembly offer an exciting prospect of more accessible chromosome-level genome sequencing in the near future. We sequenced and assembled a genome of the Hairy-crested Antbird (Rhegmatorhina melanosticta), which represents the first publicly available genome for any antbird (Thamnophilidae). Our objectives were to (1) assemble scaffolds to chromosome level based on multiple reference genomes, and report on differences relative to other genomes, (2) assess genome completeness and compare content to other related genomes, and (3) assess the suitability of linked-read sequencing technology for future studies in comparative phylogenomics and population genomics studies. Our R. melanosticta assembly was both highly contiguous (de novo scaffold N50 = 3.3 Mb, reference based N50 = 53.3 Mb) and relatively complete (contained close to 90% of evolutionarily conserved single-copy avian genes and known tetrapod ultraconserved elements). The high contiguity and completeness of this assembly enabled the genome to be successfully mapped to the chromosome level, which uncovered a consistent structural difference between R. melanosticta and other avian genomes. Our results are consistent with the observation that avian genomes are structurally conserved. Additionally, our results demonstrate the utility of linked-read sequencing for non-model genomics. Finally, we demonstrate the value of our R. melanosticta genome for future researchers by mapping reduced representation sequencing data, and by accurately reconstructing the phylogenetic relationships among a sample of thamnophilid species.