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Geographic barriers are frequently invoked to explain genetic structuring across the landscape. However, inferences on the spatial and temporal origins of population variation have been largely limited to evolutionary neutral models, ignoring the potential role of natural selection and intrinsic genomic processes known as genomic architecture in producing heterogeneity in differentiation across the genome. To test how variation in genomic characteristics (e.g. recombination rate) impacts our ability to reconstruct general patterns of differentiation between species that cooccur across geographic barriers, we sequenced the whole genomes of multiple bird populations that are distributed across rivers in southeastern Amazonia. We found that phylogenetic relationships within species and demographic parameters varied across the genome in predictable ways. Genetic diversity was positively associated with recombination rate and negatively associated with species tree support. Gene flow was less pervasive in genomic regions of low recombination, making these windows more likely to retain patterns of population structuring that matched the species tree. We further found that approximately a third of the genome showed evidence of selective sweeps and linked selection, skewing genome-wide estimates of effective population sizes and gene flow between populations toward lower values. In sum, we showed that the effects of intrinsic genomic characteristics and selection can be disentangled from neutral processes to elucidate spatial patterns of population differentiation.

Rivers frequently delimit the geographic ranges of species in the Amazon Basin. These rivers also define the boundaries between genetic clusters within many species, yet river boundaries have been documented to break down in headwater regions where rivers are narrower. To explore the evolutionary implications of headwater contact zones in Amazonia, we examined genetic variation in the Blue-capped Manakin (Lepidothrix coronata), a species previously shown to contain several genetically and phenotypically distinct populations across the western Amazon Basin. We collected restriction site-associated DNA sequence data (RADcap) for 706 individuals and found that spatial patterns of genetic structure indicate several rivers, particularly the Amazon and Ucayali, are dispersal barriers for L. coronata. We also found evidence that genetic connectivity is elevated across several headwater regions, highlighting the importance of headwater gene flow for models of Amazonian diversification. The headwater region of the Ucayali River provided a notable exception to findings of headwater gene flow by harboring non-admixed populations of L. coronata on opposite sides of a < 1-km-wide river channel with a known dynamic history, suggesting that additional prezygotic barriers may be limiting gene flow in this region.

We reconstruct the species-level phylogenetic relationship among toucans, toucan-barbets, New World barbets using phylogenomic data to assess the monophyly and relationships at the family, generic, and specific levels. Our analyses confirmed (1) the monophyly of toucans (Aves: Ramphastidae), toucan-barbets (Aves: Semnornithidae), and New World barbets (Aves: Capitonidae) and that the toucan-barbets are sister to the toucans, an arrangement suggested, but poorly supported, in previously published phylogenies; (2) the paraphyly of lowland Selenidera toucanets with respect to Andigena mountain-toucans; and (3) evidence of some mitonuclear discordance, suggesting introgression or incomplete lineage sorting. For example, mitonuclear conflict in the phylogenetic placement of Ramphastos vitellinus subspecies suggests that Amazonian populations of Ramphastos vitellinus ariel may have introgressed mitogenomes derived from other Amazonian vitellinus taxa. To reconstruct the phylogenetic history of toucans, toucan-barbets, and New World barbets, we included all species-level taxa from the three families, with the addition of outgroups from the two major clades of Old World barbets (Megalaimidae and Lybiidae). We analyzed a combination of UCE sequences and whole mitochondrial genome sequences to reconstruct phylogenetic trees.

Understanding the factors that govern variation in genetic structure across species is key to the study of speciation and population genetics. Genetic structure has been linked to several aspects of life history, such as foraging strategy, habitat association, migration distance, and dispersal ability, all of which might influence dispersal and gene flow. Comparative studies of population genetic data from species with differing life histories provide opportunities to tease apart the role of dispersal in shaping gene flow and population genetic structure. Here, we examine population genetic data from sets of bird species specialized on a series of Amazonian habitat types hypothesized to filter for species with dramatically different dispersal abilities: stable upland forest, dynamic floodplain forest, and highly dynamic riverine islands. Using genome‐wide markers, we show that habitat type has a significant effect on population genetic structure, with species in upland forest, floodplain forest, and riverine islands exhibiting progressively lower levels of structure. Although morphological traits used as proxies for individual‐level dispersal ability did not explain this pattern, population genetic measures of gene flow are elevated in species from more dynamic riverine habitats. Our results suggest that the habitat in which a species occurs drives the degree of population genetic structuring via its impact on long‐term fluctuations in levels of gene flow, with species in highly dynamic habitats having particularly elevated gene flow. These differences in genetic variation across taxa specialized in distinct habitats may lead to disparate responses to environmental change or habitat‐specific diversification dynamics over evolutionary time scales.

We assessed population structure and the spatio‐temporal pattern of diversification in the Glossy AntshrikeSakesphorus luctuosus(Aves, Thamnophilidae) to understand the processes shaping the evolutionary history of Amazonian floodplains and address unresolved taxonomic controversies surrounding its species limits. By targeting ultraconserved elements (UCEs) from 32 specimens ofS.luctuosus, we identified independent lineages and estimated their differentiation, divergence times, and migration rates. We also estimated current and past demographic histories for each recovered lineage. We found evidence confirming thatS.luctuosusconsists of a single species, comprising at least four populations, with some highly admixed individuals and overall similar levels of migration between populations. We confirmed the differentiation of the Araguaia River basin population (S. l.araguayae) and gathered circumstantial evidence indicating that the taxonS.hagmannimay represent a highly introgressed population between three distinct phylogroups ofS.luctuosus. Divergences between populations occurred during the last 1.2 mya. Signs of population expansions were detected for populations attributed to subspeciesS. l.luctuosus, but not for theS. l.araguayaepopulation. Our results support thatS.luctuosushas had a complex population history, resulting from a high dependence on southeastern “clear water” seasonally flooded habitats and their availability through time. Spatial and demographic expansions toward the western “white water” flooded forests might be related to recent changes in connectivity and availability of these habitats. Our study reinforces the view that isolation due to absence of suitable habitat has been an important driver of population differentiation within Amazonian flooded forests, but also that differences betweenvárzeas(“white water” floodplains, mostly in southwestern Amazonia) andigapós(“clear water” floodplains, especially located in the east) should be further explored as drivers of micro‐evolution for terrestrial species.

A comprehensive molecular phylogeny of lowland antpittas in the generaHylopezusandMyrmotheraindicated thatHylopezus, as currently defined, is paraphyletic with respect toMyrmotheraandGrallaricula. Specifically, both species now placed inMyrmothera, Hylopezus dives,Hylopezus fulviventrisandHylopezus berlepschiform a strongly supported clade that is sister to a clade comprised byHylopezus perspicillatus,Hylopezus auricularis,Hylopezus ochroleucus,Hylopezus whittakeri,Hylopezus paraensis,Hylopezus macularius,andHylopezus dilutus. Furthermore,Hylopezus nattereriis sister to a clade glade groupingMyrmothera,Hylopezus, andGrallaricula, representing the most divergent lineage in this complex. Our approach to assess diagnosability and define generic boundaries among these taxa integrates phylogenetic relationships with morphological and acoustic traits. Given that phenotypic and ecological differences do not warrant mergingH. nattereriinto any other genus, and because there is no generic name available forH. nattereri, we describe herein a new genus for this Atlantic Forest endemic lineage,Cryptopezusgen. n. We also redefine generic limits inMyrmotheraandHylopezusto have a taxonomic classification concordant with their phylogenetic relationships.

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.