Genomic Architecture Predicts Tree Topology, Population Structuring, and Demographic History in Amazonian Birds.

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.

Implications of headwater contact zones for the riverine barrier hypothesis: a case study of the Blue-capped Manakin (Lepidothrix coronata).

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.

Amazonian birds in more dynamic habitats have less population genetic structure and higher gene flow.

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.

A compreensão dos fatores que governam a variação da estrutura genética entre as espécies é fundamental para o estudo da especiação e da genética das populações. A estrutura genética tem sido ligada a vários aspectos da história da vida, tais como estratégia de forrageio, associação ao habitat, distância de migração e capacidade de dispersão, os quais poderiam influenciar a dispersão e o fluxo gênico. Estudos comparativos usando espécies que diferem nas suas histórias de vida oferecem uma oportunidade para desvendar o papel da dispersão no estabelecimento do fluxo gênico e da estrutura genética da população. Aqui examinamos dados genéticos populacionais de diversas espécies de aves com diferentes capacidades de dispersão especializadas em três habitats amazônicos, incluindo florestas de terra-firme, florestas de várzea e ilhas fluviais, cujos ambientes ripários são altamente dinâmicos. Utilizando dados genômicos que incluem milhares de loci, mostramos que o tipo de habitat tem um efeito significativo na estruturação genética das populações; espécies de florestas de terra-firme, florestas de várzea e ilhas fluviais exibem níveis de estruturação progressivamente menores. Embora os traços morfológicos frequentemente usados como indicadores da capacidade de dispersão a nível individual não expliquem este padrão, as medidas genéticas populacionais de fluxo gênico são altas em espécies associadas a habitats ribeirinhos mais dinâmicos. Nossos resultados sugerem que o habitat no qual uma espécie é encontrada determina o grau de estruturação genética da população através de seu impacto nas flutuações de longo prazo do fluxo gênico, com espécies em habitats altamente dinâmicos tendo um fluxo gênico particularmente alto. As diferenças na variação genética dos táxons especializados em diferentes habitats podem resultar em respostas díspares às mesmas mudanças ambientais, ou dinâmicas de diversificação específicas a um determinado habitat ao longo de escalas de tempo evolutivas.

Comprender los factores que rigen la variación de la estructura genética entre especies es clave para el estudio de la especiación y la genética de poblaciones. La estructura genética se ha relacionado con varios aspectos de la historia vital, como la estrategia de búsqueda de alimento, la asociación de hábitats, la distancia de migración y la capacidad de dispersión, factores todos ellos que podrían influir en la dispersión y el flujo genético. Los estudios comparativos de datos genéticos poblacionales de especies con historias vitales diferentes ofrecen la oportunidad de desentrañar el papel de la dispersión en la conformación del flujo genético y la estructura genética poblacional. En este trabajo examinamos los datos genéticos de poblaciones de especies de aves especializadas en una serie de hábitats amazónicos que, según la hipótesis, filtran especies con capacidades de dispersión radicalmente diferentes: bosques estables de tierras altas, bosques dinámicos de llanuras aluviales e islas fluviales altamente dinámicas. Utilizando marcadores genómicos, demostramos que el tipo de hábitat tiene un efecto significativo en la estructura genética de la población, y que las especies de los bosques de tierras altas, los bosques inundables y las islas fluviales presentan niveles de estructura progresivamente más bajos. Aunque los rasgos morfológicos utilizados como indicadores de la capacidad de dispersión individual no explican este patrón, las medidas genéticas poblacionales del flujo genético son más elevadas en las especies de hábitats fluviales más dinámicos. Nuestros resultados sugieren que el hábitat en el que se encuentra una especie determina el grado de estructuración genética de la población a través de su impacto en las fluctuaciones a largo plazo de los niveles de flujo genético, siendo las especies de hábitats muy dinámicos las que presentan un flujo genético particularmente elevado. Estas diferencias en la variación genética entre taxones especializados en hábitats distintos pueden dar lugar a respuestas dispares al cambio ambiental o a dinámicas de diversificación específicas del hbitat a lo largo de escalas temporales evolutivas.

Late Pleistocene landscape changes and habitat specialization as promoters of population genomic divergence in Amazonian floodplain birds.

Although vicariant processes are expected to leave similar genomic signatures among codistributed taxa, ecological traits such as habitat and stratum can influence genetic divergence within species. Here, we combined landscape history and habitat specialization to understand the historical and ecological factors responsible for current levels of genetic divergence in three species of birds specialized in seasonally flooded habitats in muddy rivers and which are widespread in the Amazon basin but have isolated populations in the Rio Branco. Populations of the white-bellied spinetail (Mazaria propinqua), lesser wagtail-tyrant (Stigmatura napensis) and bicolored conebill (Conirostrum bicolor) are currently isolated in the Rio Branco by the black-waters of the lower Rio Negro, offering a unique opportunity to test the effect of river colour as a barrier to gene flow. We used ultraconserved elements (UCEs) to test alternative hypotheses of population history in a comparative phylogeographical approach by modelling genetic structure, demographic history and testing for shared divergence time among codistributed taxa. Our analyses revealed that (i) all three populations from the Rio Branco floodplains are genetically distinct from other populations along the Amazon River floodplains; (ii) these divergences are the result of at least two distinct events, consistent with species habitat specialization; and (iii) the most likely model of population evolution includes lower population connectivity during the Late Pleistocene transition (~250,000 years ago), with gene flow being completely disrupted after the Last Glacial Maximum (~21,000 years ago). Our findings highlight how landscape evolution modulates population connectivity in habitat specialist species and how organisms can have different responses to the same historical processes of environmental change, depending on their habitat affinity.

Quadros de ansiedade durante a pandemia: impactos no controle da diabetes mellitus 2 em mulheres jovens com sop e necessidade de revisão no manejo de atuação e inclusão de serviços de psicologia / Anxiety system during the pandemic: impacts on the control of diabetes mellitus 2 in young women with pcos and the need for review in action management and inclusion of psychology services / Sistema de ansiedad durante la pandemia: impactos en el control de la diabetes mellitus 2 en mujeres jóvenes con sop y la necesidad de revisión en la acción gestión e inclusión de los servicios de psicología

O Diabetes mellitus (DM) é uma doença crônica que apresentou um crescente aumento em sua prevalência, principalmente de DM II em mulheres com Síndrome do Ovário Policístico (SOP). Dentro deste parâmetro, o estudo verificou não só fatores de risco modificáveis ­ sobrepeso e sedentarismo, mas também fatores como a ansiedade, identificada principalmente durante a pandemia, a qual resultou em efeitos sobre a saúde mental dessas mulheres. Sendo assim, o objetivo do estudo é conhecer a influência da ansiedade no tratamento da DM II em jovens com SOP, durante a pandemia. A metodologia foi realizada em modelo de estudo observacional entre o período de junho de 2020 a outubro de 2021, via prontuários do INOVA-Secretaria Municipal de Joinville, onde foram qualificadas mulheres da Atenção Primária do Município de Joinville-SC portadoras de DM II e com idade igual ou inferior a 30 anos. Um total de 44 mulheres atendendo aos requisitos iniciais de inclusão. Como resultado, verificou-se a influência do Índice de Massa Corporal (IMC) sobre a glicemia pela mediada, tendo-se dois grupos (IMC>30 e IMC<30), sem se constatar diferença significativa. Entretanto, nas análises dos Grupos Ansiedade (GAN) e Não Ansiedade (GNAN), observou-se que o GAN concentra as participantes com glicemias mais elevadas. Portanto, conclui-se que, a ansiedade afeta condições que interferem no controle glicêmico (sistema endócrino, manejo comportamental), se tratando de uma condição a ser mais bem manejada na DM2, o que abre discussão para a reorganização da atenção à saúde mental na atenção primária à saúde nos pós pandemia.

Diabetes mellitus (DM) is a chronic disease that has shown an increasing increase in its prevalence, especially DM II in women with Polycystic Ovary Syndrome (PCOS). Within this parameter, the study verified not only modifiable risk factors ­ overweight and sedentary lifestyle, but also factors such as anxiety, identified mainly during the pandemic, which resulted in effects on the mental health of these women. Therefore, the objective of the study is to understand the influence of anxiety on the treatment of DM II in young people with PCOS, during the pandemic. The methodology was carried out in an observational study model between the period from June 2020 to October 2021, via medical records from INOVA-Joinville Municipal Secretariat, where women from Primary Care in the Municipality of Joinville-SC who had DM II and with aged 30 years or less. A total of 44 women met the initial inclusion requirements. As a result, the influence of the Body Mass Index (BMI) on glycemia was verified through mediation, with two groups (BMI>30 and BMI<30), without finding a significant difference. However, in the analyzes of the Anxiety (GAN) and Non-Anxiety (GNAN) Groups, it was observed that the GAN concentrates participants with higher blood glucose levels. Therefore, it is concluded that anxiety affects conditions that interfere with glycemic control (endocrine system, behavioral management), being a condition to be better managed in DM2, which opens discussion for the reorganization of mental health care in primary health care in the post-pandemic period.

La diabetes mellitus (DM) es una enfermedad crónica que ha mostrado un aumento creciente en su prevalencia, especialmente la DM II en mujeres con Síndrome de Ovario Poliquístico (SOP). Dentro de ese parámetro, el estudio verificó no sólo factores de riesgo modificables ­sobrepeso y sedentarismo­, sino también factores como la ansiedad, identificados principalmente durante la pandemia, que resultaron en efectos sobre la salud mental de estas mujeres. Por tanto, el objetivo del estudio es comprender la influencia de la ansiedad en el tratamiento de la DM II en jóvenes con SOP, durante la pandemia. La metodología se realizó en un modelo de estudio observacional entre el período de junio de 2020 a octubre de 2021, a través de historias clínicas de INOVA- Secretaría Municipal de Joinville, donde participaron mujeres de Atención Primaria del Municipio de Joinville-SC que tenían DM II y con 30 años. años o menos. Un total de 44 mujeres cumplieron con los requisitos de inclusión inicial. Como resultado, se verificó mediante mediación la influencia del Índice de Masa Corporal (IMC) sobre la glucemia, con dos grupos (IMC>30 e IMC<30), sin encontrar diferencia significativa. Sin embargo, en los análisis de los Grupos de Ansiedad (GAN) y No Ansiedad (GNAN), se observó que el GAN concentra a los participantes con niveles más altos de glucosa en sangre. Por lo tanto, se concluye que la ansiedad afecta condiciones que interfieren en el control glucémico (sistema endocrino, manejo conductual), siendo una condición a ser mejor manejada en la DM2, lo que abre discusión para la reorganización de la atención a la salud mental en la atención primaria de salud en el pos- período pandémico.

Gene flow, genomic homogenization and the timeline to speciation in Amazonian manakins.

Phylogeographical studies of the most species-rich region of the planet-the Amazon basin-have repeatedly uncovered genetically distinctive, allopatric lineages within currently named species, but understanding whether such lineages are reproductively isolated species is challenging. Here we harness the power of genome-wide data sets together with detailed phylogeographical sampling to both characterize the number of unique lineages and infer levels of reproductive isolation for three parapatric manakin species that make up the genus Pipra. The mitochondrial and nuclear genomes both support six distinctive lineages. The youngest lineages are now highly admixed with each other across major portions of their geographical ranges with one lineage now extinct in a genomically unadmixed state. In contrast, the oldest sets of lineages-dated to 1.4 million years-exhibit narrow hybrid zones. By fitting demographic models to parapatric lineage pairs we found that levels of gene flow and genomic homogenization decline with increasing evolutionary age. Only lineages descending from the basal node at 1.4 million years ago in the genus experience negligible gene flow, possess genomes resistant to homogenization and are separated by narrow hybrid zones. We conclude that a million years or more were required for Pipra manakins to become reproductively isolated. We suggest the six lineages be reclassified as two or three reproductively isolated species. Our unique approach to quantifying reproductive isolation in parapatric lineages could be applied broadly to other phylogeographical studies and would help determine species classification of the plethora of newly identified lineages in the Amazon basin and other regions.

River network rearrangements promote speciation in lowland Amazonian birds.

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.

Recent population differentiation in the habitat specialist Glossy Antshrike (Aves: Thamnophilidae) across Amazonian seasonally flooded forests.

We assessed population structure and the spatio-temporal pattern of diversification in the Glossy Antshrike Sakesphorus 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 of S. 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 that S. luctuosus consists 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 taxon S. hagmanni may represent a highly introgressed population between three distinct phylogroups of S. luctuosus. Divergences between populations occurred during the last 1.2 mya. Signs of population expansions were detected for populations attributed to subspecies S. l. luctuosus, but not for the S. l. araguayae population. Our results support that S. luctuosus has 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 between várzeas ("white water" floodplains, mostly in southwestern Amazonia) and igapós ("clear water" floodplains, especially located in the east) should be further explored as drivers of micro-evolution for terrestrial species.

Multiple species and deep genomic divergences despite little phenotypic differentiation in an ancient Neotropical songbird, Tunchiornis ochraceiceps (Sclater, 1860) (Aves: Vireonidae).

Several bird taxa have been recently described or elevated to full species and almost twice as many bird species than are currently recognized may exist. Defining species is one of the most basic and important issues in biological science because unknown or poorly defined species hamper subsequent studies. Here, we evaluate the species limits and evolutionary history of Tunchiornis ochraceiceps-a widespread forest songbird that occurs in the lowlands of Central America, Chocó and Amazonia-using an integrative approach that includes plumage coloration, morphometrics, vocalization and genomic data. The species has a relatively old crown age (~9 Ma) and comprises several lineages with little, if any, evidence of gene flow among them. We propose a taxonomic arrangement composed of four species, three with a plumage coloration diagnosis and one deeply divergent cryptic species. Most of the remaining lineages have variable but unfixed phenotypic characters despite their relatively old origin. This decoupling of genomic and phenotypic differentiation reveals a remarkable case of phenotypic conservatism, possibly due to strict habitat association. Lineages are geographically delimited by the main Amazonian rivers and the Andes, a pattern observed in studies of other understory upland forest Neotropical birds, although phylogenetic relationships and divergence times among populations are idiosyncratic.

Multi-character taxonomic review, systematics, and biogeography of the Black-capped/Tawny-bellied Screech Owl (emMegascops/em ematricapilla/em-emM. watsonii/em) complex (Aves: Strigidae).

Megascops is the most species-rich owl genus in the New World, with 21 species currently recognized. Phylogenetic relationships within this genus are notoriously difficult to establish due to the considerable plumage similarity among species and polymorphism within species. Previous studies have suggested that the widespread lowland Amazonian M. watsonii might include more than one species, and that the Atlantic Forest endemic M. atricapilla is closely related to the M. watsonii complex, but these relationships are as yet poorly understood. A recently published phylogeny of Megascops demonstrated that M. watsonii is paraphyletic with respect to M. atricapilla and that genetic divergences among some populations of M. watsonii are equal to or surpass the degree of differentiation between some M. watsonii and M. atricapilla. To shed light on the taxonomic status of these species and populations within them, we conducted a multi-character study based on molecular, morphological, and vocal characters. We sequenced three mitochondrial (cytb, CO1 and ND2) and three nuclear genes (BF5, CHD and MUSK) for 49 specimens, covering most of the geographic ranges of M. watsonii and M. atricapilla, and used these sequences to estimate phylogenies under alternative Bayesian, Maximum Likelihood, and multilocus coalescent species tree approaches. We studied 252 specimens and vocal parameters from 83 recordings belonging to 65 individuals, distributed throughout the ranges of M. watsonii and M. atricapilla. We used Discriminant Function Analysis (DFA) to analyze both morphometric and vocal data, and a pairwise diagnostic test to evaluate the significance of vocal differences between distinct genetic lineages. Phylogenetic analyses consistently recovered six statistically well-supported clades whose relationships are not entirely in agreement with currently recognized species limits in M. watsonii and M. atricapilla. Morphometric analyses did not detect significant differences among clades. High plumage variation among individuals within clades was usually associated with the presence of two or more color morphs. By contrast, vocal analyses detected significant differentiation among some clades but considerable overlap among others, with some lineages (particularly the most widespread one) exhibiting significant regional variation. The combined results allow for a redefinition of species limits in both M. watsonii and M. atricapilla, with the recognition of four additional species, two of which we describe here as new. We estimated most cladogenesis in the Megascops atricapilla-M. watsonii complex as having taken place during the Plio-Pleistocene, with the development of the modern Amazonian and São Francisco drainages and the expansion and retraction of forest biomes during interglacial and glacial periods as likely events accounting for this relatively recent burst of diversification.

Analysis of multiple chromosomal rearrangements in the genome of Willisornis vidua using BAC-FISH and chromosome painting on a supposed conserved karyotype.

BACKGROUND: Thamnophilidae birds are the result of a monophyletic radiation of insectivorous Passeriformes. They are a diverse group of 225 species and 45 genera and occur in lowlands and lower montane forests of Neotropics. Despite the large degree of diversity seen in this family, just four species of Thamnophilidae have been karyotyped with a diploid number ranging from 76 to 82 chromosomes. The karyotypic relationships within and between Thamnophilidae and another Passeriformes therefore remain poorly understood. Recent studies have identified the occurrence of intrachromosomal rearrangements in Passeriformes using in silico data and molecular cytogenetic tools. These results demonstrate that intrachromosomal rearrangements are more common in birds than previously thought and are likely to contribute to speciation events. With this in mind, we investigate the apparently conserved karyotype of Willisornis vidua, the Xingu Scale-backed Antbird, using a combination of molecular cytogenetic techniques including chromosome painting with probes derived from Gallus gallus (chicken) and Burhinus oedicnemus (stone curlew), combined with Bacterial Artificial Chromosome (BAC) probes derived from the same species. The goal was to investigate the occurrence of rearrangements in an apparently conserved karyotype in order to understand the evolutionary history and taxonomy of this species. In total, 78 BAC probes from the Gallus gallus and Taeniopygia guttata (the Zebra Finch) BAC libraries were tested, of which 40 were derived from Gallus gallus macrochromosomes 1-8, and 38 from microchromosomes 9-28. RESULTS: The karyotype is similar to typical Passeriformes karyotypes, with a diploid number of 2n = 80. Our chromosome painting results show that most of the Gallus gallus chromosomes are conserved, except GGA-1, 2 and 4, with some rearrangements identified among macro- and microchromosomes. BAC mapping revealed many intrachromosomal rearrangements, mainly inversions, when comparing Willisornis vidua karyotype with Gallus gallus, and corroborates the fissions revealed by chromosome painting. CONCLUSIONS: Willisornis vidua presents multiple chromosomal rearrangements despite having a supposed conservative karyotype, demonstrating that our approach using a combination of FISH tools provides a higher resolution than previously obtained by chromosome painting alone. We also show that populations of Willisornis vidua appear conserved from a cytogenetic perspective, despite significant phylogeographic structure.

Phylogenomics of manakins (Aves: Pipridae) using alternative locus filtering strategies based on informativeness.

Target capture sequencing effectively generates molecular marker arrays useful for molecular systematics. These extensive data sets are advantageous where previous studies using a few loci have failed to resolve relationships confidently. Moreover, target capture is well-suited to fragmented source DNA, allowing data collection from species that lack fresh tissues. Herein we use target capture to generate data for a phylogeny of the avian family Pipridae (manakins), a group that has been the subject of many behavioral and ecological studies. Most manakin species feature lek mating systems, where males exhibit complex behavioral displays including mechanical and vocal sounds, coordinated movements of multiple males, and high speed movements. We analyzed thousands of ultraconserved element (UCE) loci along with a smaller number of coding exons and their flanking regions from all but one species of Pipridae. We examined three different methods of phylogenetic estimation (concatenation and two multispecies coalescent methods). Phylogenetic inferences using UCE data yielded strongly supported estimates of phylogeny regardless of analytical method. Exon probes had limited capability to capture sequence data and resulted in phylogeny estimates with reduced support and modest topological differences relative to the UCE trees, although these conflicts had limited support. Two genera were paraphyletic among all analyses and data sets, with Antilophia nested within Chiroxiphia and Tyranneutes nested within Neopelma. The Chiroxiphia-Antilophia clade was an exception to the generally high support we observed; the topology of this clade differed among analyses, even those based on UCE data. To further explore relationships within this group, we employed two filtering strategies to remove low-information loci. Those analyses resulted in distinct topologies, suggesting that the relationships we identified within Chiroxiphia-Antilophia should be interpreted with caution. Despite the existence of a few continuing uncertainties, our analyses resulted in a robust phylogenetic hypothesis of the family Pipridae that provides a comparative framework for future ecomorphological and behavioral studies.

The evolution of a tropical biodiversity hotspot.

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.

Postzygotic isolation drives genomic speciation between highly cryptic Hypocnemis antbirds from Amazonia.

How species evolve reproductive isolation in the species-rich Amazon basin is poorly understood in vertebrates. Here, we sequenced a reference genome and used a genome-wide sample of SNPs to analyze a hybrid zone between two highly cryptic species of Hypocnemis warbling-antbirds-the Rondonia warbling-antbird (H. ochrogyna) and Spix's warbling-antbird (H. striata)-in a headwater region of southern Amazonia. We found that both species commonly hybridize, producing F1 s and a variety of backcrosses with each species but we detected only one F2 -like hybrid. Patterns of heterozygosity, hybrid index, and interchromosomal linkage disequilibrium in hybrid populations closely match expectations under strong postzygotic isolation. Hybrid zone width (15.4 km) was much narrower than expected (211 km) indicating strong selection against hybrids. A remarkably high degree of concordance in cline centers and widths across loci, and a lack of reduced interspecific Fst between populations close to versus far from the contact zone, suggest that genetic incompatibilities have rendered most of the genome immune to introgression. These results support intrinsic postzygotic isolation as a driver of speciation in a moderately young cryptic species pair from the Amazon and suggest that species richness of the Amazon may be grossly underestimated.

Quaternary climate changes as speciation drivers in the Amazon floodplains.

The role of climate as a speciation driver in the Amazon has long been discussed. Phylogeographic studies have failed to recover synchronous demographic responses across taxa, although recent evidence supports the interaction between rivers and climate in promoting speciation. Most studies, however, are biased toward upland forest organisms, while other habitats are poorly explored and could hold valuable information about major historical processes. We conducted a comparative phylogenomic analysis of floodplain forest birds to explore the effects of historical environmental changes and current connectivity on population differentiation. Our findings support a similar demographic history among species complexes, indicating that the central portion of the Amazon River basin is a suture zone for taxa isolated across the main Amazonian sub-basins. Our results also suggest that changes in the fluvial landscape induced by climate variation during the Mid- and Late Pleistocene drove population isolation, leading to diversification with subsequent secondary contact.

Phylogenomics and biogeography of the world's thrushes (Aves, Turdus): new evidence for a more parsimonious evolutionary history.

To elucidate the relationships and spatial range evolution across the world of the bird genus Turdus (Aves), we produced a large genomic dataset comprising ca 2 million nucleotides for ca 100 samples representing 53 species, including over 2000 loci. We estimated time-calibrated maximum-likelihood and multispecies coalescent phylogenies and carried out biogeographic analyses. Our results indicate that there have been considerably fewer trans-oceanic dispersals within the genus Turdus than previously suggested, such that the Palaearctic clade did not originate in America and the African clade was not involved in the colonization of the Americas. Instead, our findings suggest that dispersal from the Western Palaearctic via the Antilles to the Neotropics might have occurred in a single event, giving rise to the rich Neotropical diversity of Turdus observed today, with no reverse dispersals to the Palaearctic or Africa. Our large multilocus dataset, combined with dense species-level sampling and analysed under probabilistic methods, brings important insights into historical biogeography and systematics, even in a scenario of fast and spatially complex diversification.

Genomic data reveal a protracted window of introgression during the diversification of a neotropical woodcreeper radiation.

The incidence of introgression during the diversification process and the timespan following divergence when introgression is possible are poorly understood in the neotropics where high species richness could provide extensive opportunities for genetic exchange. We used thousands of genome-wide SNPs to infer phylogenetic relationships, calculate ages of splitting, and to estimate the timing of introgression in a widespread avian neotropical genus of woodcreepers. Five distinct introgression events were reconstructed involving taxa classified both as subspecies and species including lineages descending from the basal-most split, dated to 7.3 million years ago. Introgression occurred between just a few hundred thousand to about 2.5 million years following divergence, suggesting substantial portions of the genome are capable of introgressing across taxa boundaries during a protracted time window of a few million years following divergence. Despite this protracted time window, we found that the proportion of the genome introgressing (6-11%) declines with the time of introgression following divergence, suggesting that the genome becomes progressively more immune to introgression as reproductive isolation increases.

Diversity and evolution of Amazonian birds: implications for conservation and biogeography.

Amazonia has been a focus of interest since the early days of biogeography as an intrinsically complex and extremely diverse region. This region comprises an intricate mosaic that includes diverse types of forest formations, flooded environments and open vegetation. Increased knowledge about the distribution of species in Amazonia has led to the recognition of complex biogeographic patterns. The confrontation of these biogeographic patterns with information on the geological and climatic history of the region has generated several hypotheses dedicated to explain the origin of the biological diversity. Genomic information, coupled with knowledge of Earth's history, especially the evolution of the Amazonian landscape, presents fascinating possibilities for understanding the mechanisms that govern the origin and maintenance of diversity patterns in one of the most diverse regions of the world. For this we will increasingly need more intense and coordinated interactions between researchers studying biotic diversification and the evolution of landscapes. From the interaction between these two fields of knowledge that are in full development, an increasingly detailed understanding of the historical mechanisms related to the origin of the species will surely arise.

Diversification history in the Dendrocincla fuliginosa complex (Aves: Dendrocolaptidae): Insights from broad geographic sampling.

Dendrocincla woodcreepers are ant-following birds widespread throughout tropical America. Species in the genus are widely distributed and show little phenotypic variation. Notwithstanding, several subspecies have been described, but the validity of some of these taxa and the boundaries among them have been discussed for decades. Recent genetic evidence based on limited sampling has pointed to the paraphyly of D. fuliginosa, showing that its subspecies constitute a complex that also includes D. anabatina and D. turdina. In this study we sequenced nuclear and mitochondrial markers for over two hundred individuals belonging to the D. fuliginosa complex to recover phylogenetic relationships, describe intraspecific genetic diversity and provide historical biogeographic scenarios of diversification. Our results corroborate the paraphyly of D. fuliginosa, with D. turdina and D. anabatina nested within its recognized subspecies. Recovered genetic lineages roughly match the distributions of described subspecies and congruence among phylogenetic structure, phenotypic diagnosis and distribution limits were used to discuss current systematics and taxonomy within the complex, with special attention to Northern South America. Our data suggest the origin of the complex in western Amazonia, associated with the establishment of upland forests in the area during the early Pliocene. Paleoclimatic cycles and river rearrangements during the Pleistocene could have, at different times, both facilitated dispersal across large Amazonian rivers and the Andes and isolated populations, likely playing an important role in differentiation of extant species. Previously described hybridization in the headwaters of the Tapajós river represents a secondary contact of non-sister lineages that cannot be used to test the role of the river as primary source of diversification. Based on comparisons of D. fuliginosa with closely related understory upland forest taxa, we suggest that differential habitat use could influence diversification processes in a historically changing landscape, and should be considered for proposing general mechanisms of diversification.

A dynamic continental moisture gradient drove Amazonian bird diversification.

The Amazon is the primary source of Neotropical diversity and a nexus for discussions on processes that drive biotic diversification. Biogeographers have focused on the roles of rivers and Pleistocene climate change in explaining high rates of speciation. We combine phylogeographic and niche-based paleodistributional projections for 23 upland terra firme forest bird lineages from across the Amazon to derive a new model of regional biological diversification. We found that climate-driven refugial dynamics interact with dynamic riverine barriers to produce a dominant pattern: Older lineages in the wetter western and northern parts of the Amazon gave rise to lineages in the drier southern and eastern parts. This climate/drainage basin evolution interaction links landscape dynamics with biotic diversification and explains the east-west diversity gradients across the Amazon.