Aim Assess how local variations in bird taxon composition across lowland Amazonia are associated with environmental factors and rivers. Location Lowland Amazonia below 500 m a.s.l., South America. Time Period Contemporary. Major Taxa Studied Birds. Methods We constructed maps illustrating changes in bird taxon composition across lowland Amazonia and calculated Jaccard dissimilarity between adjacent localities. We then applied...

Humans have profoundly impacted the distribution of plant and animal species over thousands of years. The most direct example of these effects is human‐mediated movement of individuals, either through translocation of individuals within their range or through the introduction of species to new habitats. While human involvement may be suspected in species with obvious range disjunctions, it can be difficult to detect natural ve...

Aim Distribution maps for Amazonian birds are often limited to species‐level taxonomy even though many subspecies represent biological species. We provide digital maps depicting subspecies‐level distributions of Neotropical birds in the Amazonas River basin and adjoining areas. Location Amazon region, which includes the entire Amazon basin, the east slope of the tropical Andes, French Guiana, Suriname, Guyana, south Venezuela...

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 differi...

Aim Continental evolutionary radiations provide opportunities to understand how landscape evolution and biotic factors interact to generate species diversity. Additionally, understanding whether diversification dynamics differ between montane and lowland environments is a long‐standing question with few comparative analyses in the Neotropics. To address these questions, we investigated the biogeographical patterns and the evol...

Geographic range shifts can cause secondary contact and hybridization between closely related species, revealing mechanisms of species formation and integrity. These dynamics typically play out in restricted geographic regions, but highly vagile species may experience major distributional changes resulting in broad areas of contact. The Glossy Ibis ( Plegadis falcinellus ) is a dispersive waterbird of the Old World and Austral...

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 genus Rhegmatorhina at multiple taxonomic and temporal scales. Location Amazonia. Taxon Antbirds (Thamnophilidae). Methods We sequenced four mt DNA and nuclear gene regions of 120 individuals from 50 loca...

During the process of ecological speciation, reproductive isolation results from divergent natural selection and leads to a positive correlation between genetic divergence and adaptive phenotypic divergence, that is, isolation by adaptation ( IBA ). In natural populations, phenotypic differentiation is often autocorrelated with geographic distance, making IBA difficult to distinguish from the neutral expectation of isolation b...

Divergence in sexual signals may drive reproductive isolation between lineages, but behavioural barriers can weaken in contact zones. Here, we investigate the role of song as a behavioural and genetic barrier in a contact zone between two subspecies of white‐crowned sparrows ( Zonotrichia leucophrys ). We employed a reduced genomic data set to assess population structure and infer the history underlying divergence, gene flow a...

Aim To examine the effect of geographical barriers and habitat dynamics related to climatic oscillations on the phylogeography of a widespread passerine of Neotropical cloud forests, the spotted barbtail ( Premnoplex brunnescens ). Location Neotropical humid forests of montane areas in lower Central America and South America. Methods We sequenced two mitochondrial genes and one nuclear intron from specimens collected across th...

Aim To evaluate the role of historical processes in the evolution of Sclerurus leaftossers by integrating phylogenetic and phylogeographical approaches. Location Humid forests of the Neotropical region. Methods We reconstructed the evolutionary history of Sclerurus based on DNA sequences representing all species and 20 of the 26 recognized subspecies using one autosomal nuclear locus and three protein‐coding mitochondrial gene...

The negative effects of human‐induced habitat disturbance and modification on multiple dimensions of biological diversity are well chronicled ( Turner 1996 ; Harding et al. 1998 ; Lawton et al. 1998 ; Sakai et al. 2001 ). Among the more insidious consequences is secondary contact between formerly allopatric taxa ( Anderson & Hubricht 1938 ; Perry et al. 2002 ; Seehausen 2006 ). How the secondary contact will play out is unpred...

Hybrid zones are often characterized by narrow, coincident clines for diverse traits, suggesting that little introgression occurs across them. However, this pattern may result from a bias in focussing on traits that are diagnostic of parental populations. Such choice of highly differentiated traits may cause us to overlook differential introgression in nondiagnostic traits and to distort our perception of hybrid zones. We test...

Sex‐chromosomes are thought to play an important role in speciation, but few studies of non‐model organisms have investigated the relative influence of multiple sex‐linked markers on reproductive isolation. We collected 222 individuals along a geographical transect spanning the hybrid zone between Passerina amoena and P. cyanea (Aves: Cardinalidae). Using maximum‐likelihood cline fitting methods, we estimated locus‐specific in...

As modern genomic tools are developed for ecologically compelling models, field manipulation experiments will become important for establishing the role of functional genomic variation in physiological acclimation and evolutionary adaptation along environmental clines. High‐altitude habitats expose individuals to hypoxic and thermal stress, necessitating physiological acclimation, which may result in evolutionary adaptation. W...