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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 versus human‐mediated dispersal events for populations at the edge of a species' range, and this uncertainty muddles how we understand the evolutionary history of populations and broad biogeographical patterns. Studies combining genetic data with archaeological, linguistic and historical evidence have confirmed prehistoric examples of human‐mediated dispersal; however, it is unclear whether these methods can disentangle recent dispersal events, such as species translocated by European colonizers during the past 500 years. We use genomic DNA from historical museum specimens and historical records to evaluate three hypotheses regarding the timing and origin of Northern Bobwhites (Colinus virginianus) in Cuba, whose status as an endemic or introduced population has long been debated. We discovered that bobwhites from southern Mexico arrived in Cuba between the 12th and 16th centuries, followed by the subsequent introduction of bobwhites from the southeastern USA to Cuba between the 18th and 20th centuries. These dates suggest the introduction of bobwhites to Cuba was human‐mediated and concomitant with Spanish colonial shipping routes between Veracruz, Mexico and Havana, Cuba during this period. Our results identify endemic Cuban bobwhites as a genetically distinct population born of hybridization between divergent, introduced lineages. see also the Perspective by Silu Wang [ABSTRACT FROM AUTHOR]

Extinction is a dominant force shaping patterns of biodiversity through time; however its role as a catalyst of speciation through its interaction with intraspecific variation has been overlooked. Here, we synthesize ideas alluded to by Darwin and others into the model of "speciation-by-extinction" in which speciation results from the extinction of intermediate populations within a single geographically variable species. We explore the properties and distinguishing features of speciation-by-extinction with respect to other established speciation models. We demonstrate its plausibility by showing that the experimental extinction of populations within variable species can result in speciation. The prerequisites for speciation-by-extinction, geographically structured intraspecific variation and local extinction, are ubiquitous in nature. We propose that speciation-by-extinction may be a prevalent, but underappreciated, speciation mechanism. [ABSTRACT FROM AUTHOR]

Black-throated Flowerpiercers (Diglossa brunneiventris) are one species representing a phenotypically specialized group of tanagers (Thraupidae) that have hooked bills which allow them to feed by stealing nectar from the base of flowers. Members of the genus are widely distributed in montane regions from Mexico to northern Argentina, and previous studies of Diglossa have focused on their systematics, phylogenetics, and interesting natural history. Despite numerous studies of species within the genus, no genome assembly exists to represent these nectivorous tanagers. We described the assembly of a genome sequence representing a museum-vouchered, wild, female D. brunneiventris collected in Peru. By combining Pacific Biosciences Sequel long-read technology with 10x linked-read and referencebased scaffolding, we produced a 1.08 Gbp pseudochromosomal assembly including 600 scaffolds with a scaffold N50 of 67.3 Mbp, a scaffold L50 of 6, and a BUSCO completeness score of 95%. This new assembly improves representation of the diverse species that comprise the tanagers, improves on scaffold lengths and contiguity when compared to existing genomic resources for tanagers, and provides another avenue of research into the genetic basis of adaptations common to a nectivorous lifestyle among vertebrates. [ABSTRACT FROM AUTHOR]

Intraspecific geographic phenotypic variation is a crucial theme in evolutionary biology. Comparing its magnitude across species can provide insights into its ecological and genetic correlates. Here, we developed an index, which we dub the V index, to quantify intraspecific plumage colour variation in typical antbirds (Thamnophilidae), a family which has long interested ornithologists due to a high prevalence of intraspecific variation. The V index is based on a bivariate colour space defined by brightness and redness. Its value for each species equals the mean area occupied by each of its subspecies in that colour space, divided by the area of the species. Lower values indicate greater intraspecific geographic variation. Based on this index, Thamnophilus caerulescens (Variable Antshrike) was exceptionally geographically variable compared to other thamnophilids, as previously suggested based on qualitative evidence. In general, we found that the most variable species had disjunct distributions and deep phylogeographic structure, suggesting an effect of historical population dynamics in producing geographic variation. The V index can be adapted for use with other taxa, traits, and taxonomic levels, and we expect it will instigate novel ways of thinking about phenotypic variation in birds and other animals. [ABSTRACT FROM AUTHOR]

Both natural and sexual selection are thought to affect the evolution of bird color. Most studies of the topic have focused on sexually dichromatic taxa and showy plumages, which are expected to be more influenced by social selection and usually result in increased conspicuousness. However, many bird clades display dull brown or gray plumages that vary greatly in brightness (lightness), but little in hue (shade). Here, we examine the macroevolution of brightness in one such clade, the Furnariida. We make comparisons across light environments, body parts, monochromatic lineages, and each sex of dichromatic lineages. We found that support for models including light environments is greater for the dorsum than for the venter, and that brightness evolution is more constrained in the former than in the latter. Plumages in this clade have evolved to be darker in darker habitats, consistent with natural selection for increased crypsis. Finally, the features of brightness macroevolution are broadly similar across the sexes of the dichromatic clade, challenging the view that sexual dichromatism is driven by different evolutionary processes acting in each sex. We conclude that, in the Furnariida, light environments and dorsal–ventral variation are more important than sex as axes of color evolution. [ABSTRACT FROM AUTHOR]

The article offers information on study according to which species turnover across the Rio Negro basin, Brazil encompasses a mixture of histories, supporting a dual role for Amazonian rivers in the generation and maintenance of biological diversity. It mentions that phylogenies can provide information concerning the potential role of geographic barriers as vicariant forces and offer clues regarding the primary or secondary nature of riverine barriers.

Abstract: 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 by distance (IBD). We examined these two alternatives in a dramatic case of clinal phenotypic variation in an Andean songbird, the Line‐cheeked Spinetail (Cranioleuca antisiensis). At its geographic extremes, this species shows a near threefold difference in body mass (11.5 to 31.0 g) with marked plumage differences. We analysed phenotypic, environmental and genetic data (5,154 SNPs) from 172 individuals and 19 populations sampled along its linear distribution in the Andes. We found that body mass was tightly correlated with environmental temperature, consistent with local adaptation as per Bergmann's rule. Using a PST–FST analysis, we found additional support for natural selection driving body mass differentiation, but these results could also be explained by environment‐mediated phenotypic plasticity. When we assessed the relative support for patterns of IBA and IBD using variance partitioning, we found that IBD was the best explanation for genetic differentiation along the cline. Adaptive phenotypic or environmental divergence can reduce gene flow, a pattern interpreted as evidence of ecological speciation's role in diversification. Our results provide a counterexample to this interpretation. Despite conditions conducive to ecological speciation, our results suggest that dramatic size and environmental differentiation within C. antisiensis are not limiting gene flow. [ABSTRACT FROM AUTHOR]

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 (Bolivar and Amazonas departments), parts of the Brazilian Cerrado and the Araguaia‐Tocantins basin. Taxon: Birds (Class Aves). Methods: To build the distribution maps, we compiled a point‐locality database of 620,000 records, 90% of which represent specimens vouchered in research collections. After manually cleaning and optimising the quality of the point localities, we generated extent‐of‐occurrence polygons at the subspecies level using a concave hull function. We corrected each polygon based on the literature and expert knowledge. We used this data set to define zoogeographical regions based on multidimensional scaling and clustering analyses, and then compared subspecies‐defined regions to zoogeographic regions inferred from species‐level data. Results: We inferred range polygons for 3990 subspecies, representing 2043 species from 65 families. The average distribution size was 955,739 km2, with half of the taxa having range sizes smaller than 230,484 km2 (median value) and nearly one‐quarter of all subspecies having ranges smaller than 50,000 km2. We identified 10 zoogeographical regions from the subspecies data set in comparison with four areas based on a species‐level analysis of the same data. The 10 zoogeographical regions are largely congruent with previously identified areas of endemism. Main Conclusions: The new maps of Amazonian bird subspecies distributions allow biodiversity studies (e.g. macroecology, evolution, and conservation) to be conducted at the subspecies level, and facilitate biogeographic, ecological, evolutionary and conservation research on birds in the most biologically diverse region in the world. [ABSTRACT FROM AUTHOR]

The demographic and phylogeographic histories of species provide insight into the processes responsible for generating biological diversity, and genomic datasets are now permitting the estimation of species histories with unprecedented accuracy. We used a genomic single nucleotide polymorphism (SNP) dataset generated using a RAD-Seq method to investigate the historical demography and phylogeography of a widespread lowland Neotropical bird ( Xenops minutus ). As expected, we found that prominent landscape features that act as dispersal barriers, such as Amazonian rivers and the Andes Mountains, are associated with the deepest phylogeographic breaks, and also that isolation by distance is limited in areas between these barriers. In addition, we inferred positive population growth for most populations and detected evidence of historical gene flow between populations that are now physically isolated. Although we were able to reconstruct the history of Xenops minutus with unprecedented resolution, we had difficulty conclusively relating this history to the landscape events implicated in many Neotropical diversification hypotheses. We suggest that even if many traditional diversification hypotheses remain untestable, investigations using genomic datasets will provide greater resolution of species histories in the Neotropics and elsewhere. [ABSTRACT FROM AUTHOR]

The article provides an overview of the challenges that avian diversification research on the lowland humid Neotropics are facing. It cites several diversification studies of Neotropical birds that focused on their attention on attempts to disentangle the relative effects of various landscape features. A discussion on the shift of a research in Neotropical biogeography toward statistical inference is discussed. An insight on studies of the family Furnariidae is provided.

Second-generation sequencing is increasingly being used in combination with genome-enrichment techniques to amplify a large number of loci in many individuals for the purpose of population genetic and phylogeographic analysis. Compiling all the necessary tools to analyse these data is complex and time-consuming. Here, we assemble a set of programs and pipe them together with Perl, enabling research laboratories without a dedicated bioinformatician to utilize second-generation sequencing. User input is a folder of the second-generation sequencing reads sorted by individual (in FASTA format) and pipeline output is a folder of multi-FASTA files that correspond to loci (with 2 alleles called per individual). Additional output includes a summary file of the number of individuals per locus, observed and expected heterozygosity for each locus, distribution of multiple hits and summary statistics (θ, Tajima's D, etc.). This user-friendly, open source pipeline, which requires no a priori reference genome because it constructs its own, allows the user to set various parameters (e.g. minimum coverage) in the dependent programs (CAP BWA SAM and VS) and facilitates evaluation of the nature and quality of data collected prior to analysis in software packages. [ABSTRACT FROM AUTHOR]

The negative effects of human-induced habitat disturbance and modification on multiple dimensions of biological diversity are well chronicled (; ; ; ). Among the more insidious consequences is secondary contact between formerly allopatric taxa (; ; ). How the secondary contact will play out is unpredictable (), but if the taxa are not fully reproductively isolated, hybridization is likely, and if the resulting progeny are fertile, the eventual outcome is often devastating from a conservation perspective (; ; ). In this issue of Molecular Ecology, present an analysis of hybridization between two avian species, one of which is critically endangered and the other of which is invasive. Their discovery that the endangered species has not yet been hybridized to extinction is promising and not what one would necessarily expect from theory. [ABSTRACT FROM AUTHOR]

Despite the theoretical link between the ecology and the population genetics of species, little empirical evidence is available that corroborates the association. Here, we examined genetic variation in 40 codistributed species of lowland Neotropical rain forest birds that have populations isolated on either side of the Andes, the Amazon River, and the Madeira River. We found widely varying levels of genetic divergence among these taxa across the same biogeographic barriers. Our investigation of the extent to which ecological traits predicted the amount of cross-barrier divergence revealed a strongly significant relationship between the forest stratum at which a species forages and the level of cross-barrier genetic differentiation. Canopy species had statistically lower genetic divergence values across the Andes and the two Amazonian rivers than did understory birds. We hypothesize that the association reflects an effect of dispersal propensity, which is greater in canopy birds, on the movement of alleles among demes (i.e., migration) and, consequently, on the interdemic proportion of the genetic variance. Differences in dispersal propensity may also explain the observation that understory species contain a significantly greater number of subspecies than do canopy species. This result indicates that higher rates of diversification may occur in lineages with lower dispersal propensity. [ABSTRACT FROM AUTHOR]

Variable selection pressures across heterogeneous landscapes can lead to local adaptation of populations. The extent of local adaptation depends on the interplay between natural selection and gene flow, but the nature of this relationship is complex. Gene flow can constrain local adaptation by eroding differentiation driven by natural selection, or local adaptation can itself constrain gene flow through selection against maladapted immigrants. Here we test for evidence that natural selection constrains gene flow among populations of a widespread passerine bird ( Zonotrichia capensis) that are distributed along an elevational gradient in the Peruvian Andes. Using multilocus sequences and microsatellites screened in 142 individuals collected along a series of replicate transects, we found that mitochondrial gene flow was significantly reduced along elevational transects relative to latitudinal control transects. Nuclear gene flow, however, was not similarly reduced. Clines in mitochondrial haplotype frequency were strongly associated with transitions in environmental variables along the elevational transects, but this association was not observed for the nuclear markers. These results suggest that natural selection constrains mitochondrial gene flow along elevational gradients and that the mitonuclear discrepancy may be due to local adaptation of mitochondrial haplotypes. [ABSTRACT FROM AUTHOR]

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 introgression rates for 10 z-linked markers. Although the cline width estimates ranged from 2.8 to 584 km, eight of 10 loci had cline widths between 224 and 271 km. We also used coalescent-based estimates of locus-specific divergence times between P. amoena and P. cyanea to test a recently proposed hypothesis of an inverse relationship between divergence time and cline width but did not find a significant association. The narrow width (2.8 km) of the cline estimated from the VLDLR9 locus indicates strong selection retarding introgression of alleles at this locus across the hybrid zone. Interestingly, a mutation in the very low density lipoprotein receptor ( VLDLR) gene, in which VLDLR9 is an intron, is known to reduce the egg-laying ability of some chickens, suggesting a possible link between this gene region and reproductive isolation between P. amoena and P. cyanea. These results underscore the importance of sampling multiple loci to investigate introgression patterns across a chromosome or genome and support previous findings of the importance of sex-linked genes in speciation. [ABSTRACT FROM AUTHOR]

Using cline fitting and divergence population genetics, we tested a prediction of Haldane's rule: autosomal alleles should introgress more than z-linked alleles or mitochondrial haplotypes across the Passerina amoena/ Passerina cyanea (Aves: Cardinalidae) hybrid zone. We screened 222 individuals collected along a transect in the Great Plains of North America that spans the contact zone for mitochondrial (two genes), autosomal (four loci) and z-linked (two loci) markers. Maximum-likelihood cline widths estimated from the mitochondrial (223 km) and z-linked (309 km) datasets were significantly narrower on average than the autosomal cline widths (466 km). We also found that mean coalescent-based estimates of introgression were larger for the autosomal loci (0.63 genes/generation, scaled to the mutation rate μ) than for both the mitochondrial (0.27) and z-linked loci (0.59). These patterns are consistent with Haldane's rule, but the among-locus variation also suggests many independently segregating loci are required to investigate introgression patterns across the genome. These results provide the first comprehensive comparison of mitochondrial, sex-linked, and autosomal loci across an avian hybrid zone and add to the body of evidence suggesting that sex chromosomes play an important role in the formation and maintenance of reproductive isolation between closely related species. [ABSTRACT FROM AUTHOR]

Although the power of multi-locus data in estimating species trees is apparent, it is also clear that the analytical methodologies for doing so are still maturing. For example, of the methods currently available for estimating species trees from multiocus data, the Bayesian method introduced by Liu and Pearl (2007; BEST) is the only one that provides nodal support values. Using gene sequences from five nuclear loci, we explored two analytical methods (deep coalescence and BEST) to reconstruct the species tree of the five primary Manacus OTUs: M. aurantiacus, M. candei, M. vitellinus, populations of M. manacus from west of the Andes (M. manacus (w)), and populations of M. manacus from east of the Andes (M. manacus (e)). Both BEST and deep coalescence supported a sister relationship between M. vitellinus and M. manacus (w). A lower probability tree from the BEST analysis and one of the most parsimonious deep coalescence trees also supported a sister relationship between M. candei and M. aurantiacus. Because hybrid zones connect the distributions of most Manacus species, we examined the potential influence of post-divergence gene flow on the sister relationship of parapatrically distributed M. vitellinus and M. manacus (w). An isolation-with-migration (IM) analysis found relatively high levels of gene flow between M. vitellinus and M. manacus (w). Whether the gene flow is obscuring a true sister relationship between M. manacus (w) and M. manacus (e) remained unclear, pointing to the need for more detailed models accommodating multispecies, multilocus DNA sequence data. [ABSTRACT FROM AUTHOR]

Phylogenetic and population genetic analyses of DNA sequence data from 10 nuclear loci were used to test species divergence hypotheses within Passerina buntings, with special focus on a strongly supported, but controversial, sister relationship between Passerina amoena and P caerulea inferred from a previous mitochondrial study. Here, a maximum-likelihood analysis of a concatenated 10-locus data set, as well as minimize-deep-coalescences and maximum-likelihood analyses of the locus-specific gene trees, recovered the traditional sister relationship between P. amoena and P. cyanea. In addition, a more recent divergence time estimate between P. amoena and P. cyanea than between P. amoena and P. caerulea provided evidence for the traditional sister relationship. These results provide a compelling example of how lineage sorting stochasticity can lead to incongruence between gene trees and species trees, and illustrate how phylogenetic and population genetic analyses can be integrated to investigate evolutionary relationships between recently diverged taxa. [ABSTRACT FROM AUTHOR]

Abstract: One of the most novel foraging strategies in Neotropical birds is army-ant-following, in which birds prey upon arthropods and small vertebrates flushed from the forest floor by swarm raids of the army-ant Eciton burchellii. This specialization is most developed in the typical antbirds (Thamnophilidae) which are divisible into three specialization categories: (1) those that forage at swarms opportunistically as army-ants move through their territories (occasional followers), (2) those that follow swarms beyond their territories but also forage independently of swarms (regular followers), and (3) those that appear incapable of foraging independently of swarms (obligate followers). Although army-ant-following is one of the great spectacles of tropical forests, basic questions about its evolution remain unaddressed. Using a strongly resolved molecular phylogeny of the typical antbirds, we found that army-ant-following is phylogenetically conserved, with regular following having evolved only three times, and that the most likely evolutionary progression was from least (occasional) to more (regular) to most (obligate) specialized, with no reversals from the obligate state. Despite the dependence of the specialists on a single ant species, molecular dating indicates that army-ant-following has persisted in antbirds since the late Miocene. These results provide the first characterization of army-ant-following as an ancient and phylogenetically conserved specialization. [Copyright &y& Elsevier]

The Andean uplift played important roles in the historical diversification of Neotropical organisms, both by producing new high-elevation habitats that could be colonized and by isolating organisms on either side of the mountains. Here, we present a molecular phylogeny of Thamnophlius antshrikes, a clade of 30 species whose collective distribution spans nearly the entirety of lowland habitats in tropical South America, the eastern slope foothills of the Andes, and the tepuis of northern South America. Our goal was to examine the role of the Andes in the diversification of lowland and foothill species. Using parsimony and Bayesian ancestral state reconstructions of a three-state distribution character (lowland-restricted, lowland-to-highland, highland-restricted), we found that the Andes were colonized twice independently and the tepuis once from lowland-restricted ancestors. Over the entire evolutionary history of Thamnophilus, the highest transition rates were between highland-restricted and lowland-to-highland distributions, with extremely low rates into and out of lowland-restricted distributions. This pattern suggests lowland-restricted distributions are limited not by physiological constraints, but by other forces, such as competition. These results highlight the need for additional comparative studies in elucidating processes associated with the colonization of high-elevation habitats and the differentiation of populations within them. [ABSTRACT FROM AUTHOR]

The Variable Antshrike (Thamnophilus caerulescens) is arguably the most polytypic thamnophilid, with males ranging from almost entirely jet black to nearly white. The four subspecies that occur in Bolivia are strikingly divergent in male plumage: T. c. aspersiventer (black with white-barred belly), T. c. connectens (black back and bib with white belly), T. c. dinellii (gray throat and back with rufous belly), and T. c. paraguayensis (light gray with white belly). To assess the genetic structure of those taxa in Bolivia, sequence variation at the mitochondrial cytochrome-b gene was screened in 126 individuals collected across transects spanning the plumage and vocal variation in the four forms. A 95-km-wide cline in haplotype frequencies from T. c. aspersiventer to T. c. dinellii was centered in the Serrania Cochabamba across an ecotone from humid to dry Andean foothill habitats, Thamnophilus caerulescens connectens is not a valid taxon, instead representing an introgressed population near the dinellii tail of the T. c. aspersiventer-T. c. dinellii hybrid zone. Although direct contact between T. c. dinellii and T. c. paraguayensis remains undocumented, the mitochondrial data were consistent with introgression along a broad cline extending across most of southern Bolivia. Overall, the transitions in mitochondrial frequencies were remarkably concordant with clinal changes in vocalizations among those same populations (Isler et al. 2005). Both studies highlight the need for increased sampling, in both the geographic extent and number of individuals per population, to address adequately the potential for clinal variation between populations that are not isolated geographically. A more restricted sampling design in the present study might have led to the erroneous conclusion that T. c. aspersiventer, T. c. dinellii, and T. c. paraguayensis have reciprocally monphyletic mitochondrial lineages, making them full species according to some species concepts. [ABSTRACT FROM AUTHOR]

Single nucleotide polymorphisms (SNPs) represent the most widespread type of sequence variation in genomes, yet they have only emerged recently as valuable genetic markers for revealing the evolutionary history of populations. Their occurrence throughout the genome also makes them ideal for analyses of speciation and historical demography, especially in light of recent theory suggesting that many unlinked nuclear loci are needed to estimate population genetic parameters with statistical confidence. In spite of having lower variation compared with microsatellites, SNPs should make the comparison of genomic diversities and histories of different species (the core goal of comparative biogeography) more straightforward than has been possible with microsatellites. The most pervasive, but correctable, complication to SNP analysis is a bias towards analyzing only the most variable loci, an artifact that is usually introduced by the limited number of individuals used to screen initially for polymorphisms. Although the use of SNPs as markers in population studies is still new, innovative methods for SNP identification, automated screening, haplotype inference and statistical analysis might quickly make SNPs the marker of choice. [Copyright &y& Elsevier]

Considers a method of approximating Weir and Cockerham's θ, an unbiased estimator of genetic population structure. Discussion of variation among species and patterns among different groups of organisms or within life zones; Factors that led to the creation of θ Role of estimation algorithm in model population and real world avian population; Effect of θ bias removing power on empirical datasets.

Presents information on a study which examined genetic and morphology of the hybrid zone in western Panama between white-collared Manacus candei and golden-collared manakins, Manacus vitellinus. Materials and methods; Results and discussion.

Contends that male plumage color in the genus Manacus is an unreliable taxonomic marker. Allospecies of manakins that are readily identifiable by differences in the color of the definitive male throat and belly plumage; Hybrid zones of Manacus; Distribution pattern of manakins; Evolution of male secondary characteristics.

Studies the historical diversification of birds in northwestern South America. Areas of endemism in South America; Estimation of phylogenetic relationships among endemic Choco, Central American and Amazonian forms in 14 species groups of birds from eight families; Role of vicariant mechanisms such as the Forest Refugia hypothesis and the Andean uplift.

Examines the geographic variation of morphometric and plumage characters in bird populations treated as a single species, the Sepia-brown Wren of the Andes mountains. Patterns of variation; Identification of the recognized sub-species of Cinnycerthia peruana; Plumage coloration; Discussions on zoogeography, species limits and Bergmann's Rule.

Evaluates the taxonomic status of the House Wren, Troglodytes aedon, species group. Background on the study; Methods used in the study; Levels and patterns of genetic differentiation.

Tarphonomus, a new genus of ovenbird (Aves: Passeriformes: Furnariidae) from South America, is described. Species included in the new genus, formerly placed in Upucerthia, are T. certhioides and T. harterti. [ABSTRACT FROM AUTHOR]

Relationships of the Neotropical finches in the genera Euphonia and Chlorophonia (Fringillidae: Euphoniinae) have been clarified by recent molecular studies, but species-level relationships within this group have not been thoroughly addressed. In this study, we sampled specimens representing every recognized species of these genera, in addition to 2 outgroup taxa, and used target enrichment to sequence thousands of ultraconserved element (UCE) loci, as well as mitochondrial DNA reconstructed from off-target reads, from each specimen to infer these relationships. We constructed both concatenation and coalescent-based estimates of phylogeny from this dataset using matrices of varying levels of completeness, and we generated a time-scaled ultrametric tree using a recently published fossil-based external calibration. We found uniformly strong support for a monophyletic subfamily Euphoniinae and genus Chlorophonia, but a paraphyletic Euphonia across UCEs and mitochondrial genomes. Otherwise, our inferred relationships were largely concordant with previous studies. Our time-tree indicated a stem divergence time of 13.8 million years ago for this lineage, followed by a relatively young crown age of only 7.1 myr. Reconstructions of biogeographic history based on this tree suggest a South American origin for crown Euphoniinae, possibly resulting from a transoceanic dispersal event from the Eastern Hemisphere, followed by 2 dispersal events into the Caribbean and as many as 6 invasions of North America coinciding with recent estimates of the age at which the Isthmus of Panama had completely formed. We recommend splitting Euphonia and resurrecting the genus Cyanophonia for the 3 blue-hooded species more closely related to Chlorophonia. Based on our results, we suspect that there is undescribed species-level diversity in at least one, possibly many, widespread and phenotypically diverse species. [ABSTRACT FROM AUTHOR]

Animal culture evolves alongside genomes, and the two modes of inheritance—culture and genes—interact in myriad ways. For example, stable geographic variation in culture can act as a reproductive barrier, thereby facilitating genetic divergence between "cultural populations." White-crowned sparrows (Zonotrichia leucophrys) are a well-established model species for bird song learning and cultural evolution, as they have distinct, geographically discrete, and culturally transmitted song types (i.e., song dialects). In this study, we tested the hypothesis that divergence between culturally transmitted songs drives genetic divergence within Nuttall's white-crowned sparrows (Z. l. nuttalli). In accordance with sexual selection theory, we hypothesized that cultural divergence between mating signals both preceded and generated genetic divergence. We characterized the population structure and song variation in the subspecies and found two genetically differentiated populations whose boundary coincides with a major song boundary at Monterey Bay, California. We then conducted a song playback experiment that demonstrated males discriminate between songs based on their degree of divergence from their local dialect. These results support the idea that discrimination against non-local songs is driving genetic divergence between the northern and southern populations. Altogether, this study provides evidence that culturally transmitted bird songs can act as the foundation for speciation by sexual selection. [ABSTRACT FROM AUTHOR]

Gloger's rule is a classic ecogeographical principle that, in its simplest version, predicts animals should be darker in warmer and wetter climates. In a rarely tested more complex version, it also predicts animals should be more rufous in warmer and drier climates. The Variable Antshrike (Thamnophilus caerulescens) is a widely distributed South American passerine that presents an impressive amount of plumage color variation and occupies a wide variety of climatic conditions. Moreover, genetic and vocal evidence indicate ongoing hybridization in south-central Bolivia among 3 populations with very distinct plumages. We collected color data from 232 specimens from throughout this species' distribution to test the predictions of Gloger's rule. We found a negative correlation between brightness and precipitation, consistent with the simple version of Gloger's rule. In contrast, we found that birds were darker in cooler climates, contrary to the simple version of Gloger's rule, but consistent with recent findings in other taxa. We found support for both predictions of the complex Gloger's rule and suggest it might be driven by background matching. We conclude by concurring with a recent suggestion that the simple version of Gloger's rule should be reformulated exclusively in terms of humidity. [ABSTRACT FROM AUTHOR]

Relationships of the Neotropical finches in the genera Euphonia and Chlorophonia (Fringillidae: Euphoniinae) have been clarified by recent molecular studies, but species-level relationships within this group have not been thoroughly addressed. In this study, we sampled specimens representing every recognized species of these genera, in addition to 2 outgroup taxa, and used target enrichment to sequence thousands of ultraconserved element (UCE) loci, as well as mitochondrial DNA reconstructed from off-target reads, from each specimen to infer these relationships. We constructed both concatenation and coalescent-based estimates of phylogeny from this dataset using matrices of varying levels of completeness, and we generated a time-scaled ultrametric tree using a recently published fossil-based external calibration. We found uniformly strong support for a monophyletic subfamily Euphoniinae and genus Chlorophonia , but a paraphyletic Euphonia across UCEs and mitochondrial genomes. Otherwise, our inferred relationships were largely concordant with previous studies. Our time-tree indicated a stem divergence time of 13.8 million years ago for this lineage, followed by a relatively young crown age of only 7.1 myr. Reconstructions of biogeographic history based on this tree suggest a South American origin for crown Euphoniinae, possibly resulting from a transoceanic dispersal event from the Eastern Hemisphere, followed by 2 dispersal events into the Caribbean and as many as 6 invasions of North America coinciding with recent estimates of the age at which the Isthmus of Panama had completely formed. We recommend splitting Euphonia and resurrecting the genus Cyanophonia for the 3 blue-hooded species more closely related to Chlorophonia. Based on our results, we suspect that there is undescribed species-level diversity in at least one, possibly many, widespread and phenotypically diverse species. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Can knowledge about genome architecture inform biogeographic and phylogenetic inference? Selection, drift, recombination, and gene flow interact to produce a genomic landscape of divergence wherein patterns of differentiation and genealogy vary nonrandomly across the genomes of diverging populations. For instance, genealogical patterns that arise due to gene flow should be more likely to occur on smaller chromosomes, which experience high recombination, whereas those tracking histories of geographic isolation (reduced gene flow caused by a barrier) and divergence should be more likely to occur on larger and sex chromosomes. In Amazonia, populations of many bird species diverge and introgress across rivers, resulting in reticulated genomic signals. Herein, we used reduced representation genomic data to disentangle the evolutionary history of 4 populations of an Amazonian antbird, Thamnophilus aethiops , whose biogeographic history was associated with the dynamic evolution of the Madeira River Basin. Specifically, we evaluate whether a large river capture event ca. 200 Ka, gave rise to reticulated genealogies in the genome by making spatially explicit predictions about isolation and gene flow based on knowledge about genomic processes. We first estimated chromosome-level phylogenies and recovered 2 primary topologies across the genome. The first topology (T1) was most consistent with predictions about population divergence and was recovered for the Z-chromosome. The second (T2), was consistent with predictions about gene flow upon secondary contact. To evaluate support for these topologies, we trained a convolutional neural network to classify our data into alternative diversification models and estimate demographic parameters. The best-fit model was concordant with T1 and included gene flow between non-sister taxa. Finally, we modeled levels of divergence and introgression as functions of chromosome length and found that smaller chromosomes experienced higher gene flow. Given that (1) genetrees supporting T2 were more likely to occur on smaller chromosomes and (2) we found lower levels of introgression on larger chromosomes (and especially the Z-chromosome), we argue that T1 represents the history of population divergence across rivers and T2 the history of secondary contact due to barrier loss. Our results suggest that a significant portion of genomic heterogeneity arises due to extrinsic biogeographic processes such as river capture interacting with intrinsic processes associated with genome architecture. Future phylogeographic studies would benefit from accounting for genomic processes, as different parts of the genome reveal contrasting, albeit complementary histories, all of which are relevant for disentangling the intricate geogenomic mechanisms of biotic diversification. [Amazonia; biogeography; demographic modeling; gene flow; gene tree; genome architecture; geogenomics; introgression; linked selection; neural network; phylogenomic; phylogeography; reproductive isolation; speciation; species tree.] [ABSTRACT FROM AUTHOR]

Genetic divergence among isolated populations is not always reflected in phenotypic differentiation. We investigated the genetic and phenotypic differentiation in Diglossa cyanea (Thraupidae; Masked Flowerpiercer), a widely distributed species in the tropical Andes. We found strong evidence for 2 main lineages separated by the Marañón River valley in the Northern Peruvian Low (NPL). These 2 lineages show a deep sequence divergence in mitochondrial DNA (mtDNA; ~6.7% uncorrected p-distance, n = 122), spectral frequency and song structure (with exclusive final whistles in southern populations, n = 88), and wing length (the northern populations are smaller, n = 364). The 2 divergent D. cyanea mitochondrial lineages were not sister to each other, suggesting a possible paraphyly with respect to D. caerulescens (Bluish Flowerpiercer) that remains to be tested with nuclear genomic data. No genetic variation, size difference, or song structure was observed within the extensive range of the southern group (from the NPL to central Bolivia) or within all sampled northern populations (from the NPL to Venezuela). These vocal differences appear to have consequences for song discrimination, and species recognition, according to a previously published playback experiment study. We propose that the southern taxon be elevated to species rank as D. melanopis, a monotypic species (with the proposed name Whistling Masked-Flowerpiercer). In turn, we provide a redefinition of D. cyanea (Warbling Masked-Flowerpiercer), which is now restricted to the northern half of the tropical Andes as a polytypic species with 3 subspecies (tovarensis, obscura, and cyanea). Based on our results, the subspecies dispar should be treated as a junior synonym of cyanea. Our study highlights the need to continue amassing complementary data sets from field observations, experiments, and collection-based assessments to better characterize the evolutionary history, biogeography, bioacoustics, and taxonomy of Neotropical montane birds. [ABSTRACT FROM AUTHOR]

Rapid diversification may be caused by ecological adaptive radiation via niche divergence. In this model, speciation is coupled with niche divergence and lineage diversification is predicted to be correlated with rates of niche evolution. Studies of the role of niche evolution in diversification have generally focused on ecomorphological diversification but climatic-niche evolution may also be important. We tested these alternatives using a phylogeny of 298 species of ovenbirds (Aves: Furnariidae). We found that within Furnariidae, variation in species richness and diversification rates of subclades were best predicted by rate of climatic-niche evolution than ecomorphological evolution. Although both are clearly important, univariate regression and multivariate model averaging more consistently supported the climatic-niche as the best predictor of lineage diversification. Our study adds to the growing body of evidence, suggesting that climatic-niche divergence may be an important driver of rapid diversification in addition to ecomorphological evolution. However, this pattern may depend on the phylogenetic scale at which rate heterogeneity is examined. [ABSTRACT FROM AUTHOR]

A revision of the avian Neotropical genus Automolus and the Furnariidae family points to the paraphyly of A. infuscatus and reveals a species complex comprising A. infuscatus , A. ochrolaemus , A. paraensis , A. leucophthalmus , A. lammi and A. subulatus , the latter historically classified in the genus Hyloctistes . Detailed knowledge of the taxonomy, geographic distribution, phylogenetic relationship and divergence times of a taxon allows exploration of its evolutionary history and the testing of different scenarios of diversification. In this context, we studied the A. infuscatus complex using molecular data in order to unveil its cryptic diversity and reveal its evolutionary history. For that we sequenced two mitochondrial (ND2 and cytb) and three nuclear markers (G3PDH, ACO, Fib7) for 302 individuals belonging to all species in the complex and most described subspecies. Our analysis supports the paraphyly of A. infuscatus , indicating the existence of at least two distinct clades not closely related. The remaining species were all recovered as monophyletic. Notwithstanding, a well-structured intraspecific diversity was found with 19 lineages suggesting substantial cryptic diversity within the described species. A. subulatus was recovered within the complex, corroborating its position inside the genus. In spite of the high congruence between distributions of different lineages, with several sister lineages currently separated by the same barriers, the temporal incongruence between divergences over the same barriers reveals a complex evolutionary history. While older events might be related to the emergence of barriers such as the Andes and major Amazonian rivers, younger events suggest dispersal after the consolidation of those barriers. Our analysis suggests that the complex had its origin around 6 million years (Ma) and inhabited Western Amazonia in Late Miocene-Early Pliocene. Considering the riparian habit of species in its sister clade, the rise and early diversifications of the complex may be related to the establishment of terra firme forests as it changed from a floodplain to a fluvial system. The late Amazonian colonization by A. subulatus and A. ochrolaemus lineages may have been hampered by the previous existence of well established A. infuscatus lineages in the region. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Gene tree discordance is expected in phylogenomic trees and biological processes are often invoked to explain it. However, heterogeneous levels of phylogenetic signal among individuals within data sets may cause artifactual sources of topological discordance. We examined how the information content in tips and subclades impacts topological discordance in the parrots (Order: Psittaciformes), a diverse and highly threatened clade of nearly 400 species. Using ultraconserved elements from 96% of the clade's species-level diversity, we estimated concatenated and species trees for 382 ingroup taxa. We found that discordance among tree topologies was most common at nodes dating between the late Miocene and Pliocene, and often at the taxonomic level of the genus. Accordingly, we used two metrics to characterize information content in tips and assess the degree to which conflict between trees was being driven by lower-quality samples. Most instances of topological conflict and nonmonophyletic genera in the species tree could be objectively identified using these metrics. For subclades still discordant after tip-based filtering, we used a machine learning approach to determine whether phylogenetic signal or noise was the more important predictor of metrics supporting the alternative topologies. We found that when signal favored one of the topologies, the noise was the most important variable in poorly performing models that favored the alternative topology. In sum, we show that artifactual sources of gene tree discordance, which are likely a common phenomenon in many data sets, can be distinguished from biological sources by quantifying the information content in each tip and modeling which factors support each topology. [Historical DNA; machine learning; museomics; Psittaciformes; species tree.] [ABSTRACT FROM AUTHOR]

Some phylogenetic problems remain unresolved even when large amounts of sequence data are analyzed and methods that accommodate processes such as incomplete lineage sorting are employed. In addition to investigating biological sources of phylogenetic incongruence, it is also important to reduce noise in the phylogenomic dataset by using appropriate filtering approach that addresses gene tree estimation errors. We present the results of a case study in manakins, focusing on the very difficult clade comprising the genera Antilophia and Chiroxiphia. Previous studies suggest that Antilophia is nested within Chiroxiphia , though relationships among Antilophia + Chiroxiphia species have been highly unstable. We extracted more than 11,000 loci (ultra-conserved elements and introns) from whole genomes and conducted analyses using concatenation and multispecies coalescent methods. Topologies resulting from analyses using all loci differed depending on the data type and analytical method, with 2 clades (Antilophia + Chiroxiphia and Manacus + Pipra + Machaeopterus) in the manakin tree showing incongruent results. We hypothesized that gene trees that conflicted with a long coalescent branch (e.g. the branch uniting Antilophia + Chiroxiphia) might be enriched for cases of gene tree estimation error, so we conducted analyses that either constrained those gene trees to include monophyly of Antilophia + Chiroxiphia or excluded these loci. While constraining trees reduced some incongruence, excluding the trees led to completely congruent species trees, regardless of the data type or model of sequence evolution used. We found that a suite of gene metrics (most importantly the number of informative sites and likelihood of intralocus recombination) collectively explained the loci that resulted in non-monophyly of Antilophia + Chiroxiphia. We also found evidence for introgression that may have contributed to the discordant topologies we observe in Antilophia + Chiroxiphia and led to deviations from expectations given the multispecies coalescent model. Our study highlights the importance of identifying factors that can obscure phylogenetic signal when dealing with recalcitrant phylogenetic problems, such as gene tree estimation error, incomplete lineage sorting, and reticulation events. [Birds; c-gene; data type; gene estimation error; model fit; multispecies coalescent; phylogenomics; reticulation] [ABSTRACT FROM AUTHOR]

Results of a comprehensive molecular phylogeny of the family Thamnophilidae were consistent with earlier findings that almost all obligate army-ant-followers of the family form a monophyletic group that contains five well-supported clades and encompasses six currently recognized genera: Phaenostictus, Pithys, Willisornis, Gymnopithys, Rhegmatorhina, and Phlegopsis. A comparative analysis of seven suites of morphological, behavioral, and ecological traits within the context of the phylogeny reinforced the validity of five of these genera, but results for the sixth, Gymnopithys, were internally inconsistent and required the description of a new genus, Oneillornis. [ABSTRACT FROM AUTHOR]

[Display omitted] • First subspecies-level phylogeny for Lepidothrix manakins clarifies relationships. • Results suggest Blue-crowned Manakins comprise two biological species. • An F1 hybrid between two manakin species suggests postmating reproductive barriers. Although recent molecular phylogenetic analyses of Lepidothrix manakins (family Pipridae) have helped clarify their evolutionary relationships, the placement of several lineages remains in question because of low or conflicting branch support. In particular, the relationship of L. coronata to other members of the genus and relationships within the L. nattereri + L. vilasboasi + L. iris clade have been difficult to resolve. We used RADcap to collect restriction site-associated DNA sequence data and estimate the first subspecies-level phylogeny of the genus Lepidothrix (17 of 18 currently recognized subspecies), and we included extensive geographic representation of the widespread and phenotypically variable L. coronata. We found strong support for the phylogenetic position and monophyly of L. coronata , and we resolved two clades separated by the Andes that, along with previous divergence time estimates and our assessment of morphological and vocal evidence, suggest the presence of two biological species: Velvety Manakin (L. velutina) west of the Andes and Blue-capped Manakin (L. coronata) east of the Andes. Species-level relationships within the L. nattereri + L. vilasboasi + L. iris clade remained poorly resolved in concatenated and coalescent-based analyses, with SNAPP analyses suggesting that the lack of reciprocal monophyly is due to extensive allele sharing among these taxa. Finally, we confirmed a previously documented hybrid between L. coronata and L. suavissima as an F1 individual, consistent with the view that hybridization between these two species is a rare event and that postmating reproductive barriers prevent successful backcrossing. [ABSTRACT FROM AUTHOR]

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 evolutionary processes underlying the diversification of a songbird genus, and compared diversification dynamics of clades occurring in lowland and montane Neotropical habitats. Location: Neotropical montane and lowland forests. Taxon: Arremon(Aves: Passerellidae). Methods: We sequenced genomic data (ultra‐conserved elements, UCEs) of 92 individuals (including historical skin specimens) comprising 47 of 50 currently recognized subspecies in the genus and collected habitat association data to (1) build the most complete phylogenetic hypothesis for the genus to date using maximum likelihood and Bayesian methods with a concatenated matrix, and a multi‐species coalescent method based on quartets; and (2) reconstruct the evolution of their ancestral ranges, habitat association and diversification rates. Results: All phylogenetic methods recovered essentially the same topology with strong support values for most interspecific nodes revealing relationships among species. We found evidence for a montane and humid ancestral range in Central America in the late Miocene and a later expansion into the lowlands of Central America, as well as into the lowlands and mountains of South America. Despite some temporal variation in diversification rate, we found overall similar diversification dynamics between montane and lowland clades. Main conclusion: Species diversity within the genus is likely underestimated by the current taxonomic arrangement. The colonization of lowlands and dry forests, and expansion across South America, may have provided new geographical and ecological opportunities for speciation resulting in high species diversification. Overall diversification dynamics were comparable between montane and lowland clades, contrasting with previous studies focused on such comparisons for Neotropical birds. [ABSTRACT FROM AUTHOR]

Phylogenetic niche conservatism (PNC) and convergence are contrasting evolutionary patterns that describe phenotypic similarity across independent lineages. Assessing whether and how adaptive processes give origin to these patterns represent a fundamental step toward understanding phenotypic evolution. Phylogenetic model-based approaches offer the opportunity not only to distinguish between PNC and convergence, but also to determine the extent that adaptive processes explain phenotypic similarity. The Myrmotherula complex in the Neotropical family Thamnophilidae is a polyphyletic group of sexually dimorphic small insectivorous forest birds that are relatively homogeneous in size and shape. Here, we integrate a comprehensive species-level molecular phylogeny of the Myrmotherula complex with morphometric and ecological data within a comparative framework to test whether phenotypic similarity is described by a pattern of PNC or convergence, and to identify evolutionary mechanisms underlying body size and shape evolution. We show that antwrens in the Myrmotherula complex represent distantly related clades that exhibit adaptive convergent evolution in body size and divergent evolution in body shape. Phenotypic similarity in the group is primarily driven by their tendency to converge toward smaller body sizes. Differences in body size and shape across lineages are associated to ecological and behavioral factors. [ABSTRACT FROM AUTHOR]

Bachman's Sparrow (Peucaea aestivalis) is a fire-dependent species that has undergone range-wide population declines in recent decades. We examined genetic diversity in Bachman's Sparrows to determine whether natural barriers have led to distinct population units and to assess the effect of anthropogenic habitat loss and fragmentation. Genetic diversity was examined across the geographic range by genotyping 226 individuals at 18 microsatellite loci and sequencing 48 individuals at mitochondrial and nuclear genes. Multiple analyses consistently demonstrated little genetic structure and high levels of genetic variation, suggesting that populations are panmictic. Based on these genetic data, separate management units/subspecies designations or translocations to promote gene flow among fragmented populations do not appear to be necessary. Panmixia in Bachman's Sparrow may be a consequence of an historical range expansion and retraction. Alternatively, high vagility in Bachman's Sparrow may be an adaptation to the ephemeral, fire-mediated habitat that this species prefers. In recent times, high vagility also appears to have offset inbreeding and loss of genetic diversity in highly fragmented habitat. [ABSTRACT FROM AUTHOR]

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 the distribution of P. brunnescens. Phylogenetic relationships were inferred using Bayesian and maximum-likelihood methods. Groups with maximum differentiation were estimated with spatial analysis of molecular variance ( SAMOVA). We estimated timing of differentiation and relationships among groups with a species-tree approach and historical demography with extended Bayesian skyline plots. Results Six highly differentiated clades of P. brunnescens are distributed in lower Central America, Sierra Nevada de Santa Marta, northern Venezuelan mountains, the Northern Andes, central Peru, and southern Peru and Bolivia. Within the Northern Andes clade, six phylogroups were identified associated with different slopes and isolated cordilleras. Most clades occupy opposite sides of low-lying valleys and ridgelines, but little differentiation was observed across several putative barriers. Population divergence occurred in the late Miocene and Pliocene, perhaps in association with Andean uplift. Historical fluctuations in population sizes suggest that populations tracked the spatial dynamics of montane forests associated with glacial cycles. Main conclusions Extensive genetic differentiation in mitochondrial and nuclear DNA exists among populations of P. brunnescens. Such marked divergence was probably promoted by the rugged topography and dynamic ecological history of the Neotropical mountains. Our study sheds light on mechanisms promoting population differentiation in the montane Neotropics. [ABSTRACT FROM AUTHOR]

Secondary contact between species often results in the formation of a hybrid zone, with the eventual fates of the hybridizing species dependent on evolutionary and ecological forces. We examine this process in the Amazon Basin by conducting the first genomic and phenotypic characterization of the hybrid zone formed after secondary contact between two obligate army‐ant‐followers: the White‐breasted Antbird (Rhegmatorhina hoffmannsi) and the Harlequin Antbird (Rhegmatorhina berlepschi). We found a major geographic displacement (∼120 km) between the mitochondrial and nuclear clines, and we explore potential hypotheses for the displacement, including sampling error, genetic drift, and asymmetric cytonuclear incompatibilities. We cannot exclude roles for sampling error and genetic drift in contributing to the discordance; however, the data suggest expansion and unidirectional introgression of hoffmannsi into the distribution of berlepschi. [ABSTRACT FROM AUTHOR]

Polyphyletic arrangements in DNA phylogenies are often indicators of cryptic species diversity masked by erroneous taxonomic treatments that are frequently based on morphological data. Although mitochondrial (mt) DNA polyphyly is detected relatively rarely in phylogenetic studies, it has recently been found in a variety of tyrant-flycatcher ( Tyrannidae) groups. In the present study, we provide a DNA phylogeny for a mitochondrial and a nuclear locus with a complete species sampling in Zimmerius flycatchers, showing that the genus is characterized by multiple mtDNA polyphyly. Based on phylogenetic and life-history information, we suggest the elevation of a number of taxa to species status, leading to a doubling of Zimmerius species-level diversity compared to taxonomic treatments conducted before 2001. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, ●●, ●●-●●. [ABSTRACT FROM AUTHOR]

Ecological theories of adaptive radiation predict that ecological opportunity stimulates cladogenesis through its effects on competitive release and niche expansion. Given that key innovations may confer ecological opportunity, we investigated the effect of the acquisition of climbing adaptations on rates of cladogenesis in a major avian radiation, the Neotropical bird family Furnariidae, using a species-level phylogeny. Morphological specializations for vertical climbing originated in the woodcreepers ~23 million years ago, well before that adaptation occurred in woodpeckers (Picidae) or in other potential competitors in South America. This suggests that the acquisition of climbing adaptations conferred ample ecological opportunity to early woodcreepers. Nonetheless, we found that increases in speciation rates in Furnariidae did not coincide with the acquisition of climbing adaptations and that the relationship between the accumulation of climbing adaptations and rates of speciation was negative. In addition, we did not detect a diversity-dependent decline in woodcreeper diversification rates consistent with saturation of the trunk-climbing niche. These findings do not Support the hypothesis that ecological opportunity related to trunk foraging stimulated cladogenesis in this radiation. The negative effect of climbing on diversification may be mediated by an indirect positive effect of climbing on dispersal ability, which may reduce speciation rates over evolutionary timescales. [ABSTRACT FROM AUTHOR]