Ana S. Barreira

Probing Evolutionary Patterns in Neotropical Birds through DNA Barcodes

Background The Neotropical avifauna is more diverse than that of any other biogeographic region, but our understanding of patterns of regional divergence is limited. Critical examination of this issue is currently constrained by the limited genetic information available. This study begins to address this gap by assembling a library of mitochondrial COI sequences, or DNA barcodes, for Argentinian birds and comparing their patterns of genetic diversity to those of North American birds. Methodology and Principal Findings Five hundred Argentinian species were examined, making this the first major examination of DNA barcodes for South American birds. Our results indicate that most southern Neotropical bird species show deep sequence divergence from their nearest-neighbour, corroborating that the high diversity of this fauna is not based on an elevated incidence of young species radiations. Although species ages appear similar in temperate North and South American avifaunas, patterns of regional divergence are more complex in the Neotropics, suggesting that the high diversity of the Neotropical avifauna has been fueled by greater opportunities for regional divergence. Deep genetic splits were observed in at least 21 species, though distribution patterns of these lineages were variable. The lack of shared polymorphisms in species, even in species with less than 0.5M years of reproductive isolation, further suggests that selective sweeps could regularly excise ancestral mitochondrial polymorphisms. Conclusions These findings confirm the efficacy of species delimitation in birds via DNA barcodes, even when tested on a global scale. Further, they demonstrate how large libraries of a standardized gene region provide insight into evolutionary processes.

DNA barcodes provide new evidence of a recent radiation in the genus Sporophila (Aves: Passeriformes)

The capuchinos are a group of birds in the genus Sporophila that has apparently radiated recently, as evidenced by their lack of mitochondrial genetic diversity. We obtained cytochrome c oxidase I (COI) sequences (or DNA barcodes) for the 11 species of the group and various outgroups. We compared the patterns of COI variability of the capuchinos with those of the largest barcode data set from neotropical birds currently available (500 species representing 51% of avian richness in Argentina), and subjected COI sequences to neighbour‐joining, maximum parsimony and Bayesian phylogenetic analyses as well as statistical parsimony network analysis. A clade within the capuchinos, the southern capuchinos, showed higher intraspecific and lower interspecific divergence than the remaining Argentine species. As most of the southern capuchinos shared COI haplotypes and pairwise distances within species were in many cases higher than distances between them, the phylogenetic affinities within the group remained unresolved. The observed genetic pattern is consistent with both incomplete lineage sorting and gene flow between species. The southern capuchinos constitute the only large group of species among the neotropical birds barcoded so far that are inseparable when using DNA barcodes, and one of few multispecies avian groups known to lack reciprocal monophyly. Extending the analysis to rapidly evolving nuclear and mitochondrial markers will be crucial to understanding this radiation. Apart from giving insights into the evolution of the capuchinos, this study shows how DNA barcoding can rapidly flag species or groups of species worthy of deeper study.

DNA Barcode Libraries Provide Insight into Continental Patterns of Avian Diversification

Background The causes for the higher biodiversity in the Neotropics as compared to the Nearctic and the factors promoting species diversification in each region have been much debated. The refuge hypothesis posits that high tropical diversity reflects high speciation rates during the Pleistocene, but this conclusion has been challenged. The present study investigates this matter by examining continental patterns of avian diversification through the analysis of large-scale DNA barcode libraries. Methodology and Principal Findings Standardized COI datasets from the avifaunas of Argentina, the Nearctic, and the Palearctic were analyzed. Average genetic distances between closest congeners and sister species were higher in Argentina than in North America reflecting a much higher percentage of recently diverged species in the latter region. In the Palearctic genetic distances between closely related species appeared to be more similar to those of the southern Neotropics. Average intraspecific variation was similar in Argentina and North America, while the Palearctic fauna had a higher value due to a higher percentage of variable species. Geographic patterning of intraspecific structure was more complex in the southern Neotropics than in the Nearctic, while the Palearctic showed an intermediate level of complexity. Conclusions and Significance DNA barcodes can reveal continental patterns of diversification. Our analysis suggests that avian species are older in Argentina than in the Nearctic, supporting the idea that the greater diversity of the Neotropical avifauna is not caused by higher recent speciation rates. Species in the Palearctic also appear to be older than those in the Nearctic. These results, combined with the patterns of geographic structuring found in each region, suggest a major impact of Pleistocene glaciations in the Nearctic, a lesser effect in the Palearctic and a mild effect in the southern Neotropics.

Continental-scale analysis reveals deep diversification within the polytypic Red-crowned Ant Tanager (Habia rubica, Cardinalidae).

We explored the phylogeographic patterns of intraspecific diversity in the Red-crowned Ant Tanager (Habia rubica) throughout its continent-wide distribution, in order to understand its evolutionary history and the role of evolutionary drivers that are considered to promote avian diversification in the Neotropics. We sampled 100 individuals of H. rubica from Mexico to Argentina covering the main areas of its disjunct distribution. We inferred phylogenetic relationships through Bayesian and maximum parsimony methodologies based on mitochondrial and nuclear markers, and complemented genetic analyses with the assessment of coloration and behavioral differentiation. We found four deeply divergent phylogroups within H. rubica: two South American lineages and two Mexican and Middle American lineages. The divergence event between the northern and southern phylogroups was dated to c. 5.0 Ma, seemingly related to the final uplift of the Northern Andes. Subsequently, the two South American phylogroups split c. 3.5 Ma possibly due to the development of the open vegetation corridor that currently isolates the Amazonian and Atlantic forests. Diversification throughout Mexico and Middle America, following dispersion across the Isthmus of Panama, was presumably more recent and coincident with Pleistocene climatic fluctuations and habitat fragmentations. The analyses of vocalizations and plumage coloration showed significant differences among main lineages that were consistent with the phylogenetic evidence. Our findings suggest that the evolutionary history of H. rubica has been shaped by an assortment of diversification drivers at different temporal and spatial scales resulting in deeply divergent lineages that we recommend should be treated as different species.

Intraspecific and interspecific vocal variation in three Neotropical cardinalids (Passeriformes : Fringillidae) and its relationship with body mass

Abstract Several studies, of a large number of bird species, have shown that song frequencies have a strong negative relationship with body size. However, mixed results were obtained at the intraspecific level or when comparing closely related species. Here, we compared the vocalisations of the monotypic Glaucous-blue Grosbeak (Cyanoloxia glaucocaerulea), three of five subspecies of the Ultramarine Grosbeak (Cyanocompsa brissonii) and all four subspecies of the Blue-black Grosbeak (Cyanocompsa cyanoides). These taxa of Neotropical cardinalids differ significantly in body size, so we compared them to examine the allometric relationship of body size with song frequencies, using body mass as a proxy of body size. The maximum frequency and the emphasised frequency (i.e. the frequency of the song of highest amplitude) showed the expected negative correlation with body mass, supporting the idea that the aforementioned relationship stands when comparing closely related lineages in Cyanoloxia and Cyanocompsa. We also found that the duration of notes, rate of production of notes and duration of inter-note interval correlated with body mass: heavier species had longer notes produced at a lower rate and separated by longer intervals. The correlation of temporal variables with body mass suggests that body size could also influence the temporal structure of song. Our findings highlight once again the importance of considering the role of avian morphology when studying the evolution of song, even if differences in frequency and temporal variables of songs are small.

SUBSPECIFIC AND TEMPORAL VARIATION IN THE STRUCTURALLY BASED COLORATION OF THE ULTRAMARINE GROSBEAK

Abstract ABSTRACT Ultramarine Grosbeaks (Cyanocompsa brissonii) possess a striking sexual dichromatism, with males dark blue and females brown. There are two subspecies in Argentina: the larger-bodied C. b. argentina, which is common in shrubs and semiopen areas, and the smaller C. b. sterea that inhabits forests. We measured reflectance spectra of six plumage patches from study skins to evaluate the possibility of color differences between males of each subspecies and temporal variation in plumage coloration. We found differences between subspecies in color brightness, hue, saturation, and UV chroma in the plumage patches of more conspicuous coloration, which could be related to ambient light differences between the environments that each subspecies inhabits. We also documented temporal color variation in some plumage patches, in particular a gradual decrease of UV reflectance and a gradual increase in hue after molting, possibly attributable to feather wear.

Structural colour in Tersina viridis

espanolEl color del plumaje de las aves se debe tanto a la presencia de pigmentos como a efectos estructurales selectivos en frecuencia producidos por la interaccion de la luz con la microestructura fotonica que constituye las barbas de las plumas. El plumaje de la especie Tersina viridis, de la familia Thraupidae, presenta dicromatismo sexual: los machos tienen plumaje azul y las hembras son verdes. Ademas, las plumas muestran una reflectancia iridiscente que varia con el angulo entre la direccion de incidencia y la de observacion. Para investigar los mecanismos de generacion de color en las plumas de Tersina viridis estudiamos su respuesta electromagnetica. En primer lugar, se obtuvieron imagenes TEM de la seccion transversal de las barbas, las cuales revelaron una microestructura formada por cavidades cuasi-esfericas de aire inmersas en una matriz de β-queratina. Para obtener sus parametros geometricos relevantes, se realizo un analisis estadistico detallado de las imagenes. Dichos parametros, junto con las propiedades opticas de los materiales involucrados, determinan el comportamiento electromagnetico de la estructura. Para calcular la reflectancia de la barba se utilizaron dos metodos teoricos. En primer lugar, se aplico un modelo simplificado basado en el analisis de Fourier que solo tiene en cuenta eventos de esparcimiento simple. Este metodo provee informacion util acerca de la posicion espectral del pico de reflectancia dominante en la zona visible del espectro. Sin embargo, este analisis no considera las interacciones entre las esferas, las cuales podrian afectar significativamente la respuesta optica. Para tener esto en cuenta, se aplico el metodo conocido como Korringa-Kohn-Rostoker (KKR), que es un formalismo teorico riguroso para el calculo de la reflectancia de estructuras formadas por apilamientos de esferas inmersas en un medio material. Se realizaron simulaciones numericas prestando especial atencion a la influencia de las caracteristicas geometricas de la microestructura. Las curvas obtenidas muestran un pico de reflectancia en la zona del UV, tal como muestran las mediciones de los espectros de reflectancia de la especie. Estos resultados muestran el potencial del metodo KKR para reproducir en forma precisa la respuesta electromagnetica de estructuras naturales y para reproducir caracteristicas que no pueden ser explicadas utilizando el metodo de Fourier. Los resultados obtenidos confirman que la estructura fotonica cuasi-periodica de la barba produce esparcimiento coherente y por lo tanto es la responsable del color de la especie Tersina viridis. EnglishThe colour of birds’ plumage is due to the presence of pigments as well as to frequency selective structural effects produced by the interaction of light with the photonic microstructure that constitutes the feather barbs. The species Swallow Tanager, of the family Thraupidae, exhibits sexual dichromatism: males have blue plumage and females green. In addition, the feathers show an iridescent reflectance, which changes as the angle between the directions of incidence and observation is varied. In order to investigate the mechanisms of colour generation in the feathers of the Swallow Tanager species, we study their electromagnetic response. First, we obtained TEM images of the barbs’ cross section, which revealed a microstructure consisting of quasi-spherical air cavities embedded in a β-keratin matrix. To obtain the relevant geometric parameters of the structure, we performed a detailed statistical analysis of the images. These parameters, together with the optical properties of the constituent materials, determine the electromagnetic behaviour of the structure. To calculate the reflectance of a barb, we used two theoretical approaches. First, we applied a simplified model based on Fourier analysis, which relies on the single-particle scattering hypothesis. This method provides useful information about the spectral position of the dominant reflectance peak in the visible region of the spectrum. However, this approach does not account for multiple scattering effects which could produce additional features. Then, we investigate the optical response by applying the Korringa-Kohn-Rostoker (KKR) method, which is a rigorous theoretical formalism for the calculation of the reflectance of structures formed by a stack of spheres embedded in a material medium. We performed numerical simulations, paying special attention to the influence of the geometrical characteristics of the microstructure on the optical response of the barbs. The KKR curves exhibit an enhancement in the UV region, which is in agreement with the measured reflectance of Swallow Tanager. These results evidence the potential of the KKR formalism to accurately reproduce the electromagnetic response of natural structures and to reveal features that cannot be explained using the Fourier approach. The results obtained confirm that the quasi-ordered spongy structure produces coherent scattering and therefore is the responsible for the colour of the Swallow Tanager.

Viewing geometry affects sexual dichromatism and conspicuousness of noniridescent plumage of Swallow Tanagers (Tersina viridis)

ABSTRACT Some types of plumage color are difficult to characterize spectrophotometrically because the properties of the reflected light change with viewing geometry (i.e. the relative positions of the light source and the observer, and the orientation of the feather). This is the case for the noniridescent plumage coloration of the Swallow Tanager (Tersina viridis), which seems to change from a human perspective as the angle between the light source and the observer varies. In this study, we measured plumage reflectance with different angles of illumination and/or observation, and used avian visual models to evaluate the change in sexual dichromatism and conspicuousness with viewing geometry from a birds perspective. We also calculated different color parameters to assess how these changed with viewing conditions. Sexual dichromatism showed large changes, with its maximum coinciding with the angle combination between illuminant and observer that produced both the highest conspicuousness for males and the highest crypsis for females. The conspicuousness of males also varied with viewing geometry, and was consistently less when viewed by the visual system of a potential avian predator (VS) than by that of a conspecific (UVS). The change in perceived coloration was mainly related to large variation in hue and chroma in the plumage of males as the relative angle between the illumination and observation probes changed. Our results show that viewing geometry can alter color perception, even for noniridescent plumage coloration. Therefore, the relative position of the light source and the observer should be considered in studies of avian visual communication, particularly for species with plumage coloration similar to that of Swallow Tanagers.