A fundamental question in evolutionary genetics concerns the extent to which adaptive phenotypic convergence is attributable to convergent or parallel changes at the molecular sequence level. Here we report a comparative analysis of hemoglobin (Hb) function in eight phylogenetically replicated pairs of high- and low-altitude waterfowl taxa to test for convergence in the oxygenation properties of Hb, and to assess the extent to which convergence in biochemical phenotype is attributable to repeated amino acid replacements. Functional experiments on native Hb variants and protein engineering experiments based on site-directed mutagenesis revealed the phenotypic effects of specific amino acid replacements that were responsible for convergent increases in Hb-O2 affinity in multiple high-altitude taxa. In six of the eight taxon pairs, high-altitude taxa evolved derived increases in Hb-O2 affinity that were caused by a combination of unique replacements, parallel replacements (involving identical-by-state variants with independent mutational origins in different lineages), and collateral replacements (involving shared, identical-by-descent variants derived via introgressive hybridization). In genome scans of nucleotide differentiation involving high- and low-altitude populations of three separate species, function-altering amino acid polymorphisms in the globin genes emerged as highly significant outliers, providing independent evidence for adaptive divergence in Hb function. The experimental results demonstrate that convergent changes in protein function can occur through multiple historical paths, and can involve multiple possible mutations. Most cases of convergence in Hb function did not involve parallel substitutions and most parallel substitutions did not affect Hb-O2 affinity, indicating that the repeatability of phenotypic evolution does not require parallelism at the molecular level.

The idea of an area of endemism implies that different groups of plants and animals should have largely coincident distributions. This paper analyses an area of 1152 000 km2, between parallels 21 and 32°S and meridians 70 and 53°W to examine whether a large and taxonomically diverse data set actually displays areas supported by different groups. The data set includes the distribution of 805 species of plants (45 families), mammals (25 families), reptiles (six families), amphibians (five families), birds (18 families), and insects (30 families), and is analysed with the optimality criterion (based on the notion of endemism) implemented in the program NDM/VNDM. Almost 50% of the areas obtained are supported by three or more major groups; areas supported by fewer major groups generally contain species from different genera, families, or orders. © The Willi Hennig Society 2011.

Behavioral isolation can catalyze speciation and permit the slow accumulation of additional reproductive barriers between co-occurring organisms. We illustrate how this process occurs by examining the genomic and behavioral bases of pre-mating isolation between two bird species (Sporophila hypoxantha and the recently discovered S. iberaensis) that belong to the southern capuchino seedeaters, a recent, rapid radiation characterized by variation in male plumage coloration and song. Although these two species co-occur without obvious ecological barriers to reproduction, we document behaviors indicating species recognition by song and plumage traits and strong assortative mating associated with genomic regions underlying male plumage patterning. Plumage differentiation likely originated through the reassembly of standing genetic variation, indicating how novel sexual signals may quickly arise and maintain species boundaries.

Consistent responses by various organisms to common environmental pressures represent strong evidence of natural selection driving geographical variation. According to Bergmann's and Allen's rules, animals from colder habitats are larger and have smaller limbs than those from warmer habitats to minimize heat loss. Although evidence supporting both rules in different organisms exists, most studies have considered only elevational or latitudinal temperature gradients. We tested for the effects of temperature associated with both elevation and latitude on body and appendage size of torrent ducks (Merganetta armata), a widespread species in Andean rivers. We found a negative relationship between body size and temperature across latitude consistent with Bergmann's rule, whereas there was a positive relationship between these variables along replicate elevational gradients at different latitudes. Limb‐size variation did not support Allen's rule along latitude, nor along elevation. High‐elevation ducks were smaller and had longer wings than those inhabiting lower elevations within a river. We hypothesize that temperature is likely a major selective pressure acting on morphology across latitudes, although hypoxia or air density may be more important along elevational gradients. We conclude that the effect of temperature on morphology, and hence the likelihood of documenting ecogeographical ‘rules’, depends on the environmental context in which temperature variation is examined. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 111, 850–862.

Because the tropical regions of America harbor the highest concentration of butterfly species, its fauna has attracted considerable attention. Much less is known about the butterflies of southern South America, particularly Argentina, where over 1,200 species occur. To advance understanding of this fauna, we assembled a DNA barcode reference library for 417 butterfly species of Argentina, focusing on the Atlantic Forest, a biodiversity hotspot. We tested the efficacy of this library for specimen identification, used it to assess the frequency of cryptic species, and examined geographic patterns of genetic variation, making this study the first large-scale genetic assessment of the butterflies of southern South America. The average sequence divergence to the nearest neighbor (i.e. minimum interspecific distance) was 6.91%, ten times larger than the mean distance to the furthest conspecific (0.69%), with a clear barcode gap present in all but four of the species represented by two or more specimens. As a consequence, the DNA barcode library was extremely effective in the discrimination of these species, allowing a correct identification in more than 95% of the cases. Singletons (i.e. species represented by a single sequence) were also distinguishable in the gene trees since they all had unique DNA barcodes, divergent from those of the closest non-conspecific. The clustering algorithms implemented recognized from 416 to 444 barcode clusters, suggesting that the actual diversity of butterflies in Argentina is 3%–9% higher than currently recognized. Furthermore, our survey added three new records of butterflies for the country (Eurema agave, Mithras hannelore, Melanis hillapana). In summary, this study not only supported the utility of DNA barcoding for the identification of the butterfly species of Argentina, but also highlighted several cases of both deep intraspecific and shallow interspecific divergence that should be studied in more detail.

Hypoxia is a key factor determining survival, and haemoglobins are targets of selection in species native to high-altitude regions. We studied population genetic structure and evaluated evidence for local adaptation in the crested duck (Lophonetta specularioides). Differentiation, gene flow and time since divergence between highland and lowland populations were assessed for three haemoglobin genes (α(A) , α(D) , β(A) ) and compared to seven reference loci (six autosomal introns and mtDNA). Four derived amino acid replacements were found in the globin genes that had elevated Φ(ST) values between the Andean highlands and Patagonian lowlands. A single β(A) -globin polymorphism at a site known to influence O(2) affinity was fixed for different alleles in the two populations, whereas three α(A) - and α(D) -globin polymorphisms exhibited high heterozygosity in the highlands but not in the lowlands. Coalescent analyses supported restricted gene flow for haemoglobin alleles and mitochondrial DNA but nonzero gene flow for the introns. Simulating genetic data under a drift-migration model of selective neutrality, the β(A) -globin fell outside the 95% confidence limit of simulated data, suggesting that directional selection is maintaining different variants in the contrasting elevational environments, thereby restricting migration of β(A) -globin alleles. The α(A) - and α(D) -globins, by contrast, did not differ from the simulated values, suggesting that variants in these genes are either selectively neutral, or that the effects of selection could not be differentiated from background levels of population structure and linkage disequilibrium. This study illustrates the combined effects of selection and population history on inferring levels of population divergence for a species distributed across an altitudinal gradient in which selection for hypoxia resistance has likely played an important role.

The riverine barrier hypothesis proposes that large rivers represent geographical barriers to gene flow for terrestrial organisms, leading to population differentiation and ultimately allopatric speciation. Here we assess for the first time if the subtropical Paraná–Paraguay River system in the Del Plata basin, second in size among South American drainages, acts as a barrier to gene flow for birds. We analysed the degree of mitochondrial and nuclear genomic differentiation in seven species with known subspecies divided by the Paraná–Paraguay River axis. Only one species showed genetic differentiation concordant with the current river channel, but another five species have an east/west genetic split broadly coincident with the Paraná River's dynamic palaeochannel, suggesting this fluvial axis has had a past role in shaping present‐day genetic structure. Moreover, dating analyses show that these splits have been asynchronous, with species responding differently to the riverine barrier. Comparisons informed by the geological history of the Paraná River and its influence on the ecological and climatic differences among ecoregions in the study area further bolster the finding that responses to this geographical barrier have been species‐specific.

We assessed the relationship between function and tail structure of woodcreepers (Dendrocolaptidae) and Neotropical ovenbirds (Furnariidae) using a comparative analysis of independent contrasts. Because woodcreepers are scansorial (they use their tail for body support), we predicted that the structure of the rectrix rachis should be reinforced both at the tip and at the base, whereas the nonscansorial Neotropical ovenbirds should lack reinforcement of the rectrix tips. For each species, we measured the length of the rachis of the medial rectrix and its diameter both at the tip and base of the feather. Rachis diameters were positively associated with body mass in both groups as expected if tail structure were a simple allometric product of body size. However, woodcreepers had larger rachis diameters for a given body mass and higher slopes in the allometric regressions than Neotropical ovenbirds. In addition, we found positive relationships between rachis width at both the tip and base of the rectrix and tail length in woodcreepers, but in Neotropical ovenbirds only rachis width at the base was associated with tail length. These results considered together are consistent with the hypothesis that the tip of the woodcreeper tail rachis is adapted to both support body mass and to prevent Euler buckling failure. Modificaciones Adaptativas de la Estructura de la Cola en Relación a la Masa Corporal y al Pandeo en Pájaros Trepadores Resumen. Se evaluó la relación entre la función y la estructura de la cola en los trepadores (Dendrocolaptidae) y los furnáridos (Furnariidae) usando un análisis comparativo de contrastes independientes. Debido a que los trepadores son escansoriales (es decir que usan su cola para el soporte del cuerpo), se predijo que la estructura del raquis de la rectriz debería estar reforzada tanto en la punta como en la base mientras que la de los furnáridos que no son escansoriales debería carecer del reforzamiento en la punta. Para cada especie se midió el largo del raquis de la rectriz medial y su diámetro, tanto en la punta como en la base de la pluma. Los diámetros del raquis estuvieron positivamente asociados con la masa corporal en ambos grupos, tal como se esperaría si la cola fuera el simple producto de una relación alométrica con el tamaño corporal. Sin embargo, los diámetros del raquis para una dada masa corporal y las pendientes de las regresiones alométricas fueron mayores en los trepadores que en los furnáridos. Además, se encontraron relaciones postivas entre el ancho del raquis en la punta y en la base de la rectriz y el largo de la cola en trepadores, pero solamente el ancho del raquis en la base estuvo asociado con el largo de la cola en furnáridos. Estos resultados considerados en su conjunto son consistentes con la hipótesis de que la punta del raquis en la cola de los trepadores está adaptada para soportar la masa corporal y prevenir el pandeo de Euler.