Cecilia Kopuchian

Convergent Evolution of Hemoglobin Function in High-Altitude Andean Waterfowl Involves Limited Parallelism at the Molecular Sequence Level

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.

Detecting areas of endemism with a taxonomically diverse data set: plants, mammals, reptiles, amphibians, birds, and insects from Argentina

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.

Temporal stability and change in a microgeographical pattern of song variation in the rufous-collared sparrow

We studied the pattern of song variation in the rufous-collared sparrow, Zonotrichia capensis, in the 1987 and 2000 breeding seasons in a 7-km2 area covering open and closed habitats. We measured 14 quantitative song variables over a total of 390 individuals and found consistent differences between habitats in both years. In particular, songs of individuals from closed habitat sites had trills with longer trill intervals and lower frequencies than those of individuals from open habitats. This pattern of variation is interpreted as a song cline that correlates with the environmental gradient. Although this cline was stable in location and shape, it also showed several differences between years. The songs recorded during 2000 had trills with longer trill intervals and lower minimum frequencies than those recorded during 1987. Thus, this study is the first to directly document temporal changes in song variables in a Z. capensis population. This change would be expected if all the habitats studied were more closed in 2000 than in 1987, but we did not find obvious differences in habitat features between seasons. However, this modification of song structure is compatible with alternative explanations, such as subtle differences in habitat characteristics, changes in climatic variables, a delayed effect of a past modification of the environment and neutrality of the change.

Multilocus coalescent analysis of haemoglobin differentiation between low‐ and high‐altitude populations of crested ducks (Lophonetta specularioides)

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 (αA, αD, βA) 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 ΦST values between the Andean highlands and Patagonian lowlands. A single βA‐globin polymorphism at a site known to influence O2 affinity was fixed for different alleles in the two populations, whereas three αA‐ and αD‐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 βA‐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 βA‐globin alleles. The αA‐ and αD‐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.

ADAPTIVE MODIFICATION OF TAIL STRUCTURE IN RELATION TO BODY MASS AND BUCKLING IN WOODCREEPERS

Abstract 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.

Behaviour of resampling methods under different weighting schemes, measures and variable resampling strengths

We compared general behaviour trends of resampling methods (bootstrap, bootstrap with Poisson distribution, jackknife, and jackknife with symmetric resampling) and different ways to summarize the results for resampling (absolute frequency, F, and frequency difference, GC′) for real data sets under variable resampling strengths in three weighting schemes. We propose an equivalence between bootstrap and jackknife in order to make bootstrap variable across different resampling strengths. Specifically, for each method we evaluated the number of spurious groups (groups not present in the strict consensus of the unaltered data set), of real groups, and of inconsistencies in ranking of groups under variable resampling strengths. We found that GC′ always generated more spurious groups and recovered more groups than F. Bootstrap methods generated more spurious groups than jackknife methods; and jackknife is the method that recovered more real groups. We consistently obtained a higher proportion of spurious groups for GC′ than for F; and for bootstrap than for jackknife. Finally, we evaluated the ranking of groups under variable resampling strengths qualitatively in the trajectories of “support” against resampling strength, and quantitatively with Kendall coefficient values. We found fewer ranking inconsistencies for GC′ than for F, and for bootstrap than for jackknife.

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.

Molecular phylogeny of the South American sheldgeese with implications for conservation of Falkland Islands (Malvinas) and continental populations of the Ruddy-headed Goose Chloephaga rubidiceps and Upland Goose C. picta

Sheldgeese of the genus Chloephaga are waterfowl (Anatidae) endemic to mainland South America and the Falkland Islands (Malvinas). Continental populations of three species C. picta , C. poliocephala , and C. rubidiceps breed in Patagonia and Tierra del Fuego and migrate northwards to winter in central Argentina and Chile. These continental populations have declined by > 50% in the past 30 years due to direct hunting to control crop damage and by the introduction of the grey fox Dusicyon griseus to their breeding grounds in Tierra del Fuego. The continental population of C. rubidiceps is critically endangered, estimated to be C. rubidiceps in its wintering grounds, the breeding population in Tierra del Fuego was estimated to number several thousand individuals in the 1950s. In contrast, the C. rubidiceps population in the Falkland Islands (Malvinas) is non-migratory and stable with > 42,000 individuals, as is the Falkland Islands (Malvinas) population of C. picta leucoptera with > 138,000 individuals. Here we use sequence data from the mitochondrial DNA control region to quantify genetic divergence between insular and continental populations of these two species of sheldgeese. Chloephaga rubidiceps and C. picta showed significant intraspecific differentiation of 1.0% and 0.6%, respectively. In both cases, mainland and insular populations were reciprocally monophyletic and did not share mtDNA haplotypes. These results suggest that the insular and continental populations of C. rubidiceps and C. picta are genetically distinct and that female-mediated gene flow is restricted. We recommend a reevaluation of the threat category status of the continental C. rubidiceps population, under IUCN guidelines. It is necessary to implement urgent actions for the conservation of this critically endangered population.

A striking case of deceptive woodpecker colouration: the threatened Helmeted Woodpecker Dryocopus galeatus belongs in the genus Celeus

The Helmeted Woodpecker Dryocopus galeatus is a threatened species of the Atlantic Forest in southeastern South America. It has traditionally been placed in the genus Dryocopus, but it shows similarities in plumage and structure with woodpeckers in the genus Celeus. We sequenced mitochondrial and nuclear DNA that was sampled from live captured Helmeted Woodpeckers. We found that the Helmeted Woodpecker has a phylogenetic position embedded within the genus Celeus, and recommend its taxonomic treatment as Celeus galeatus. The Helmeted Woodpecker belongs to a clade within Celeus that includes Kaempfer’s Woodpecker C. obrieni, Rufous-headed Woodpecker C. spectabilis, and Cream-coloured Woodpecker C. flavus. It has the southernmost distribution range of the woodpeckers in this clade. The Helmeted Woodpecker is sympatric throughout its range with Lineated Woodpecker Dryocopus lineatus and Robust Woodpecker Campephilus robustus and these species from three different genera show a remarkable convergence in plumage colours and patterns. With the inclusion of Helmeted Woodpecker in Celeus, this genus has four out of 15 species on the International Union for Conservation of Nature (IUCN) red list, a higher proportion of red listed species than in the woodpecker family overall.ZusammenfassungEin Fall verblüffend irreführender Spechtfärbung: der bedrohte WellenohrspechtDryocopus galeatusist einCeleus Der Wellenohrspecht ist eine bedrohte Spechtart der atlantischen Wälder im Südosten Südamerikas. Er wurde traditionellerweise in das Genus Dryocopus eingeordnet, weist aber in Gefieder und Struktur Ähnlichkeiten zur Gattung Celeus auf. Wir sequenzierten mitochondriale und nukleare DNA aus Proben, die lebend gefangenen Individuen entnommen worden waren. Wir fanden heraus, dass der Wellenohrspecht phylogenetisch innerhalb der Gattung Celeus positioniert ist und empfehlen, ihn in dieses Genus zu klassifizieren. Dieser Specht gehört zu einer Stammlinie innerhalb von Celeus, die den Kaempferspecht Celeus obrieni, Zimtkopfspecht C. spectabilis und den Strohspecht C. flavus enthält. Er stellt den südlichsten Vertreter dieser Gruppe dar. Sein Verbreitungsgebiet deckt sich mit jenen des Linienspechts Dryocopus lineatus und des Scharlachkopfspechts Campephilus robustus und diese drei Arten aus verschiedenen Genera weisen eine bemerkenswerte Konvergenz in Gefiederfärbung und -muster auf. Zusammen mit dem Wellenohrspecht beinhaltet die 15 Arten zählende Gattung Celeus vier auf der Roten Liste der IUCN stehende Arten, mehr als der Durchschnitt der Familie.

Stability and change through time in the dialects of a Neotropical songbird, the Rufous-collared Sparrow

Abstract Behavioural characters that are learned can show temporal variation resulting from changes introduced in new generations during the learning process. The song of the Rufous-collared Sparrow (Zonotrichia capensis) shows significant geographical variation associated with habitat, delimiting song dialects. To study the temporal stability or change in dialects of Rufous-collared Sparrows at a microgeographical scale, we compared recordings made at Reserva El Destino, in north-eastern coastal Buenos Aires Province, Argentina, during 1987 and 2000 with recordings made during 2010 and 2011. We found that the geographical boundaries of the dialects remained stable over the period of 24 years. As we did not detect gross changes in the habitat of the study area over that period, we conclude that habitat is an important factor in maintaining geographical boundaries of dialects. Within the dialects, variation in some variables detected between 1987 and 2000 persisted to 2010–11 whereas other variables showed reversal over that period. These findings are consistent with the hypothesis that some changes in song were the result of neutral variation, whereby changes resulting from random factors, such as copying error, could have been maintained or introduced across generations. Our results show that comparing more than two points in time is fundamental to a better understanding of temporal variation of song and its possible causes.