Juliana Araripe

Phylogenetic analyses of the genera Pipra, Lepidothrix and Dixiphia (Pipridae, Passeriformes) using partial cytochrome b and 16S mtDNA genes

The piprids (manakins) are small‐bodied Neotropical birds characterized by sexual dimorphism of the plumage and elaborate courtship rituals. The phylogenetic relationships of some of piprid genera, in particular Pipra, are not well defined. Recently, Pipra was divided into three distinct groups, and the recognition of two new genera — Lepidothrix and Dixiphia— was suggested, based on the characteristic of the syringial morphology. In the present study, we analyse the phylogenetic relationships among these genera on the basis of data from the mitochondrial genes rRNA 16S and cytochrome b. Bayesian Inference (BI), Maximum Parsimony (MP) and Maximum Likelihood (ML) methods of analyses produced phylogenetic trees with very similar topologies with regard to the groupings formed by the species representing the three genera. These results indicate that the genera Pipra, Lepidothrix and Dixiphia do not constitute a single monophyletic clade, and support the current hypothesis of polyphyletism for the former representatives of the genus Pipra. However, the topologies presented do not coincide exactly with the phylogeny suggested by the morphological data with regard to the relationship between these three groups and the remaining piprid genera analysed here, emphasizing the need for further studies of this group of birds. The agreement between the molecular data presented here and the biogeographical information available for some of the species analysed appears to confirm the potential of using segments of the mitochondrial genome for the study of phylogeographical patterns in this group of organisms.

Tocantins river as an effective barrier to gene flow in Saguinus niger populations

The Saguinus represent the basal genus of the Callitrichinae subfamily. Traditionally this genus is divided into three groups: Hairy, Mottled and Bare-face, however, molecular data failed to validate these groups as monophyletic units, as well as raised some subspecies to the species status. This is the case of the former subspecies Saguinus midas midas and S. midas niger, which are now considered as different species. In the present study, we sequenced a portion of the D-loop mtDNA region in populations from the East bank of the Xingu and from both banks of the Tocantins river, in order to test the effectiveness of large rivers as barriers to the gene flow in Saguinus. According to our results, the populations from the East and West banks of the Tocantins river are more divergent than true species like S. mystax and S. imperator. The Tocantins river may be acting as a barrier to gene flow, and consequently these very divergent populations may represent distinct taxonomic entities (species?).

Dispersal Capacity and Genetic Structure of Arapaima gigas on Different Geographic Scales Using Microsatellite Markers

Despite the ecological and economic importance of the Arapaima gigas (Cuvier 1817), few data about its dispersal capacity are available. The present study was based on the analysis of microsatellite markers in order to estimate the dispersal capacity of the species on fine, meso, and large geographic scales. For this, 561 specimens obtained from stocks separated by distances of up to 25 km (fine scale), 100 km (meso scale), and 1300–2300 km (large scale) were analyzed. The fine scale analysis indicated a marked genetic similarity between lakes, with low genetic differentiation, and significant differences between only a few pairs of sites. Low to moderate genetic differentiation was observed between pairs of sites on a meso scale (100 km), which could be explained by the distances between sites. By contrast, major genetic differentiation was recorded in the large scale analysis, that is, between stocks separated by distances of over 1300 km, with the analysis indicating that differentiation was not related solely to distance. The genetic structuring analysis indicated the presence of two stocks, one represented by the arapaimas of the Mamirauá Reserve, and the other by those of Santarém and Tucuruí. The dispersal of arapaimas over short distances indicates a process of lateral migration within the várzea floodplains, which may be the principal factor determining the considerable homogeneity observed among the várzea lakes. The populations separated by distances of approximately 100 km were characterized by reduced genetic differentiation, which was associated with the geographic distances between sites. Populations separated by distances of over 1300 km were characterized by a high degree of genetic differentiation, which may be related primarily to historical bottlenecks in population size and the sedentary behavior of the species. Evidence was found of asymmetric gene flow, resulting in increasing genetic variability in the population of the Mamirauá Reserve.

High Levels of Genetic Connectivity among Populations of Yellowtail Snapper, Ocyurus chrysurus (Lutjanidae – Perciformes), in the Western South Atlantic Revealed through Multilocus Analysis

In the present study, five loci (mitochondrial and nuclear) were sequenced to determine the genetic diversity, population structure, and demographic history of populations of the yellowtail snapper, Ocyurus chrysurus, found along the coast of the western South Atlantic. O. chrysurus is a lutjanid species that is commonly associated with coral reefs and exhibits an ample geographic distribution, and it can therefore be considered a good model for the investigation of phylogeographic patterns and genetic connectivity in marine environments. The results reflected a marked congruence between the mitochondrial and nuclear markers as well as intense gene flow among the analyzed populations, which represent a single genetic stock along the entire coast of Brazil between the states of Pará and Espírito Santo. Our data also showed high levels of genetic diversity in the species (mainly mtDNA), as well a major historic population expansion, which most likely coincided with the sea level oscillations at the end of the Pleistocene. In addition, this species is intensively exploited by commercial fisheries, and data on the genetic structure of its populations will be essential for the development of effective conservation and management plans.

Molecular phylogenetics of large‐bodied tamarins, Saguinus spp. (Primates, Platyrrhini)

With 33 recognized taxa, the tamarins, Saguinus spp., constitute the most diverse genus of New World monkeys (Platyrrhini), and are found almost exclusively within the Amazon basin. This diversity can be subdivided into three main morphological groups, based primarily on pelage characteristics, although there is also an ecologically important division between the small‐ and large‐bodied forms (adult body weight ± 300 g vs. > 450 g, respectively). In the present study, the phylogenetic relationships among the large‐bodied forms were analysed using the sequences of a fragment of the mitochondrial rRNA16S gene, from which 58 informative sites were identified. The analysis revealed the existence of four main lineages, three of which coincided with geographical and/or morphological patterns. However, Saguinus leucopus formed a highly distinct clade, contradicting expectations based on its morphology and distribution, but corroborating a previous study of the NADH dehydrogenase subunit I (ND1) gene. Whereas genetic differences between some closely related species were relatively small (< 1%), that observed between the two specimens of S. imperator was twice higher (± 2%), indicating the possible presence of distinct species within this taxon. Previous molecular clock analysis suggested that the earliest radiation event of the large‐bodied tamarins occurred sometime in the lower Miocene, whereas the most recent events, such as the division of the closely related S. midas and S. niger would have occurred during the Pleistocene. Most of these events would thus have taken place before the formation of the present‐day river system, which now constitutes a considerable barrier to gene flow among many populations.

Molecular data indicate the presence of a novel species of Centropomus (Centropomidae - Perciformes) in the Western Atlantic

Centropomus undecimalis is distributed in the coastal waters of the western Atlantic between North Carolina and São Paulo, although very little is known of the genetic structure of its populations. Here, 148 C. undecimalis samples were obtained from six sites in the southwestern Atlantic, representing the Brazilian distribution of this species. Segments of three mitochondrial (Cytb, COI and 16S) and one nuclear (IGF1) gene were sequenced. The results of all analyses indicated the presence of a previously undetected lineage of Centropomus in the northern extreme of Brazil (Amapá) in the region of the Oiapoque estuary. This taxon is genetically distinct from all 12 recognized species of Centropomus. The populations from the Brazilian states of Pará, Maranhão, Ceará, Rio Grande do Norte, Rio de Janeiro and São Paulo were genetically similar to C. undecimalis from coastal areas of the Caribbean and USA. Nucleotide divergence between C. undecimalis and the new Oiapoque taxon are greater than or similar to those found between a number of valid Centropomus species. The estimated time of divergence between C. undecimalis and the new taxon is approximately 2 millionyears. The findings of the present study emphasize the need for a thorough taxonomic revision of this genus.

Molecular and plumage analyses indicate the incomplete separation of two woodpeckers (Aves, Picidae)

We evaluated the relationship between Celeus undatus and Celeus grammicus, with the objective of clarifying their evolutionary history. We analysed fragments of the mitochondrial and nuclear genes of 57 specimens. For comparative purposes, we inspected the plumage patterns of 77 skins. Our findings highlight the absence of reciprocal monophyly between the two taxa, given their reduced genetic divergence, and the lack of any clear separation of the two forms in the haplotype networks. A similar situation was found in the STRUCTURE analysis, with reciprocal contributions from the two taxa to the respective clusters, indicating that C. grammicus and C. undatus cannot be differentiated using the molecular markers. Corroborating the genetic data, our plumage analyses also failed to find any clear diagnostic characters between the polytypic C. undatus and C. grammicus, as they are defined at present. The genetic profile is consistent with either extensive historical gene flow between the species or, alternatively, incomplete lineage sorting, rather than recent secondary contact. The lack of monophyly between the two taxa impeded subspecies‐level phylogeographic inferences, with the subspecific variation being interpreted as a probable artefact of the phenotypic plasticity of the two forms. These findings indicate clearly that the two taxa form a single evolutionary unit, in which the morphological differentiation used to diagnose the species, combined with their geographic distribution, is at odds with the incomplete separation of the taxa. This may reflect disparities in the rates of differentiation between molecular and phenotypic markers, which is possibly due to the variation in selection pressures along a humidity gradient in Amazonia.

Recent chapters of Neotropical history overlooked in phylogeography: Shallow divergence explains phenotype and genotype uncoupling in Antilophia manakins

Establishing links between phenotypic and genotypic variation is a central goal of evolutionary biology, as they might provide important insights into evolutionary processes shaping genetic and species diversity in nature. One of the more intriguing possibilities is when no genetic divergence is found to be associated with conspicuous phenotypic divergence. In that case, speciation theory predicts that phenotypic divergence may still occur in the presence of significant gene flow—thereby resulting in little genomic divergence—when genetic loci underpinning phenotypes are under strong divergent selection. However, a finding of phenotypic distinctiveness with weak or no population genetic structure may simply result from low statistical power to detect shallow genetic divergences when small data sets are used. Here, we used a subgenomic data set of 2,386 ultraconserved elements to explore genomewide divergence between two species of Antilophia manakins, which are phenotypically distinct yet evidently lack strong genetic differentiation according to previous studies based on a limited number of loci. Our results revealed clear population structure that matches the two phenotypes, supporting the idea that smaller data sets lacked the power to detect this recent divergence event (likely <100 k ya). Indeed, we found little or no introgression between the species, as well as evidence of genomewide divergence. One implication of our study is that the Araripe plateau may be a hot spot of cryptic‐diverging forest Cerrado populations. Besides their use in biogeography, subgenomic data sets may help redefine local conservation programmes by revealing cryptic population structure that may be key to population management.

Mutations in the melanocortin-1 receptor (MC1R) gene have no influence on the distinct patterns of melanic plumage found in the manakins of the genus Antilophia (Aves: Pipridae)

The melanocortin-1 receptor gene is the most widely-used marker for the investigation of the genetic determination of melanic plumage patterns. Studies of a number of wild bird species have shown an association between non-synonymous mutations of the MC1R gene and the presence of melanic variants. The genus Antilophia (Pipridae) includes only two manakin species (A. galeata and A. bokermanni), which are distinguished primarily by the differences in the pattern of melanic coloration of the plumage of the mantle in the adult males. In A. galeata, this plumage is black, while in A. bokermanni, it is predominantly white. This study investigates the possible association between mutations of the MC1R marker and the variation in plumage coloration observed in the two species. The MC1R sequences of the two species was analyzed, and the observed nucleotide variation was compared. Six polymorphic sites were identified, representing seven distinct genotypes. Five of these polymorphic mutations were non-synonymous, but were not related to the different phenotypes. Neutral evolution and the absence of any systematic association between the variants of the MC1R and plumage coloration in the Antilophia species indicate that alternative mechanisms regulate the expression of the coloration of the plumage in the adult males.

Low Genetic Diversity and Structuring of the Arapaima (Osteoglossiformes, Arapaimidae) Population of the Araguaia-Tocantins Basin

The arapaima, Arapaima gigas, is a fish whose populations are threatened by both overfishing and the ongoing destruction of its natural habitats. In the Amazon basin, varying levels of population structure have been found in A. gigas, although no data are available on the genetic diversity or structure of the populations found in the Araguaia-Tocantins basin, which has a topographic profile, hydrological regime, and history of fishing quite distinct from those of the Amazon. In this context, microsatellite markers were used to assess the genetic diversity and connectivity of five wild A. gigas populations in the Araguaia-Tocantins basin. The results of the analysis indicated low levels of genetic diversity in comparison with other A. gigas populations, studied in the Amazon basin. The AMOVA revealed that the Arapaima populations of the Araguaia-Tocantins basin are structured significantly. No correlation was found between pairwise FST values and the geographical distance among populations. The low level of genetic variability and the evidence of restricted gene flow may both be accounted for by overfishing, as well as the other human impacts that these populations have been exposed to over the years. The genetic fragility of these populations demands attention, given that future environmental changes (natural or otherwise) may further reduce these indices and eventually endanger these populations. The results of this study emphasize the need to take the genetic differences among the study populations into account when planning management measures and conservation strategies for the arapaima stocks of the Araguaia-Tocantins basin.