Molecular systematics,species limits,and diversification of the genus Dendrocolaptes (Aves: Furnariidae): Insights on biotic exchanges between dry and humid forest types in the Neotropics

The true diversity and interspecific limits in the Neotropical endemic avian genus Dendrocolaptes (Furnariidae) remain a highly controversial subject, with previous genus‐wide assessments, based mostly on morphological characters, producing poorly resolved phylogenies. The lack of well‐resolved, robust, and taxonomically densely sampled phylogenies for Dendrocolaptes prevents reliable inferences on the genus’ actual species diversity and evolutionary history. Here, we analyzed 2,741 base pairs of mitochondrial and nuclear genes from 43 specimens belonging to all species and the majority of subspecies described for Dendrocolaptes to evaluate species limits and reconstruct its diversification through time. Our phylogenies recovered a monophyletic Dendrocolaptes, with two main highly supported internal clades corresponding to the D. certhia and D. picumnus species complexes. Also, our analyses supported the monophyly of most Dendrocolaptes species recognized today, except D. picumnus, which was consistently recovered as paraphyletic with respect to D. hoffmannsi. A coalescent‐based test supported a total of 15 different lineages in Dendrocolaptes and indicated that the number of currently accepted species within the genus may be greatly underestimated. Particularly relevant, when combined with previous analyses based on plumage characters, comparative high levels of genetic differentiation and coalescent analyses support the recognition of D. picumnus transfasciatus as a full species that is already under threat. Ancestral area reconstructions suggest that diversification in Dendrocolaptes was centered in lowland Amazonia, with several independent dispersal events leading to differentiation into different adjacent dry and high elevation forest types throughout the Neotropics, mainly during the Middle and Late Pleistocene.     

Patterns of Genetic Variability in Island Populations of the Cane Toad (Rhinella marina) from the Mouth of the Amazon

The Amazonian coast has several unique geological characteristics resulting from the interaction between drainage pattern of the Amazon River and the Atlantic Ocean. It is one of the most extensive and sedimentologically dynamic regions of the world, with a large number of continental islands mostly formed less than 10,000 years ago. The natural distribution of the cane toad (Rhinella marina), one of the world’s most successful invasive species, in this complex Amazonian system provides an intriguing model for the investigation of the effects of isolation or the combined effects of isolation and habitat dynamic changes on patterns of genetic variability and population differentiation. We used nine fast-evolving microsatellite loci to contrast patterns of genetic variability in six coastal (three mainlands and three islands) populations of the cane toad near the mouth of the Amazon River. Results from Bayesian multilocus clustering approach and Discriminant Analyses of Principal Component were congruent in showing that each island population was genetically differentiated from the mainland populations. All F_ST values obtained from all pairwise comparisons were significant, ranging from 0.048 to 0.186. Estimates of both recent and historical gene flow were not significantly different from zero across all population pairs, except the two mainland populations inhabiting continuous habitats. Patterns of population differentiation, with a high level of population substructure and absence/restricted gene flow, suggested that island populations of R. marina are likely isolated since the Holocene sea-level rise. However, considering the similar levels of genetic variability found in both island and mainland populations, it is reliable to assume that they were also isolated for longer periods. Given the genetic uniqueness of each cane toad population, together with the high natural vulnerability of the coastal regions and intense human pressures, we suggest that these populations should be treated as discrete units for conservation management purposes.     

DNA barcode reveals candidate species of Scinax and Ololygon (Anura: Hylidae) in Atlantic Forest

Molecular species delimitation methods are efficient tools to identify species, including the discovery of new taxa and cryptic organisms, thus being useful to biodiversity studies. In the present work, 16S mitochondrial sequences and cytochrome oxidase I (COI) were used to evaluate the richness of species in the genus Scinax and Ololygon from a biodiversity hotspot in Atlantic Forest. A total of 109 specimens formally belonging to eight species of Scinax and three species of Ololygon were collected in 13 localities along the state of Bahia (northeastern Brazil) and one site in Espírito Santo (southeastern Brazil). Of the Scinax species collected in this study, three were morphologically differentiated from other described species and identified as putative new species (Scinax sp.1, Scinax sp.2 and Scinax sp.3). The species delimitations were inferred using three different methods: ABGD, PTP and mPTP which allowed recognizing 11 Scinax species and five Ololygon species. Scinax sp. 1, Scinax sp. 2 and Scinax sp. 3, have been confirmed as new putative species and Ololygon argyreornata possibly contains cryptic species. We suggest additional studies, including morphological and bioacoustic data to validate these new putative species.     

Phylogeny and biogeography of the Rhinella marina species complex (Amphibia,Bufonidae) revisited: implications for Neotropical diversification hypotheses

Vallinoto, M., Sequeira, F., Sodré, D., Bernardi, J. A. R., Sampaio, I. & Schneider, H. (2009). Phylogeny and biogeography of the Rhinella marina species complex (Amphibia, Bufonidae) revisited: implications for Neotropical diversification hypotheses. —Zoologica Scripta, 39, 128–140. A number of distinct hypotheses have been proposed to account for the origin of the considerable biological diversity found in the Neotropics, which is still a matter of intense debate. Here, we conducted a phylogenetic analysis of the Rhinella marina complex, a group of species widely distributed in Central and South America, combining published data with new sequences of three mtDNA genes (12S, 16S and cyt b) in order to clarify the evolutionary relationships and biogeographical history of the group. We included eight of the ten currently recognized R. marina group species and several outgroups. Maximum parsimony, maximum likelihood, and Bayesian inference analyses produced similar topologies, with two well‐supported main clades, each characterized by a deep subdivision. One of these major clades includes the samples of R. marina from Central America and Ecuador (west of the Andes), whereas the other comprises the remaining species of the group and samples of R. marina from the Amazon basin and other areas east of the Andes. A Bayesian coalescent‐based method (BEAST) dated the divergence between the two major clades, and between the Central American and Ecuadorian clades to the Miocene, matching the timing of other Central‐South American faunal divergences. Taken together, the results highlight the importance of Tertiary events such as the Pebas/marine incursions into the Amazon basin and Andean uplift for the diversification and historical biogeography of R. marina, making such taxa paraphyletic, and provide new perspectives on the debate on its species status.     

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.     

Molecular phylogeny of mangrove oysters (Crassostrea) from Brazil

As a result of phenotypic plasticity, the cupped oysters (Crassostrea)are difficult to identify by means of their morphology. However,molecular DNA markers are a useful means of discriminating amongthese species. Cupped oysters are one of the most widely culturedmarine invertebrates and correct species identification is importantin aquaculture. Moreover, the molecular phylogeny of the genusCrassostrea and the subfamily Crassostreinae is still not clear.In order to identify the Brazilian cupped oysters and to clarifythe phylogenetic relationships of these species, we sequenceda fragment of mitochondrial DNA (16S rRNA gene) from 120 specimenscollected at nine different sites distributed along the Braziliancoast. The results identified two native species of oyster:Crassostrea gasar, from the Amazon to the Parnaíba delta;and Crassostrea rhizophorae, from the northeast (Fortim) tothe south of Brazil. An exotic Crassostrea species, closelyrelated to Indo-Pacific Crassostrea, was found in one locationin the north of Brazil. Crassostrea showed monophyly and theAtlantic oysters are clearly separated from the Indo-Pacificcluster. (Received 30 May 2006; accepted 12 April 2007)     

Influence of Th1/Th2 Cytokines and Nitric Oxide in Murine Systemic Infection Induced by Sporothrix schenckii

In an attempt to elucidate the effects of Sporothrix schenckii infection on the immune response, our laboratory has developed a murine model of disseminated sporotrichosis. Helper T cells can be further subdivided into Th1 and Th2 phenotypes. The differentiation of two subsets of T lymphocytes is driven by IL-12 and IL-4 cytokines, respectively. Th1 cells produce IFN-γ that activate macrophages and promote cell-mediated immunity. In addition, we found low levels of iNOS and NO production in the initial (1st and 2nd weeks) and final (9th and 10th weeks) periods of the infection, in contrast with the period of week 4 to 7 of elevated values. The determination of IFN-γ and IL-12 are in agreement with NO/iNOS detection, showing the presence of cellular immune response throughout the infectious process. However, the production of IL-4 shows an increase in levels after the 5th and 6th weeks suggesting a participation of Th2 response in this period as well. Regarding these results, the study demonstrated that in experimental sporotrichosis infection the cellular immune response participated throughout the period analyzed as a nitric oxide dependent mechanism. In contrast, the presence of Th2 response began in the 5th week, suggesting the participation of humoral immune response in advanced stages of sporotrichosis.