Molecular phylogeny of the genus Saguinus (Platyrrhini, Primates) based on the ND1 mitochondrial gene and implications for conservation

The systematics of the subfamily Callitrichinae (Platyrrhini, Primates), a group of small monkeys from South America and Panama, remains an area of considerable discussion despite many investigations, there being continuing controversy over subgeneric taxonomic classifications based on morphological characters. The purpose of our research was to help elucidate the phylogenetic relationships within the monkey genus Saguinus (Callitrichinae) using a molecular approach to discover whether or not the two different sections containing hairy-faced and bare-faced species are monophyletic, whether Saguinus midas midas and Saguinus bicolor are more closely related than are S. midas midas and Saguinus midas niger, and if Saguinus fuscicollis melanoleucus and Saguinus fuscicollis weddelli really are different species. We sequenced the 957 bp ND1 mitochondrial gene of 21 Saguinus monkeys (belonging to six species and nine morphotypes) and one Cebus monkey (the outgroup) and constructed phylogenetic trees using maximum parsimony, neighbor joining, and maximum likelihood methods. The phylogenetic trees obtained divided the genus Saguinus into two groups, one containing the small-bodied species S. fuscicollis and the other, the large-bodied species S. mystax, S. leucopus, S. oedipus, S. midas, S. bicolor. The most derived taxa, S. midas and S. bicolor, grouped together, while S. fuscicollis melanoleucus and S. f. weddelli showed divergence values that did not support the division of these morphotypes into subspecies. On the other hand, S. midas individuals showed divergence compatible with the existence of three subspecies, two of them with the same morphotype as the subspecies S. midas niger. The results of our study suggest that there is at least one Saguinus subspecies that has not yet been described and that the conservation status of Saguinus species and subspecies should be carefully revised using modern molecular approaches.

Molecular studies of Callithrix pygmaea (Primates, Platyrrhini) based on transferrin intronic and ND1 regions: implications for taxonomy and conservation

As classificações tradicionais envolvendo os macacos da infraordem Platyrrhini, principalmente baseadas em características morfológicas, têm sido contestadas por dados moleculares recentes. A subfamília Callitrichinae (Platyrrhine, Primates) engloba um diverso grupo de espécies, muitas das quais consideradas em perigo de extinção. A presente análise de duas regiões do DNA, um gene mitocondrial (ND1) e um gene nuclear (regiões intrônicas da transferrina), sugerem que Callithrix pygmaea apresenta variabilidade suficiente para justificar a existência de subespécies ou até mesmo de espécies distintas. As árvores filogenéticas baseadas na região do ND1 indicam que esta espécie está relacionada mais proximamente aos marmosets amazônicos do que aos da mata Atlântica. Estes resultados reabrem a discussão sobre diversidade e programas de conservação baseados apenas em classificações taxonômicas tradicionais.

Molecular identification, phylogeny and geographic distribution of Brazilian mangrove oysters (Crassostrea)

Oysters (Ostreidae) manifest a high degree of phenotypic plasticity, whereby morphology is of limited value for species identification and taxonomy. By using molecular data, the aim was to genetically characterize the species of Crassostrea occurring along the Brazilian coast, and phylogenetically relate these to other Crassostrea from different parts of the world. Sequencing of the partial cytochrome oxidase c subunit I gene (COI), revealed a total of three species of Crassostrea at 16 locations along the Brazilian coast. C. gasar was found from Curuçá (Pará state) to Santos (São Paulo state), and C. rhizophorae from Fortim (Ceará state) to Florianópolis (Santa Catarina state), although small individuals of the latter species were also found at Ajuruteua beach (municipality of Bragança, Pará state). An unidentified Crassostrea species was found only on Canela Island, Bragança. Crassostrea gasar and C. rhizophorae grouped with C. virginica, thereby forming a monophyletic Atlantic group, whereas Crassostrea sp. from Canela Island was shown to be more similar to Indo-Pacific oysters, and either arrived in the Atlantic Ocean before the convergence of the Isthmus of Panama or was accidentally brought to Brazil by ship.

Phylogenetic relationships among Brazilian howler monkeys, genus Alouatta (Platyrrhini, Atelidae), based on γ¹-globin pseudogene sequences

Os guaribas, do gênero Alouatta, que são os primatas do Novo Mundo com maior distribuição geográfica, têm sido colocados em três grupos de espécies: o grupo Alouatta palliata da América central, e os grupos sulamericanos Alouatta seniculus e Alouatta caraya. Este último é monotípico, mas o grupo A. seniculus inclui pelo menos três espécies (A. seniculus, A. belzebul e A. fusca). Neste estudo, foram seqüenciados aproximadamente 600 pares de base do pseudogene globina g1 nas quatro espécies brasileiras (A. seniculus, A. belzebul, A. fusca e A. caraya). Os métodos de máxima parcimônia e máxima verossimilhança produziram árvores filogenéticas com o mesmo arranjo: {A. caraya [A. seniculus (A. fusca, A. belzebul)]}. A árvore mais parcimoniosa apresentou valores de bootstrap maiores de 82% para todos os agrupamentos, e valores de força de ligação de pelo menos 2, apoiando o agrupamento irmão de A. fusca e A. belzebul. O estudo também confirmou a presença em A. fusca do elemento de inserção Alu, com 150 pares de base, e uma deleção de 1,8 kb no pseudogene globina g1 já conhecidos nas demais espécies de guaribas. A classificação cladística baseada em dados moleculares é congruente com as de estudos morfológicos, com um isolamento claro do grupo monoespecífico A. caraya em relação ao grupo A. seniculus.

Taxonomic implications of molecular studies on Northern Brazilian Teredinidae (Mollusca: Bivalvia) specimens

The current taxonomy of the Teredinidae (shipworms) is wholly based on morphology and up to now no molecular studies of the phylogeny of this group have been published. In the present study the relationships between four genera of the subfamilies Teredininae and Bankiinae were established and the efficiency of the 16S rRNA gene in characterizing four Teredinidae species was tested. Phylogenetic trees support the grouping of Bankia fimbriatula with Nausitora fusticula and of Neoteredo reynei with Psiloteredo healdi, but the genetic distances do not justify the classification of these species into two distinct subfamilies. The results show that B. fimbriatula, N. reynei and P. healdi specimens from the coast of the Brazilian state of Pará have five distinct 16S rRNA haplotypes, with one N. reynei haplotype differing from the other haplotypes in respect to at least seven sequences sites, indicating the existence of two very distinct sympatric lineages.

Genetic characterization of native and introduced populations of the neotropical cichlid genus Cichla in Brazil

A molecular phylogenetic analysis based on mitochondrial 16S ribosomal DNA and Control Region sequences from native and introduced populations was undertaken, in order to characterize the introduction of Cichla (peacock bass or tucunaré) species in Brazil. Mitochondrial DNA haplotypes found in introduced fish from Minas Gerais state (southeastern Brazil) clustered only with those from native species of the Tocantins River (Cichla piquiti and C. kelberi), thereby suggesting a single or, at most, few translocation acts in this area, even though with fish from the same source-population. Our study contributes to an understanding of the introduction of Cichla in regions of Brazil outside the Amazon basin, and adds phylogenetic data to the recently describe Cichla species, endemic from the Tocantins-Araguaia basin.

Identification and phylogenetic inferences on stocks of sharks affected by the fishing industry off the Northern coast of Brazil

The ongoing decline in abundance and diversity of shark stocks, primarily due to uncontrolled fishery exploitation, is a worldwide problem. An additional problem for the development of conservation and management programmes is the identification of species diversity within a given area, given the morphological similarities among shark species, and the typical disembarkation of processed carcasses which are almost impossible to differentiate. The main aim of the present study was to identify those shark species being exploited off northern Brazil, by using the 12S-16S molecular marker. For this, DNA sequences were obtained from 122 specimens collected on the docks and the fish market in Bragança, in the Brazilian state of Pará. We identified at least 11 species. Three-quarters of the specimens collected were either Carcharhinus porosus or Rhizoprionodon sp, while a notable absence was the daggernose shark, Isogomphodon oxyrhyncus, previously one of the most common species in local catches. The study emphasises the value of molecular techniques for the identification of cryptic shark species, and the potential of the 12S-16S marker as a tool for phylogenetic inferences in a study of elasmobranchs.

Novel 12S mtDNA findings in sloths (Pilosa, Folivora) and anteaters (Pilosa, Vermilingua) suggest a true case of long branch attraction

We sequenced 12S RNA mtDNA for the majority of the extant species of sloths and anteaters and compared our results with previous data obtained by our group using 16S RNA mtDNA in the same specimens and to GenBank sequences of the extinct giant sloth Mylodon. Our results suggest that pigmy-anteaters may be a case of the long-branch attraction phenomenon and also show the large genetic difference between the Amazonian and Atlantic forest three-toed sloths, contrasting with the small differences observed between the two non-Atlantic forest forms of sloths. These results have important implications for the taxonomy of sloths and anteaters and strongly suggest the placement of pigmy anteaters in their own family (Cyclopidae) and raising the taxonomic status of Bradypus torquatus to a genus.

Can Lutjanus purpureus (South red snapper) be "legally" considered a red snapper (Lutjanus campechanus)?

Red snappers (Lutjanus purpureus in Brazil and Lutjanus campechanus in USA and Gulf of Mexico) are both under clear effect of overfishing. Because of their high morphological similarity it has already been suggested that they could possibly be considered as a single species. To investigate the degree of similarity and the genetic structure of red snapper populations we constructed a common dataset of partial D-loop mtDNA sequences of L. purpureus from Brazil (Amapá, Pará and Maranhão) and L. campechanus from the Atlantic coast of the USA (Florida, Louisiana and Mississippi). Phylogenetic and population genetic analyses surprisingly depicted high similarity between L. campechanus and L. purpureus, compatible with the hypothesis of a single species of red snapper for the Western Atlantic Ocean. These preliminary but very curious findings open an important discussion regarding the legislation involved on the capture of this overexploited fish resources as well as regarding their taxonomy.

Low levels of genetic diversity depicted from mitochondrial DNA sequences in a heavily exploited marine fish (Cynoscion acoupa, Sciaenidae) from the Northern coast of Brazil

The acoupa weakfish (Cynoscion acoupa - Sciaenidae) is a marine species of croaker with estuarine-dependent behavior, found in the western Atlantic from Panama to Argentina. It is one of the most exploited food fish on the northern coast of Brazil. In this study, DNA sequences were determined from the entire control region (D-loop) of the mitochondrial genome of 297 individuals collected during seven different months between December 2003 and August 2005 on the northern coast of Brazil (Amapá and Pará). Genetic variability expressed by haplotype (h = 0,892) and nucleotide (p = 0,003) diversities were low compared to other heavily exploited marine fish species from the western Atlantic and eastern Asia. AMOVA depicted a lack of genetic structuring among the samples from different years, indicating the presence of a single stock of C. acoupa within the sample area. The possible reasons for the low levels of genetic diversity are discussed. These results demonstrate a need for the monitoring of C. acoupa harvesting and the preservation of the estuaries within its geographic range, considering that this large fish depends on estuarine ecosystems during part of its life cycle.

Molecular discrimination of pouched four-eyed opossums from the Mamirauá Reserve in the Brazilian Amazon

Previous cytochrome B (CytB) mtDNA studies have suggested four species for the opossum genus Philander (four-eyed opossums), three (P. mcilhennyi, P. andersoni and P. opossum) from the Amazon and one (P. frenata) from the Brazilian Atlantic forest. During a faunal survey nine specimens of Philander sp. and four of Didelphis marsupialis were collected in the Mamirauá Sustainable Reserve, Amazonas State, Brazil. Preliminary analyses based on morphology and geographical distributions were not conclusive, suggesting that Philander specimens could belong to either P. andersoni or P. opossum. In order to elucidate the relationship of this taxon to the remaining Amazonian taxa, seven Philander and two Didelphis specimens animals were sequenced for the cytB mtDNA gene and compared to other previously studied taxa. The maximum likelihood (ML), neighbor-Joining (NJ) and maximum parsimony (MP) consensus bootstrap trees depicted six groups: Didelphis., P. frenata, P andersoni, P. mcilhennyi, P.o. opossum and Philander sp. and Philander canus in a common assemblage supported by significant bootstrap values, suggesting that the Philander sp. from Mamiraua in fact belongs to the species Philander canus.

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?).

Phylogenetic analysis of 16S mitochondrial DNA data in sloths and anteaters

We sequenced part of the 16S rRNA mitochondrial gene in 17 extant taxa of Pilosa (sloths and anteaters) and used these sequences along with GenBank sequences of both extant and extinct sloths to perform phylogenetic analysis based on parsimony, maximum-likelihood and Bayesian methods. By increasing the taxa density for anteaters and sloths we were able to clarify some points of the Pilosa phylogenetic tree. Our mitochondrial 16S results show Bradypodidae as a monophyletic and robustly supported clade in all the analysis. However, the Pleistocene fossil Mylodon darwinii does not group significantly to either Bradypodidae or Megalonychidae which indicates that trichotomy best represents the relationship between the families Mylodontidae, Bradypodidae and Megalonychidae. Divergence times also allowed us to discuss the taxonomic status of Cyclopes and the three species of three-toed sloths, Bradypus tridactylus, Bradypus variegatus and Bradypus torquatus. In the Bradypodidae the split between Bradypus torquatus and the proto-Bradypus tridactylus / B. variegatus was estimated as about 7.7 million years ago (MYA), while in the Myrmecophagidae the first offshoot was Cyclopes at about 31.8 MYA followed by the split between Myrmecophaga and Tamandua at 12.9 MYA. We estimate the split between sloths and anteaters to have occurred at about 37 MYA.

The current status of the new world monkey phylogeny

Four DNA datasets were combined in tandem (6700 bp) and Maximum parsimony and Neighbor-Joining analyses were performed. The results suggest three groups emerging almost at the same time: Atelidae, Pitheciidae and Cebidae. The total analysis strongly supports the monophyly of the Cebidae family, grouping Aotus, Cebus and Saimiri with the small callitrichines. In the callitrichines, the data link Cebuela to Callithrix, place Callimico as a sister group of Callithrix/Cebuella, and show Saguinus to be the earliest offshoot of the callitrichines. In the family Pithecidae, Callicebus is the basal genus. Finally, combined molecular data showed congruent branching in the atelid clade, setting up Alouatta as the basal lineage and Brachyteles-Lagothrix as a sister group and the most derived branch. Two major points remain to be clarified in the platyrrhine phylogeny: (i) what is the exact branching pattern of Aotus, Cebus, Saimiri and the small callitrichines, and (ii), which two of these three lineages, pitheciines, atelines or cebids, are more closely related?

Cytogenetic studies in fishes of the genera Hassar, Platydoras and Opsodoras (Doradidae, Siluriformes) from Jarí and Xingú Rivers, Brazil

We studied the karyotypes of Hassar cf. orestis and an undescribed Hassar species from the Jarí River and Opsodoras ternetzi, H. orestis and Platydoras cf. costatus from the Xingú River, all with 2n = 58. Constitutive heterochromatin is located in the centromere in most metacentric pairs; in some chromosomes this banding is not present, or it is located on the whole chromosome arm or in the distal regions. The NOR is located on a single biarmed pair at a distal region of the short arm in H. cf. orestis, H. orestis and P. cf. costatus at a distal region of the long arm in O. ternetzi and at a proximal region of the long arm in the Hassar species. In all species (except for Hassar sp.) the CMA3 analysis revealed a rich G-C region coincident with the NOR. Probably inversions occurred in the NOR chromosome during the chromosomal differentiation of the Doradidae species here described.