Microsatellites for the Amazonian Fish Hypophthalmus marginatus

We isolated 41 and characterized 17 microsatellite loci for evaluating the genetic structure of the Amazonian fish Hypophthalmus marginatus, from the Tocantins and Araguaia River in the Eastern Amazonia. Of the 17 selected microsatellite sequences, 15 were dinucleotide repeats, 9 of which were perfect (5–31 repetitions) and 6 were composite motifs. Among these 17 microsatellites, only two were polymorphic. The average number of alleles (Na) observed in the five examined populations ranged from 3.5 to 4.5, while the average observed heterozygosity (Ho) ranged from 0.3 to 0.6. The allelic frequency was less homogeneous at the locus Hm 5 than that for the Hm 13. Genetic diversity was measured in three upstream and two downstream populations under the influence of the Tucuruí Hydroelectric Dam. Our findings provide evidence for low levels of genetic diversity in H. marginatus of the Tocantis basin possibility related to the Dam construction. The Fst and Rst analysis fits well with migratory characteristics of H. marginatus, suggesting the existence of a gene flow mainly in the upstream or downstream directions. To test the hypothesis that the Dam was responsible for the detected reduction on this species genetic diversity, a large number of genetic markers are recommended, covering geographic distribution range of the fish species

Genetic structure of red-handed howler monkey populations in the fragmented landscape of Eastern Brazilian Amazonia

We genotyped 15 microsatellite loci in order to evaluate the effects of habitat fragmentation, caused by flooding of the Tucuruí reservoir, on the genetic structure of Alouatta belzebul in eastern Amazonia. The analysis included two populations sampled in 1984, representing both margins of the Tocantins river, and three populations sampled 18 years later. Minimal differences in the diversity levels between present-day (Ho = 0.62-0.69 and A R = 6.07-7.21) and pre-flooding (Ho = 0.60-0.62 and A R = 6.27-6.77) populations indicated there was no significant loss of genetic variability, possibly because of successful management strategies applied during the flooding. The changes observed were limited to shifts in the composition of alleles, which presumably reflect the admixture of subpopulations during flooding. Given this, there were significant differences in the Rst values (p = 0.05) in all but one between-site comparison. Both present-day and original populations showed a deficit of heterozygotes, which suggests that this may be typical of the species, at least at a local level, perhaps because of specific ecological characteristics. The relatively large number of private alleles recorded in all populations may be a consequence of the Wahlund effect resulting from population admixture or a process of expansion rather than the loss of rare alleles through genetic drift. Additionally, the levels of genetic variability observed in this study were higher than those reported for other species of Neotropical primates, suggesting good fitness levels in these A. belzebul populations. Regular genetic monitoring of remnant populations, especially on islands, should nevertheless be an integral component of long-term management strategies

Performance of intron 7 of the β-fibrinogen gene for phylogenetic analysis: An example using gladiator frogs, Boana Gray, 1825 (Anura, Hylidae, Cophomantinae)

Boana, the third largest genus of Hylinae, has cryptic morphological species. The potential applicability of b-fibrinogen intron 7 – FGBI7 is explored to propose a robust phylogeny of Boana. The phylogenetic potential of FGBI7 was evaluated using maximum parsimony, MrBayes, and maximum likelihood analysis. Comparison of polymorphic sites and topologies obtained with concatenated analysis of FGBI7 and other nuclear genes (CXCR4, CXCR4, RHO, SIAH1, TYR, and 28S) allowed evaluation of the phylogenetic signal of FGBI7. Mean evolutionary rates were calculated using the sequences of the mitochondrial genes ND1 and CYTB available for Boana in GenBank. Dating of Boana and some of its groups was performed using the RelTime method with secondary calibration. FGBI7 analysis revealed high values at informative sites for parsimony. The absolute values of the mean evolutionary rate were higher for mitochondrial genes than for FGBI7. Dating of congruent Boana groups for ND1, CYTB, and FGBI7 revealed closer values between mitochondrial genes and slightly different values from those of FGBI7. Divergence times of basal groups tended to be overestimated when mtDNA was used and were more accurate when nDNA was used. Although there is evidence of phylogenetic potential arising from concatenation of specific genes, FGBI7 provides well-resolved independent gene trees. These results lead to a paradigm for linking data in phylogenomics that focuses on the uniqueness of species histories and ignores the multiplicities of individual gene histories

Evaluating the diversity of Neotropical anurans using DNA barcodes

This study tested the effectiveness of COI barcodes for the discrimination of anuran species from the Amazon basin and other Neotropical regions. Barcodes were determined for a total of 59 species, with a further 58 species being included from GenBank. In most cases, distinguishing species using the barcodes was straightforward. Each species had a distinct COI barcode or codes, with intraspecific distances ranging from 0% to 9.9%. However, relatively high intraspecific divergence (11.4–19.4%) was observed in some species, such as Ranitomeya ventrimaculata, Craugastor fitzingeri, Hypsiboas leptolineatus, Scinax fuscomarginatus and Leptodactylus knudseni, which may reflect errors of identification or the presence of a species complex. Intraspecific distances recorded in species for which samples were obtained from GenBank (Engystomops pustulosus, Atelopus varius, Craugastor podiciferus, and Dendropsophus labialis) were greater than those between many pairs of species. Interspecific distances ranged between 11–39%. Overall, the clear differences observed between most intra- and inter-specific distances indicate that the COI barcode is an effective tool for the identification of Neotropical species in most of the cases analyzed in the present study

Genetic diversity and differentiation of three Brazilian populations of Scarlet ibis (Eudocimus ruber)

The possible origin of the Scarlet ibis population of Cubatão in southern Brazil, and its levels of genetic diversity and differentiation in relation to populations from the country’s northern coast were investigated through the sequences of 980 base pairs of β-fibrinogen intron 7 from a sample of 37 specimens. A total of 19 haplotypes were recorded in the three populations. Despite observed discrepancies in the levels of genetic diversity (π = 0.0017–0.0033; h = 0.60–0.95), AMOVA, K*st and Fst values all indicated that genetic differentiation among the populations was relatively low. This suggests that the Cubatão population was isolated recently from the panmictic population that was once distributed all along the Brazilian coast, although it does not totally refute its possible derivation from a specific population on the north coast. Given our results, genetic management should focus on the minimization of inbreeding, especially in the smaller populations, such as Cubatão. However, a more definitive study, including markers with higher evolutionary rates (e.g. microsatellites) and a much larger sample, would be required before any such actions can be taken

Diagnóstico molecular da infecção por hemoplasmas em gatos domésticos naturalmente infectados da cidade de Belém, Pará

Mycoplasma haemofelis, 'Candidatus Mycoplasma haemominutum' e 'Candidatus Mycoplasma turicensis' são os agentes causadores da micoplasmose felina, que podem causar anemia aguda ou crônica. O objetivo deste trabalho foi determinar a ocorrência de hemoplasmas em gatos domésticos de Belém, Pará. Para isso, 201 gatos foram divididos em três grupos: Grupo A foi composto por 101 gatos de rua capturados pelo Centro de Controle de Zoonoses, o grupo B foi composto por 62 gatos domiciliados e saudáveis e o grupo C foi composto por 38 gatos domiciliados que apresentavam alguma afecção clínica. Foram coletadas amostras de sangue para a realização de Reação em Cadeia pela Polimerase (PCR) para detectar o DNA destes agentes, os quais foram sequenciados e alinhados. A análise estatística foi realizada para detectar a associação entre a infecção, o sexo dos animais e os grupos experimentais. O DNA de pelo menos uma das espécies de hemoplasmas pesquisados foi detectado em 19,9% (40/201) das amostras, sendo o DNA de 'Candidatus M. haemominutum' encontrado em 7,96% (16/201) das amostras, M. haemofelis em 1,49% (3/201) das amostras, enquanto que o DNA de 'Candidatus M. turicensis' foi detectado em 12,93% (26/201) das amostras. O DNA destes três agentes foi detectado em gatos dos grupos A e C, enquanto que no grupo B foi detectado apenas 'Candidatus M. turicensis' e 'Candidatus M. haemominutum' Foi detectada a influência do sexo sobre a infecção hemoplasmas apenas entre 'Candidatus M. haemominutum' e machos. Estes resultados mostraram que os hemoplasmas circulam entre os gatos domésticos em Belém e 'Candidatus M. turicensis' e 'Candidatus M. haemominutum' foram mais comuns do que M. haemofelis, especialmente em gatos vadios

Molecular characterization of Babesia vogeli in dogs from Belém, northern Brazil

Universidade Federal do Pará. Instituto de Ciências Biológicas. Laboratório de Tecnologia Biomolecular, Belém, PA, Brasil.Universidade Federal do Pará. Instituto de Ciências Biológicas. Laboratório de Tecnologia Biomolecular, Belém, PA, Brasil.Universidade Federal do Pará. Instituto de Ciências Biológicas. Laboratório de Tecnologia Biomolecular, Belém, PA, Brasil.Universidade Federal do Pará. Instituto de Ciências Biológicas. Laboratório de Tecnologia Biomolecular, Belém, PA, Brasil.Universidade Federal do Pará. Instituto de Ciências Biológicas. Laboratório de Tecnologia Biomolecular, Belém, PA, Brasil.Universidade Federal Rural da Amazônia. Instituto da Saúde e Produção Animal. Belém , PA, Brasil.Universidade Federal do Pará. Instituto de Ciências Biológicas. Laboratório de Tecnologia Biomolecular, Belém, PA, Brasil.Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Ananindeua, PA, Brasil.Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Ananindeua, PA, Brasil / Universidade Federal do Pará. Instituto de Ciências Biológicas. Laboratório de Tecnologia Biomolecular, Belém, PA, Brasil.Babesiosis is an infectious hemolytic disease that occurs worldwide, and is caused by a protozoan of the Babesia genus (Apicomplexa). Little is known about this genus; therefore, this study conducted a molecular characterization of Babesia spp in naturally infected dogs in northern Brazil. Blood samples were collected from 172 dogs from metropolitan Belém, and screened for Babesia spp using semi-nested polymerase chain reactions. Subsequently, 18S rDNA gene fragments were amplified and sequenced. Alignments of the 27 nucleotide sequences returned fragments measuring 1023 bp in size, which did not include any polymorphic sites (100 per cent identity). This genotype was very similar to the 18S rDNA gene in B. vogeli. This study provides an important molecular characterization of the parasite responsible for canine babesiosis in naturally infected dogs in metropolitan Belém. In addition, the 18S rDNA gene in B. vogeli may represent the most common genotype occurring in South America