Illegal hunting cases detected with molecular forensics in Brazil

Background: Illegal hunting is one of the major threats to vertebrate populations in tropical regions. This unsustainable practice has serious consequences not only for the target populations, but also for the dynamics and structure of tropical ecosystems. Generally, in cases of suspected illegal hunting, the only evidence available is pieces of meat, skin or bone. In these cases, species identification can only be reliably determined using molecular technologies. Here, we reported an investigative study of three cases of suspected wildlife poaching in which molecular biology techniques were employed to identify the hunted species from remains of meat.Findings: By applying cytochrome b (cyt-b) and cytochrome oxidase subunit I (COI) molecular markers, the suspected illegal poaching was confirmed by the identification of three wild species, capybara (Hydrochoerus hydrochaeris), Chaco Chachalaca (Ortalis canicollis) and Pampas deer (Ozotoceros bezoarticus). In Brazil, hunting is a criminal offense, and based on this evidence, the defendants were found guilty and punished with fines; they may still be sentenced to prison for a period of 6 to 12 months.Conclusions: The genetic analysis used in this investigative study was suitable to diagnose the species killed and solve these criminal investigations. Molecular forensic techniques can therefore provide an important tool that enables local law enforcement agencies to apprehend illegal poachers. © 2012 Sanches et al.; licensee BioMed Central Ltd.

Reproductive biology of the guitarfish Rhinobatos percellens (Chondrichthyes, Rhinobatidae) from the São Paulo Coast, Brazil, western South Atlantic Ocean

The reproductive biology of the guitarfish Rhinobatos percellens was studied from 751 specimens caught by bottom pair trawlers off the coast of São Paulo, Brazil, between c. 24° 00′ S; 45° 15′ W and c. 25° 10′ S; 47° 52′ W, from September 2007 to August 2009. The total length (LT) and total mass (MT) relationship for males and females combined was MT = 1·29E-06 LT 3·15 (r = 0·99, n = 751). The mean LT of sexually mature specimens was 548 mm for males and 583 mm for females. Clasper growth was allometric and showed three distinct phases. Most claspers were calcified in specimens of c. 550 mm LT. The mean diameter of the largest oocyte was 29·8 mm, the mean ovarian fecundity was seven oocytes and ovulation occurred between August and November. Uterine fecundity ranged from two to 13 embryos (mean of five embryos). Larger females had higher litter sizes and larger embryos; the size-at-birth was c. 200 mm LT. The hepato-somatic index oscillated seasonally for males and females; the gonado-somatic index had little variation in males, but varied seasonally in females. The presence of many non-pregnant adult females and of encapsulated eggs during two consecutive seasons suggests a resting period between gestations and the possibility of diapause. © 2012 The Authors. Journal of Fish Biology © 2012 The Fisheries Society of the British Isles.

A precautionary tale when describing species in a world of invaders: Morphology, coloration and genetics demonstrate that Lysmata rauli is not a new species endemic to Brazil but a junior synonym of the Indo-Pacific L. vittata

The objective of this study was to investigate morphological variation in traits of systematic relevance and the phylogenetic position, ecology, and reproductive biology of the shrimp Lysmata rauli Laubenheimer and Rhyne, 2010 (Caridea: Hippolytidae), described based only on a single specimen collected in Salvador, Bahia, Brazil. We analyzed a total of 89 specimens from Camamu Bay, Bahia (n = 88) and from S3o Vicente estuary, São Paulo (n = 1). Considerable morphological variation was detected in the rostral spine series, number of segments on the carpus and merus of pereiopod 2, number of spiniform setae on the ventrolateral margin of merus and on the ventral margin of propodus of pereiopods 3-5. Importantly, L rauli can be distinguished neither using morphology, nor coloration from the Indo-Pacific L. vittata (Stimpson, 1860). Furthermore, molecular phylogenetic analyses (using the 16S mt DNA fragment) did not reveal any considerable genetic dissimilarities between L rauli and L vittata. Thus, our results clearly indicate that L rauli is not a new species but a junior synonym of L vittata. The high density observed within the structures of oyster farming indicates that the invasive L vittata lives in crowds in Brazil. The studied population was composed of males, hermaphrodites, and transitional individuals (having characteristics of males and hermaphrodites). The above information suggests that L rauli is a protandric simultaneous hermaphrodite, as it has been observed in all species of Lysmata that have been investigated. Lysmata vittata has invaded the southwestern Atlantic and is present in Bahia, Rio de Janeiro and S3o Paulo, Brazil. © The Crustacean Society, 2013. Published by Brill NV, Leiden.

Comparison of the population biology of Epialtus bituberculatus from two rocky shores with distinct hydrodynamic patterns

The population biology of Epialtus bituberculatus was compared between two different intertidal localities with differing levels of wave exposure. Sampling was conducted monthly between January and December, 2001 on seaweed banks of Sargassum cymosum in the intertidal zone of the rocky shores Grande (GR) (23°23′S-45°03′W) and Domingas Dias (DD) (23°29′S-45°08′W). Four hundred and twenty-eight crabs were captured at the GR site: 111 juvenile males, 106 adult males, 57 juvenile females, 17 adult females and 137 ovigerous females; while 455 specimens were obtained at the DD site: 76 juvenile males, 113 adult males, 37 juvenile females, 40 adult females and 189 ovigerous females. The population from GR showed a non-normal distribution and from DD a normal distribution. The sex-ratio (female/male) was 1:0.97 at GR (χ2 = 0.77, P = 0.084), whereas it was 1:1.41 at DD (χ2 = 13.03, P < 0.001). The largest individuals occurred at DD (U = 78249.0, P < 0.001). The estimated size at sexual maturity was 6.3 and 5.0 mm carapace width (CW) for males, and 5.4 and 5.2 mm CW for females, from GR and DD, respectively. The observed differences in E. bituberculatus between the studied localities might be explained by the different degrees of wave exposure between sites. However, other factors that might also explain the observed differences (e.g. temperature, salinity and food availability) cannot be discarded as relevant in influencing the population structure between sites herein studied. © 2012 Marine Biological Association of the United Kingdom.

Reproductive biology of two macrourid fish, Nezumia aequalis and Coelorinchus mediterraneus, inhabiting the NW Mediterranean continental margin (400-2000m)

Nezumia aequalis and Coelorinchus mediterraneus are abundant species on the upper and lower continental slopes, respectively, in the Mediterranean Sea. A study on the reproductive strategy of the two species was conducted on the Catalan margin (NW Mediterranean). The reproductive cycle of both species was investigated using visual analyses of gonads and histological screening. The shallower species, N. aequalis, showed continuous reproduction with a peak of spawning females in winter months. In contrast, the deeper-living species, C. mediterraneus, showed semi-continuous reproduction with a regression period during the spring. Juveniles of N. aequalis were present in all seasons, but most abundant in the spring. Only two juveniles of C. mediterraneus were found. Both species had asynchronous oocyte development. The average fecundity of N. aequalis was 10,630 oocytes per individual, lower than known for the same species in the Atlantic Ocean. The fecundity of C. mediterraneus was measured for the first time in this study, with an average of 7693 oocytes per individual. Males of both species appear to have semi-cystic spermatogenesis. © 2013 Elsevier Ltd.

Avanços recentes em biologia celular e molecular, questões éticas implicadas e sua abordagem em aulas de biologia no ensino médio: um estudo de caso

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

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.

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.

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.

Caracterização sorológica e detecção molecular do HTLV em amostras de pacientes com distúrbios neurológicos no Estado do Pará, Brasil (1996-2005)

ABSTRACT: Human T-lymphotropic virus tipe 1 is recognized as the etiologic agent of tropical spastic paraparesis/HTLV-1 associated myelopathy (TSP/HAM). A very similar clinical disease has been increasingly associated to HTLV-2, whose pathogenicity still requires further assessments. This transversal, retrospective epidemiological survey aimed to determine the prevalence of HTLV among individuals with neurological disturbances and further evaluate cases of inconclusive serology using molecular biology methods. The present study involved patients inhabitants of Pará State and/or admitted at health institutions of the and who were referred to the Virology Section of Instituto Evandro Chagas (IEC) by local doctors between January of 1996 and December 2005, to search for the presence of HTLV-1/2 serum antibodies. Of these patients 353 were selected, with age between 9 months and 79 years, who presented at least one signal or symptom of the Marsh’s Complex (1996), as well as had HTLV-1/2 positive serology at screening and confirmatory ELISA. The overall prevalence of HTLV antibodies by ELISA as 8,8% (31/353), with rates of 10,6% (19/179) and 6,9% (12/174) for female and male patients, respectively. Among HTLV-1/2 the 31 ELISA-positive patients it was noted that 15 (48.4%) of 31 had paresis (n = 8), parestesis (n = 5), and paraplegia (n = 3). Of these 31 HTLV ELISA positive patients, 25 could be submitted to WB for assessment of viral types, which were distributed as follow: 80% (20/25) were HTLV-1, 12% (3/25) were HTLV-2, one case was of HTLV-1+HTLV-2 infection (4%), and serum from one patient yielded an indeterminate profile (4%). Only 14 of these 25 patients could be re-localised for collection of an additional sample for molecular analysis. It was observed that 78.6% of samples typed by WB had the proviral TAX region successfully amplified by nested-PCR. In addition, types were confirmed as based on results obtained from the amplification of the POL region using real-time PCR; this denoted good specificity and sensitivity of the WB used in this study. The sample defined as HTLV-1+HTLV-2 infection by WB was amplified in its TAX region but real time PCR confirmed HTLV-1 infection only. The patient with WB indeterminate profile and one of samples typed as HTLV-2 by WB were amplified by nested-PCR but the real time PCR was negative for HTLV-1 and HTLV-2 in both samples. One patient presenting clinical manifestations of crural myalgia and parestesia with duration of about 7 years reacted HTLV-2-positive by both WB and real-time PCR, a denoting a clear HTLV-2- related chronic myelopathy. This study has identified a case of possible vertical transmission in two distinct situations: a patient whose mother presented antibodies for HTLV-1 by WB and two sisters who reacted HTLV-1-positive by WB and real-time PCR. Although of epidemiological relevance, results from this study warrant further and broader analyses concerning the molecular epidemiology of HTLV types and subtypes HTLV. In addition, a more complete clinical assessment of neurological symptoms should be further performed, in order to better characterise cases of HTLV-related chronic myelopathy in our region.

Reproductive biology of Plagioscion magdalenae (Teleostei: Sciaenidae) (Steindachner, 1878) in the bay of Marajo, Amazon Estuary, Brazil

Plagioscion magdalenae (pescada-curuca) é um sciaenídeo bentopelágico, de importância comercial, amplamente distribuído na bacia do rio Amazonas. O objetivo deste trabalho foi descrever a biologia reprodutiva dessa espécie na baía do Marajó, estuário Amazônico, Brasil. Neste estudo foi determinado o estádio do desenvolvimento gonadal, tamanho de primeira maturação gonadal (L₅₀), proporção entre sexos, época e o tipo de desova. A coleta foi realizada bimestralmente no período de dezembro de 2005 a outubro de 2006. Foi examinado um total de 251 exemplares, variando entre 220 e 590 mm de comprimento total (CT). A relação peso-comprimento para fêmeas, machos e sexos agrupados foi altamente significativa, com alometria positiva. O L₅₀ foi de 279 mm considerando sexos agrupados, 305 e 269 mm CT para fêmeas e machos respectivamente. A proporção entre sexos para o total de indivíduos foi favorável aos machos (2,02 machos: 1 fêmea). Macroscopicamente, as gônadas foram classificadas em imatura, em maturação, matura e desovada. Considerando-se as avaliações macro e microscópicas das gônadas, foi registrado um período prolongado de desova, principalmente entre agosto e fevereiro.

New molecular evidence supports the species status of Kaempfer's Woodpecker (Aves, Picidae)

ABSTRACT: Kaempfer's Woodpecker (Celeus obrieni) is the only species of the genus Celeus endemic to Brazil. The description of this taxon as a subspecies of the Rufous-headed Woodpecker (Celeus spectabilis) was based on a single specimen. While C. obrieni and C. spectabilis are now considered separate species based on morphological and limited molecular evidence, no study has critically tested the reciprocal monophyly and degree of evolutionary independence between these taxa with several specimens. Herein, fragments of the mitochondrial and nuclear DNA of three recently-collected specimens of C. obrieni were analyzed to evaluate the degree of evolutionary differentiation of this taxon with respect to C. spectabilis. The results confirm the reciprocal monophyly between the specimens of C. obrieni and C. spectabilis. The genetic divergence values for the two taxa also support their classification as independent species, given that they are greater than the values recorded among other closely-related but separate species of the same genus. Estimates of the divergence time between C. obrieni and C. spectabilis indicate that cladogenesis occurred in the mid-Pleistocene, during a period of major climatic fluctuations and landscape change, consistent with the hypothesis of a corridor of open bamboo dominated forests and woodland stretching.

Molecular analysis of three FUT3 gene single nucleotide polymorphisms and their relationship with the lewis erythrocytary phenotype in a human population of japanese-ancestry living in Tomé Açu, a town in the Brazilian Amazon

The Lewis blood group system involves two major antigens, Le^ª and Le^b. Their antigenic determinants are not primary gene products but are synthesized by the transfer of sugar subunits to a precursory chain by a specific enzyme which is the product of the FUT3 gene (Lewis gene). The presence of three FUT3 gene single nucleotide polymorphisms (SNPs) (59T > G; 508G > A and 1067T > A) was related to the Lewis phenotype of erythrocytes from 185 individuals of Japanese ancestry living in the town of Tomé-Açu in the Brazilian Amazon region. This relationship was detected using a serological hemagglutination test and the Dot-ELISA assay along with the molecular technique PCR-RFLP. We found that the three SNPs investigated in this study only accounted for a proportion of the Lewis-negative phenotype of the erythrocytes.