Diversity and three-dimensional structures of the alpha Mcr of the methanogenic Archaea from the anoxic region of Tucuruí Lake, in Eastern Brazilian Amazonia

Methanogenic archaeans are organisms of considerable ecological and biotechnological interest that produce methane through a restricted metabolic pathway, which culminates in the reaction catalyzed by the Methyl-coenzyme M reductase (Mcr) enzyme, and results in the release of methane. Using a metagenomic approach, the gene of the a subunit of mcr (mcrα) was isolated from sediment sample from an anoxic zone, rich in decomposing organic material, obtained from the Tucuruí hydroelectric dam reservoir in eastern Brazilian Amazonia. The partial nucleotide sequences obtained were 83 to 95 percent similar to those available in databases, indicating a low diversity of archaeans in the reservoir. Two orders were identified -the Methanomicrobiales, and a unique Operational Taxonomic Unit (OTU) forming a clade with the Methanosarcinales according to low bootstrap values. Homology modeling was used to determine the three-dimensional (3D) structures, for this the partial nucleotide sequence of the mcrα were isolated and translated on their partial amino acid sequences. The 3D structures of the archaean mcrα observed in the present study varied little, and presented approximately 70 percent identity in comparison with the mcrα of Methanopyrus klanderi. The results demonstrated that the community of methanogenic archaeans of the anoxic C1 region of the Tucurui reservoir is relatively homogeneous.

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.

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.

The prion protein and New World primate phylogeny

The PrP C prion protein contains 250 amino acids with some variation among species and is expressed in several cell types. PrP C is converted to PrP Sc by a post-translational process in which it acquires amino acid sequences of three-dimensional conformation of beta-sheets. Variations in the prion protein gene were observed among 16 genera of New World primates (Platyrrhini), and resulted in amino acid substitutions when compared with the human sequence. Seven substitutions not yet described in the literature were found: W -> R at position 31 in Cebuella, T -> A at position 95 in Cacajao and Chiropotes, N-> S at position 100 in Brachyteles, L -> Q at position 130 in Leontopithecus (in the sequence responsible for generating the beta-sheet 1), D -> E at position 144 in Lagothrix (in the sequence responsible for the alpha-helix 1), D-> G at position 147 in Saguinus (also located in the alpha-helix 1 region), and M -> I at position 232 in Alouatta. The phylogenetic trees generated by parsimony, neighbor-joining and Bayesian analyses strongly support the monophyletic status of the platyrrhines, but did not resolve relationships among families. However, the results do corroborate previous findings, which indicate that the three platyrrhine families radiated rapidly from an ancient split.

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

As classificaçöes 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 extinçäo. A presente análise de duas regiöes do DNA, um gene mitocondrial (ND1) e um gene nuclear (regiöes 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 regiäo do ND1 indicam que esta espécie está relacionada mais proximamente aos marmosets amazônicos do que aos da mata Atlântica. Estes resultados reabrem a discussäo sobre diversidade e programas de conservaçäo baseados apenas em classificaçöes taxonômicas tradicionais.

Mitochondrial DNA-like sequence in the nuclear genome of Saguinus (Callitrichinae, Primates): transfer estimation

Seqüências tipo mitocondriais têm comumente sido encontradas no genoma nuclear de diversos organismos. Quando acidentalmente incluídas em estudos de seqüências mitocondriais, diversas conclusöes erröneas podem ser obtidas. No entanto, estes pseudogenes nucleares tipo mitocondriais podem ser usados para a estimativa da taxa relativa de evoluçäo de genes mitocondriais e também como grupo externo em análises filogenéticas. No presente trabalho, seqüências mitocondriais com características do tipo de pseudogene, tais como deleçöes e/ou inserçöes e códons de parada, foram encontradas em tamarins (Saguinus spp., Callitrichinae, Primates). A análise filogenética permitiu a estimativa do tempo da migraçäo da seqüência mitocondrial para o genoma nuclear e algumas inferências filogenéticas. A escolha de um grupo externo näo adequado (Aotus infulatus) näo permitiu uma reconstruçäo filogenética confiável da subfamília Callitrichinae. A divergência bastante antiga de Cebidae (Callitrichinae, Aotinae e Cebinae) pode ter favorecido o aparecimento de homoplasias, obscurecendo a análise.

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

Os guaribas, do gênero Alouatta, que säo os primatas do Novo Mundo com maior distribuiçäo 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 gamaû 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 por cento para todos os agrupamentos, e valores de força de ligaçäo de pelo menos 2, apoiando o agrupamento irmäo de A. fusca e A. belzebul. O estudo também confirmou a presença em A. fusca do elemento de inserçäo Alu, com 150 pares de base, e uma deleçäo de 1,8 kb no pseudogene globina gamaû ja conhecidos nas demais espécies de guaribas. A classificaçäao cladística baseada em dados moleculares é congruente com as de estudos morfológicos, com um isolamento claro do grupo monoespecífico A. caraya em relaçäo ao grupo A. seniculus.

Comparative study of lactate dehydrogenase in fifteen genera of New World monkeys

Electrophoretic variation of LDH was investigated in 3,200 specimens belonging to 28 species and 15 genera of New World monkeys. A small sample of (Old World) Cercopithecus aethiops was also tested for comparison. Variation was observed in seven species, five alleles being detected for both LDHA and LDHB loci. The frequency of the variant alleles was low in almost all species, the exceptions being Callithrix kuhli and Callithrix jacchus penicillata, in which the LDHA*5 allele showed frequencies of 47 per cent and 60 per cent, respectively. In the monomorphic patterns the B4 and A4 bands were the same in all fifteen genera, but differences were observed in the B3A1, B2A2 and BlA3 hybrid bands. Furthermore, only the B4 band was shared by humans, Old World and New World monkeys. An important marker was found in the genus Cebus, which clearly distinguishes the "tufted" and "untufted" groups.

Adenosine deaminase isozyme variation inn Alouatta belzebul with review of data from other primates

Dados sobre os tipos de adenosina deaminase säo reportados em 1067 espécimes de Alouatta belzebul belzebul procedentes da regiäo do rio Tocantins, na Amazônia Brasileira. Oito fenótipos eletroforéticos foram observados, codificados provavelmente por 4 alelos. O grau de polimorfismo observado pode ser classificado como moderno. Dados da literatura indicam que cerca de 40% das espécies de macacos do Velho Mundo e 2 espécies do Novo Mundo säo monomórficas para este locus, e nas espécies ocorre variaçäo, 2-3 alelos säo observados. Em Alouatta belzebul o cromossomo Y está translocado para um autossomo. O locus ADA näo está em desequilíbrio de ligaçäo com os genes determinantes do sexo masculino, e portanto, ou este locus näo está localizado no autossomo indicado, ou está distante da regiäo na qual estes genes foram relocados