Amplificação cruzada e padronização de marcadores microssatélites em Colossoma macropomum (tambaqui)

A espécie Colossoma macropomum (tambaqui), muito cultivada em piscicultura por todo o Brasil, já apresenta perda de variabilidade genética em alguns estoques. O objetivo deste trabalho foitestar para esta espécie a amplificação cruzada de 52 locos microsatélites desenvolvidos originalmente para outras espécies da ictiofauna. Para tanto, foram coletados indivíduos de tambaqui de pisciculturada região de Goiânia, Brasil, e a extração do DNA para amplificação foi feita a partir de tecido muscular. Os testes de amplificação cruzada foram realizados alterando as temperaturas de cada loco, buscando a padronização da amplificação. Dos 52 locos testados, 16 apresentaram resultados satisfatórios de amplificação cruzada, o que permitiu a definição dos genótipos. Esses resultados indicam que existeum grande potencial de transferibilidade de marcadores microssatélites entre espécies diferentes da ictiofauna. Esses marcadores podem ser usados em estudos genético-populacionais desta espécie nosprogramas de conservação, manejo e melhoramento deste recurso pesqueiro

Variabilidade genética em bandos de queixada (Tayassu pecari) do Parque Nacional das Emas utilizando marcadores RAPD (Random Amplified Polymorphic DNA)

Nowadays, the analysis of genetic variability has a highlighted roll in the definition of conservation strategies and natural populations management. In this context, the goal of this study was to evaluate the pattern of genetic variability on Tayassu pecari groups from Emas National Park, using RAPD markers. DNA from 182 individuals, distributed among eight groups, were extracted and used to amplify 10 primers previously selected through PCR. The obtained data were used to estimate the magnitude and distribution of variability within and among the groups using AMOVA. In order to analyze, in an explicit way, the patterns of spatial variation patterns, Pearson correlation coefficient (r) was estimated between the matrix of genetic distances and geographic among the groups, considering their central area of life, estimated from telemetry data. From the ten primers, 129 loci were obtained, which 88% (114) were polymorphic, ranging between 37% and 78% in the groups. The value of ?sT obtained from AMOVA was equal to 0.11 (P < 0.0001 - 10000 permutations); a high value considering the only local population distributed in regional scale. Distances among pares of groups (?sT) ranged between 4% and 29%, illustrating the heterogeneity of variability on spatial scale. Key words: Tayassu pecari, RAPD, genetic variability.O estudo das espécies presentes nos fragmentos remanescentes e/ou preservadas nos parques e reservas ainda existentes ajuda a definir estratégias de manejo, de conservação e de uso sustentado dos recursos naturais dos diferentes biomas. A análise da variabilidade genética possui hoje um papel de destaque na definição dessas estratégias. Nesse contexto, o objetivo deste trabalho foi avaliar os padrões de variabilidade genética em bandos de queixada (Tayassu pecari) do Parque Nacional das Emas (PNE), utilizando marcadores do tipo RAPD. O DNA de 182 indivíduos, distribuídos em oito bandos, foi extraído e utilizado para a amplificação via PCR (reação em cadeia da polimerase) de dez primers previamente selecionados. Os dados foram utilizados para estimar a magnitude e a distribuição da variabilidade entre bandos e dentro dos bandos por meio da Análise de Variância Molecular (AMOVA). Com base nos dez primers, foram obtidos 129 locos, dos quais 88% (114) foram polimórficos, variando entre 37% e 78% nos bandos. O valor das distâncias dos pares de bandos ?sT obtido pela AMOVA foi igual a 0,11 (P < 0,0001 - 10.000 permutações), que pode ser considerado elevado, já que se trata, de uma única grande população local distribuída em uma escala regional (PNE). As distâncias entre os pares de bandos (?sT) variaram entre 4% e 29%, ilustrando a heterogeneidade da variabilidade nessa escala espacial. Com base no cálculo indireto do fluxo gênico, podese perceber que o número médio de indivíduos migrantes, por geração, entre os bandos de queixada, foi igual a dois, valor suficiente para suprimir a maior parte dos efeitos da deriva genética sob a diferenciação entre os bandos. Palavras-chave: Tayassu pecari, RAPD, variabilidade genética

Disentangling landscape effects on population genetic structure of a Neotropical savanna tree

ABSTRACTGeographical patterns of genetic variation and population structure and their relationship with habitat loss and fragmentation have been investigated at distinct scales and extents using spatially explicit statistics. Here, we analyzed population genetic structure of Dipteryx alata (Fabaceae; the “baru” tree), an economically important tree widely distributed in Central Brazil that is endemic to the “Cerrado” (savanna) biome, relating population genetic divergence with broad-scale landscape patterns. Genetic divergence among 25 populations, estimated based on eight microsatellite loci for a total of 644 individuals, was correlated with landscape features using several forms of Mantel tests (standard Mantel correlations, Mantel correlograms, partial correlations, and multiple regression). Patterns of genetic divergence are significantly correlated with human-driven landscape features of habitat loss and fragmentation, after taking into account isolation-by-distance and historical effects of range expansion after the last glacial maximum. Our findings present important implications for the conservation of this species, because interruption of gene flow by habitat loss and fragmentation jeopardize the persistence of population in the medium- and long term due to disruption of demographic patterns, increased endogamy, and recruitment problems.© 2014 Associação Brasileira de Ciência Ecológica e Conservação. Published by Elsevier Editora Ltd

Genetic variability in natural populations of Zeyheria montana mart. from the Brazilian Cerrado

Zeyheria montana, an endemic species of the Bignoniaceae family from the Brazilian Cerrado's known for its anti-cancer properties, is widely used as imuno stimulant in the popular medicine and its therapeutic activity must be validated by scientific data. The objective of this work was to evaluate the genetic variability of eight plant populations collected within the state of São Paulo, Brazil, via Random Amplification of Polymorphic DNA (RAPD) used as molecular markers. After an optimized protocol for the amplification reaction, nine selected primers generated 105 reproducible bands, indicating up to 60% polymorphism. Analysis of molecular variance (AMOVA) revealed higher genetic variation within populations (84.03%) than among populations (15.97%). The variation values estimated by phiST (0.160) indicated moderate to high inter population structuration. Levels of similarity inter plants with genetic and geographical distances, estimated by the unweighted pair-group method analysis (UPGMA) clustering and non-metric multidimensional scaling (NMDS) ordination methods and by the Mantel test (-0.2345 p = 0.118) denoted that the structure found follows the island model, which assumes that a single population of infinite size may have initiated the existing populations of Zeyheria montana, with no spatial position correlation. Based on the obtained data, a germplasm bank from individuals representing the species variability was established. Furthermore the information here reported can be of importance to develop strategies for the conservation of Z. montana.Zeyheria montana, planta arbustiva da família Bignoniaceae, é uma espécie endêmica do Cerrado e possui atividade anti-câncer, sendo utilizada como estimulante na medicina popular. O objetivo deste estudo foi avaliar a variabilidade genética de oito populações localizadas no estado de São Paulo, utilizando marcadores moleculares de Polimorfismo de DNA Amplificado ao Acaso (RAPD). Após a otimização da reação de amplificação, nove iniciadores selecionados geraram 105 fragmentos RAPD reprodutíveis, sendo que a maioria (60,0%) foi polimórfica. A análise molecular de variância (AMOVA) mostrou que a variabilidade dentro de populações (84,03%) foi maior que entre populações (15,97%). As estimativas de variação fiST (0,1597) indicam estruturação populacional moderadamente alta. O agrupamento por meio de UPGMA, a ordenação pelo NMDS e o teste de Mantel entre as matrizes de distâncias genéticas e geográficas demonstraram que a estruturação encontrada segue um modelo de "ilhas", onde uma única população de tamanho infinito pode ter dado origem às populações atuais de Zeyheria, sem relação com sua posição espacial. Com base nos resultados obtidos foi estruturado um banco de germoplasma de indivíduos, representando a variabilidade da espécie. Adicionalmente, as informações deste estudo são importantes para dar suporte a estratégias de conservação de Z. montana

Divergence among local populations of Eugenia dysenterica in response to edaphic patterns and spatial distribution

A domesticação e a utilização de espécies nativas em sistemas de produção muitas vezes são inviabilizadas pela falta de conhecimento prévio sobre a variabilidade genética. Uma vez quantificada, esta variabilidade pode ser útil tanto para o melhoramento genético da espécie quanto em programas de conservação. O objetivo deste trabalho foi avaliar a diferenciação, com base em caracteres genéticos e fenotípicos, entre dez subpopulações de Eugenia dysenterica DC. nativas da região sudeste do Estado de Goiás. Foram utilizados testes de Mantel a fim de comparar os padrões de variação genética, com base em oito locos isoenzimáticos, e caracteres fenotípicos (caracteres morfológicos e demográficos), entre as subpopulações, e estabelecer suas relações com as diferenças geográficas e edáficas entre as regiões. Os testes de Mantel sugeriram que o principal fator determinando a divergência genética é a distribuição geográfica das subpopulações, em um modelo no qual existe um balanço entre deriva genética atuando dentro das subpopulações e fluxo gênico em curtas distâncias ligando as subpopulações. A variação fenotípica, por sua vez, é melhor explicada pelos padrões edáficos e pela distribuição espacial. Esses resultados podem servir de guia para a coleta de germoplasma visando a sua utilização em programa de melhoramento genético desta espécie.The domestication and management of native plant species for uses in agricultural systems is usually constrained by the absence of knowledge about genetic variability, population structure and evolutionary processes involved in population differentiation in geographic space. A full understanding of these patterns and processes implies in analyzing multiple characters. In this paper, differentiation among ten local populations of Eugenia dysenterica DC. from Southeastern region of Goiás state, Central Brazil, was analyzed. Mantel tests were used to evaluate the relationships between genetic (eight loci from isozymes) and phenotypic (morphological and demographic characters) patterns of population differentiation, in relation to spatial distribution and edaphic differences among regions. The results from Mantel's tests suggested that the main factor acting on genetic differentiation is the geographic distribution of local populations, in a stochastic model that balances local drift within local population and short-distance gene flow among them. The phenotypic differentiation, on the other hand, is better explained by edaphic patterns and also by the geographic distribution. These results support the idea of neutral (or quasi-neutral) evolutionary processes in isozymic markers and shows that genetic divergence among local populations is highly structured in geographic space, independently of variations in edaphic patterns and phenotypic variation

The complete mitochondrial genome of the aquatic coralsnake Micrurus surinamensis (Reptilia, Serpentes, Elapidae)

In this study, we report the first complete mitochondrial genome sequence of the Aquatic Coralsnake Micrurus surinamensis. The mitochondrial genome lengthis 17,375 bp, comprising 13 protein-coding genes, 2 rRNA (12S and 16S) and 22 tRNA, as well as two typical control regions. Phylogenetic analysis based upon 13 protein-coding genes showed clusters based on terrestrial and marine species

Population structure of Eupemphix nattereri (Amphibia, Anura, Leiuperidae) from Central Brazil

This study reports on 156 specimens of the amphibian Eupemphix nattereri, a widely distributed leiuperid, obtained from 11 municipalities of central Brazil. The extent of genetic variation was quantified by determining the mean number of alleles per locus and the proportion of polymorphic loci. An analysis of molecular variance (AMOVA) was performed on the random amplified polymorphic DNA (RAPD) haplotypes. The genetic distances obtained by calculating pairwise phist among local samples were used to determine population relationships using the unweighted pair-group method (UPGMA) and non-metric multidimensional scaling (NMDS). The cophenetic correlation was calculated to confirm agreement between the genetic matrix and the unweighted pair group method with averages (UPGMA) dendrogram. To determine if genetic distances were correlated to geographical distances we constructed pairwise genetic distance and geographical distance matrices and compared them using the Mantel test. The AMOVA results indicated significant genetic differences (p < 0.001) between E. nattereri populations, representing 69.5% of the within population genetic diversity. The Mantel test showed no significant correlation (r = 0.03; p = 0.45) between the genetic and geographical distance matrices. Our findings indicate that the genetic variation of E. nattereri populations was randomly distributed in geographic space and that gene flow for this species is probably structured at spatial scales smaller than those between our sample

Coralsnake venomics: Analyses of venom gland transcriptomes and proteomes of six Brazilian taxa

Venom gland transcriptomes and proteomes of six Micrurus taxa (M. corallinus, M. lemniscatus carvalhoi, M. lemniscatus lemniscatus, M. paraensis, M. spixii spixii, and M. surinamensis) were investigated, providing the most comprehensive, quantitative data on Micrurus venom composition to date, and more than tripling the number of Micrurus venom protein sequences previously available. The six venomes differ dramatically. All are dominated by 2–6 toxin classes that account for 91–99% of the toxin transcripts. The M. s. spixii venome is compositionally the simplest. In it, three-finger toxins (3FTxs) and phospholipases A2 (PLA2s) comprise >99% of the toxin transcripts, which include only four additional toxin families at levels ≥0.1%. Micrurus l. lemniscatus venom is the most complex, with at least 17 toxin families. However, in each venome, multiple structural subclasses of 3FTXs and PLA2s are present. These almost certainly differ in pharmacology as well. All venoms also contain phospholipase B and vascular endothelial growth factors. Minor components (0.1–2.0%) are found in all venoms except that of M. s. spixii. Other toxin families are present in all six venoms at trace levels (<0.005%). Minor and trace venom components differ in each venom. Numerous novel toxin chemistries include 3FTxs with previously unknown 8- and 10-cysteine arrangements, resulting in new 3D structures and target specificities. 9-cysteine toxins raise the possibility of covalent, homodimeric 3FTxs or heterodimeric toxins with unknown pharmacologies. Probable muscarinic sequences may be reptile-specific homologs that promote hypotension via vascular mAChRs. The first complete sequences are presented for 3FTxs putatively responsible for liberating glutamate from rat brain synaptosomes. Micrurus C-type lectin-like proteins may have 6–9 cysteine residues and may be monomers, or homo- or heterodimers of unknown pharmacology. Novel KSPIs, 3× longer than any seen previously, appear to have arisen in three species by gene duplication and fusion. Four species have transcripts homologous to the nociceptive toxin, (MitTx) α-subunit, but all six species had homologs to the β-subunit. The first non-neurotoxic, non-catalytic elapid phospholipase A2s are reported. All are probably myonecrotic. Phylogenetic analysis indicates that the six taxa diverged 15–35 million years ago and that they split from their last common ancestor with Old World elapines nearly 55 million years ago. Given their early diversification, many cryptic micrurine taxa are anticipated

Coralsnake Venomics: Analyses of Venom Gland Transcriptomes and Proteomes of Six Brazilian Taxa

Venom gland transcriptomes and proteomes of six Micrurus taxa (M. corallinus, M. lemniscatus carvalhoi, M. lemniscatus lemniscatus, M. paraensis, M. spixii spixii, and M. surinamensis) were investigated, providing the most comprehensive, quantitative data on Micrurus venom composition to date, and more than tripling the number of Micrurus venom protein sequences previously available. The six venomes differ dramatically. All are dominated by 2–6 toxin classes that account for 91–99% of the toxin transcripts. The M. s. spixii venome is compositionally the simplest. In it, three-finger toxins (3FTxs) and phospholipases A2 (PLA2s) comprise >99% of the toxin transcripts, which include only four additional toxin families at levels ≥0.1%. Micrurus l. lemniscatus venom is the most complex, with at least 17 toxin families. However, in each venome, multiple structural subclasses of 3FTXs and PLA2s are present. These almost certainly differ in pharmacology as well. All venoms also contain phospholipase B and vascular endothelial growth factors. Minor components (0.1–2.0%) are found in all venoms except that of M. s. spixii. Other toxin families are present in all six venoms at trace levels (<0.005%). Minor and trace venom components differ in each venom. Numerous novel toxin chemistries include 3FTxs with previously unknown 8- and 10-cysteine arrangements, resulting in new 3D structures and target specificities. 9-cysteine toxins raise the possibility of covalent, homodimeric 3FTxs or heterodimeric toxins with unknown pharmacologies. Probable muscarinic sequences may be reptile-specific homologs that promote hypotension via vascular mAChRs. The first complete sequences are presented for 3FTxs putatively responsible for liberating glutamate from rat brain synaptosomes. Micrurus C-type lectin-like proteins may have 6–9 cysteine residues and may be monomers, or homo- or heterodimers of unknown pharmacology. Novel KSPIs, 3× longer than any seen previously, appear to have arisen in three species by gene duplication and fusion. Four species have transcripts homologous to the nociceptive toxin, (MitTx) α-subunit, but all six species had homologs to the β-subunit. The first non-neurotoxic, non-catalytic elapid phospholipase A2s are reported. All are probably myonecrotic. Phylogenetic analysis indicates that the six taxa diverged 15–35 million years ago and that they split from their last common ancestor with Old World elapines nearly 55 million years ago. Given their early diversification, many cryptic micrurine taxa are anticipated