Gen?tica de popula??es de on?a-pintada (Panthera onca) em biomas brasileiros

Made available in DSpace on 2015-04-14T13:09:21Z (GMT). No. of bitstreams: 1 426215.pdf: 1203023 bytes, checksum: a4c95024eb4a04a350ac7a3aeb621944 (MD5) Previous issue date: 2010-02-25Atualmente, a redu??o do tamanho populacional constitui um problema real para muitas popula??es selvagens e cativas, e muitos estudos t?m sido realizados nesse contexto com o intuito de identificar ?reas de manejo e prote??o de esp?cies amea?adas. O manejo de popula??es naturais tem como objetivo assegurar h?bitats adequados para manter popula??es em tamanhos vi?veis evitando assim que os efeitos do endocruzamento se pronunciem, al?m de manter corredores para facilitar a dispers?o dos organismos e consequentemente o fluxo g?nico entre popula??es. Os grandes carn?voros, por necessitarem de grandes ?reas de vida e serem usualmente perseguidos por ca?adores, s?o bastante vulner?veis ? fragmenta??o de h?bitats Devido ao fato de serem predadores-topo, sua extin??o local geralmente leva ? altera??o de todo o ecossistema. Desta forma, sua conserva??o afeta, de maneira direta e indireta, muitos outros organismos. Os carn?voros est?o entre os organismos que causam maiores desafios e preocupa??es ?s autoridades referentes ? conserva??o. ?reas consideravelmente grandes s?o necess?rias para englobar a ?rea de vida de um ?nico individuo, e territ?rios ainda maiores s?o necess?rios para abranger uma comunidade inteira deste grupo. A on?a-pintada, o maior fel?deo das Am?ricas, encontra-se atualmente em menos de 50% da sua distribui??o original e muitas ?reas remanescentes n?o apresentam tamanho e disponibilidade suficiente de presas para manter uma popula??o saud?vel em longo prazo. No Brasil, a Bacia Amaz?nica e o Pantanal s?o as maiores ?reas de distribui??o da esp?cie onde ainda se encontra popula??es grandes o suficiente para uma viabilidade por um longo per?odo de tempo. No entanto, pouco se sabe sobre a din?mica das popula??es de on?a-pintada nesses biomas, havendo assim uma extrema necessidade de an?lises em n?vel gen?tico-populacional da esp?cie. O presente trabalho teve como objetivo analisar 52 indiv?duos provenientes do Pantanal brasileiro amostrados no per?odo de 2001 a 2008, e fazer infer?ncias gen?ticas sobre esta popula??o, bem como compar?-la com uma ?rea previamente estudada na Mata Atl?ntica, onde altos n?veis de estrutura??o foram encontrados. Foram analisados ?ndices de diversidade gen?tica intra-populacional e calculados ?ndices de estrutura??o (Fst e Rst) assim como an?lise Bayesiana de estrutura??o no programa STRUCTURE. Os n?veis de variabilidade foram bastante altos e compar?veis com aqueles encontrados para a esp?cie quando analisada de uma forma mais ampla (em escala filogeogr?fica). Quando as amostras do Pantanal foram analisadas em rela??o ? sua estrutura??o, os dados indicaram a presen?a de apenas uma popula??o, sugerindo que a regi?o amostrada (Pantanal sul) consiste de uma s? unidade gen?tica. No entanto, quando as popula??es da Mata Atl?ntica foram inclu?das na an?lise, as amostras do Pantanal foram alocadas em duas unidades gen?ticas incompletamente diferenciadas, devido provavelmente ? influ?ncia de parentesco entre alguns dos indiv?duos desta regi?o, em combina??o ? prov?vel miscigena??o hist?rica com ?reas transicionais entre os dois biomas. Este parece ter sido o caso da popula??o amostrada na ?rea de influ?ncia da UHE Porto Primavera (MS/SP), situada no limite interior do bioma Mata Atl?ntica e que atualmente encontra-se extinta por a??o humana. Os resultados obtidos ap?iam a infer?ncia de que, no passado, havia conectividade gen?tica entre popula??es do Pantanal e da Mata Atl?ntica de Interior, embasando o delineamento de poss?veis a??es de manejo a fim de retomar a conex?o entre estes dois biomas. Al?m disso, os dados do Pantanal representam a primeira amostragem de uma popula??o geneticamente saud?vel de on?as-pintadas, podendo servir como base para a avalia??o e monitoramento da variabilidade observada nesta esp?cie em regi?es fragmentadas

Genética de populações de onça-pintada (Panthera onca) em biomas brasileiros

Atualmente, a redução do tamanho populacional constitui um problema real para muitas populações selvagens e cativas, e muitos estudos têm sido realizados nesse contexto com o intuito de identificar áreas de manejo e proteção de espécies ameaçadas. O manejo de populações naturais tem como objetivo assegurar hábitats adequados para manter populações em tamanhos viáveis evitando assim que os efeitos do endocruzamento se pronunciem, além de manter corredores para facilitar a dispersão dos organismos e consequentemente o fluxo gênico entre populações. Os grandes carnívoros, por necessitarem de grandes áreas de vida e serem usualmente perseguidos por caçadores, são bastante vulneráveis à fragmentação de hábitats Devido ao fato de serem predadores-topo, sua extinção local geralmente leva à alteração de todo o ecossistema. Desta forma, sua conservação afeta, de maneira direta e indireta, muitos outros organismos. Os carnívoros estão entre os organismos que causam maiores desafios e preocupações às autoridades referentes à conservação. Áreas consideravelmente grandes são necessárias para englobar a área de vida de um único individuo, e territórios ainda maiores são necessários para abranger uma comunidade inteira deste grupo. A onça-pintada, o maior felídeo das Américas, encontra-se atualmente em menos de 50% da sua distribuição original e muitas áreas remanescentes não apresentam tamanho e disponibilidade suficiente de presas para manter uma população saudável em longo prazo.No Brasil, a Bacia Amazônica e o Pantanal são as maiores áreas de distribuição da espécie onde ainda se encontra populações grandes o suficiente para uma viabilidade por um longo período de tempo. No entanto, pouco se sabe sobre a dinâmica das populações de onça-pintada nesses biomas, havendo assim uma extrema necessidade de análises em nível genético-populacional da espécie. O presente trabalho teve como objetivo analisar 52 indivíduos provenientes do Pantanal brasileiro amostrados no período de 2001 a 2008, e fazer inferências genéticas sobre esta população, bem como compará-la com uma área previamente estudada na Mata Atlântica, onde altos níveis de estruturação foram encontrados. Foram analisados índices de diversidade genética intra-populacional e calculados índices de estruturação (Fst e Rst) assim como análise Bayesiana de estruturação no programa STRUCTURE. Os níveis de variabilidade foram bastante altos e comparáveis com aqueles encontrados para a espécie quando analisada de uma forma mais ampla (em escala filogeográfica). Quando as amostras do Pantanal foram analisadas em relação à sua estruturação, os dados indicaram a presença de apenas uma população, sugerindo que a região amostrada (Pantanal sul) consiste de uma só unidade genética. No entanto, quando as populações da Mata Atlântica foram incluídas na análise, as amostras do Pantanal foram alocadas em duas unidades genéticas incompletamente diferenciadas, devido provavelmente à influência de parentesco entre alguns dos indivíduos desta região, em combinação à provável miscigenação histórica com áreas transicionais entre os dois biomas. Este parece ter sido o caso da população amostrada na área de influência da UHE Porto Primavera (MS/SP), situada no limite interior do bioma Mata Atlântica e que atualmente encontra-se extinta por ação humana.Os resultados obtidos apóiam a inferência de que, no passado, havia conectividade genética entre populações do Pantanal e da Mata Atlântica de Interior, embasando o delineamento de possíveis ações de manejo a fim de retomar a conexão entre estes dois biomas. Além disso, os dados do Pantanal representam a primeira amostragem de uma população geneticamente saudável de onças-pintadas, podendo servir como base para a avaliação e monitoramento da variabilidade observada nesta espécie em regiões fragmentadas.Population size reduction currently constitutes a real problem for several natural populations, and many studies have focused on the identification and management of adequate protected areas for threatened species. The conservation of natural areas aims to guarantee good-quality habitats to keep populations at a viable size, which includes an avoidance of potentially deleterious effects of inbreeding. Additionally, conservation plans aim to keep dispersal corridors and consequently to maintain gene flow among populations that were originally connected. Large carnivores, due to their need for large home ranges and frequent persecution by hunters, are extremely vulnerable to habitat fragmentation. Since they are top-predators, their local elimination may cause the alteration of the whole ecosystem, while their protection might impact the persistence and demography of several co-occurring species. Carnivores usually cause major challenges to conservation managers, since considerably large areas are necessary to encompass the home range of a single individual and even larger regions are required to comprise an entire population. The jaguar is the largest predator in the Americas, and currently persists in less than 50% of its original distribution. Also, many remnant areas do not contain sufficient habitat and prey base to hold viable populations in the long term.In Brazil, the Amazon Basin and the Pantanal are the largest areas of the current distribution of the species, and where populations with high probability of long-term survival are still found. However, little is known about the dynamics of jaguar populations in these biomes, and thus population-genetic analyses are extremely necessary. The present study aimed to analyze 52 individuals sampled in the southern Pantanal from 2001 and 2008 to make genetic inferences on jaguar populations, as well as to compare them to previously investigated fragments in the Atlantic Forest biome, where high levels of structuring had been found. We estimated genetic differentiation among populations using an AMOVA approach to generate Fst and Rst indices. Population structuring analyses were also performed with the Bayesian approach implemented in the software STRUCTURE. Variability indices were quite high, and comparable to those found for the species when analyzed under on a phylogeographic scale. When Pantanal populations were assessed separately, a single genetic cluster was inferred, supporting the expectation of demographic connectivity throughout this area. However, when Atlantic Forest jaguars were also included in the analysis, the Pantanal population was divided into two groups, probably due to relatedness among some of the sampled individuals, combined with complex historical admixture with respect to transitional areas between the two biomes. One such area was likely the region adjacent to Porto Primavera dam, on the bank of the upper Paraná river, whose population has already been extirpated due to human activities.Results obtained in the present study support the idea that, in the past, there was genetic connectivity between populations from the Pantanal and the Upper Paraná region, which helps provide baseline data to aid in the design of adequate management actions that may reconnect these biomes. Moreover, the data shown here represent the first jaguar sampling of a genetically healthy local population, and may be used as a comparative reference for the evaluation and monitoring of the observed variability in fragmented regions

Variabilidade genética em três populações de cachorro-do-mato (Cerdocyon thous) inferida através da análise de microssatélites

07

Data from: Population genetics of jaguars (Panthera onca) in the Brazilian Pantanal: molecular evidence for demographic connectivity on a regional scale

Habitat loss and fragmentation are important threats to carnivores worldwide, and can be especially intense for large predators. Jaguars have already been extirpated from over half of their original area of distribution, and few regions still maintain large populations. For these, detailed understanding is crucial for setting appropriate recovery targets in impacted areas. The Pantanal is among the best examples of a region with a large jaguar population in a healthy environment. Here, we analyzed 12 microsatellite loci to characterize genetic diversity and population structure of 52 jaguars sampled in 4 localities of the southern Pantanal, and compared them with prior studies of heavily fragmented populations of the Atlantic Forest. Although we observed some internal structure among the Pantanal localities, our results indicated that this area comprises a single population with high genetic variability. Moreover, our comparative analyses supported the hypothesis that the strong population structure observed in the Atlantic Forest derives from recent, anthropogenic fragmentation. We also observed significant but low levels of genetic differentiation between the Pantanal and Atlantic Forest populations, indicating recent connectivity between jaguars occurring in these biomes. Evidence for admixture between the Pantanal and a population on the western boundary of the Atlantic Forest corroborates the transitional nature of the latter area, where the jaguar population has already been extirpated. Our results can be used to understand jaguar population dynamics in a region that is less disturbed than the Atlantic forest, and to support the design of conservation strategies that maintain and restore natural connectivity among currently isolated areas

Successful carnivore identification with faecal DNA across a fragmented Amazonian landscape

The use of scat surveys to obtain DNA has been well documented in temperate areas, where DNA preservation may be more effective than in tropical forests. Samples obtained in the tropics are often exposed to high humidity, warm temperatures, frequent rain and intense sunlight, all of which can rapidly degrade DNA. Despite these potential problems, we demonstrate successful mtDNA amplification and sequencing for faeces of carnivores collected in tropical conditions and quantify how sample condition and environmental variables influence the success of PCR amplification and species identification. Additionally, the feasibility of genotyping nuclear microsatellites from jaguar (Panthera onca) faeces was investigated. From October 2007 to December 2008, 93 faecal samples were collected in the southern Brazilian Amazon. A total of eight carnivore species was successfully identified from 71% of all samples obtained. Information theoretic analysis revealed that the number of PCR attempts before a successful sequence was an important negative predictor across all three responses (success of species identification, success of species identification from the first sequence and PCR amplification success), whereas the relative importance of the other three predictors (sample condition, season and distance from forest edge) varied between the three responses. Nuclear microsatellite amplification from jaguar faeces had lower success rates (15-44%) compared with those of the mtDNA marker. Our results show that DNA obtained from faecal samples works efficiently for carnivore species identification in the Amazon forest and also shows potential for nuclear DNA analysis, thus providing a valuable tool for genetic, ecological and conservation studies.Fundacao de Amparo a `Pesquisa do Estado de Sao Paulo (FAPESP)[Proc. 2007/01252-2]Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)CNPq, Brazil[Proc. 490594/2007-7]Wildlife Conservation SocietyWildlife Conservation SocietyConservation, Food and Health FoundationConservation, Food and Health FoundationCleveland Metro-parks ZooCleveland Metro-parks ZooCleveland Zoological SocietyCleveland Zoological SocietyRufford Small Grants FoundationRufford Small Grants FoundationConservacao Internacional do BrasilConservacao Internacional do Brasi

Metagenomic Survey of Viral Diversity Obtained from Feces of Subantarctic and South American Fur Seals.

The Brazilian South coast seasonally hosts numerous marine species, observed particularly during winter months. Some animals, including fur seals, are found dead or debilitated along the shore and may harbor potential pathogens within their microbiota. In the present study, a metagenomic approach was performed to evaluate the viral diversity in feces of fur seals found deceased along the coast of the state of Rio Grande do Sul. The fecal virome of two fur seal species was characterized: the South American fur seal (Arctocephalus australis) and the Subantarctic fur seal (Arctocephalus tropicalis). Fecal samples from 10 specimens (A. australis, n = 5; A. tropicalis, n = 5) were collected and viral particles were purified, extracted and amplified with a random PCR. The products were sequenced through Ion Torrent and Illumina platforms and assembled reads were submitted to BLASTx searches. Both viromes were dominated by bacteriophages and included a number of potentially novel virus genomes. Sequences of picobirnaviruses, picornaviruses and a hepevirus-like were identified in A. australis. A rotavirus related to group C, a novel member of the Sakobuvirus and a sapovirus very similar to California sea lion sapovirus 1 were found in A. tropicalis. Additionally, sequences of members of the Anelloviridae and Parvoviridae families were detected in both fur seal species. This is the first metagenomic study to screen the fecal virome of fur seals, contributing to a better understanding of the complexity of the viral community present in the intestinal microbiota of these animals

Successful carnivore identification with faecal DNA across a fragmented Amazonian landscape

The use of scat surveys to obtain DNA has been well documented in temperate areas, where DNA preservation may be more effective than in tropical forests. Samples obtained in the tropics are often exposed to high humidity, warm temperatures, frequent rain and intense sunlight, all of which can rapidly degrade DNA. Despite these potential problems, we demonstrate successful mtDNA amplification and sequencing for faeces of carnivores collected in tropical conditions and quantify how sample condition and environmental variables influence the success of PCR amplification and species identification. Additionally, the feasibility of genotyping nuclear microsatellites from jaguar (Panthera onca) faeces was investigated. From October 2007 to December 2008, 93 faecal samples were collected in the southern Brazilian Amazon. A total of eight carnivore species was successfully identified from 71% of all samples obtained. Information theoretic analysis revealed that the number of PCR attempts before a successful sequence was an important negative predictor across all three responses (success of species identification, success of species identification from the first sequence and PCR amplification success), whereas the relative importance of the other three predictors (sample condition, season and distance from forest edge) varied between the three responses. Nuclear microsatellite amplification from jaguar faeces had lower success rates (15-44%) compared with those of the mtDNA marker. Our results show that DNA obtained from faecal samples works efficiently for carnivore species identification in the Amazon forest and also shows potential for nuclear DNA analysis, thus providing a valuable tool for genetic, ecological and conservation studies.Fundacao de Amparo a `Pesquisa do Estado de Sao Paulo (FAPESP)[Proc. 2007/01252-2]Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)CNPq, Brazil[Proc. 490594/2007-7]Wildlife Conservation SocietyWildlife Conservation SocietyConservation, Food and Health FoundationConservation, Food and Health FoundationCleveland Metro-parks ZooCleveland Metro-parks ZooCleveland Zoological SocietyCleveland Zoological SocietyRufford Small Grants FoundationRufford Small Grants FoundationConservacao Internacional do BrasilConservacao Internacional do Brasi

Data from: Successful carnivore identification with faecal DNA across a fragmented Amazonian landscape

The use of scat surveys to obtain DNA has been well documented in temperate areas, where DNA preservation may be more effective than in tropical forests. Samples obtained in the tropics are often exposed to high humidity, warm temperatures, frequent rain, and intense sunlight, all of which can rapidly degrade DNA. Despite these potential problems, we demonstrate successful DNA amplification and sequencing for faeces of carnivores collected in tropical conditions and quantify how sample condition and environmental variables influence the success of PCR amplification and species identification. Additionally the feasibility of genotyping nuclear microsatellites from jaguar (Panthera onca) faeces was investigated. From October 2007 to December 2008, 93 faecal samples were collected in the southern Brazilian Amazon. A total of eight carnivore species was successfully identified from 71% of all samples obtained. Information theoretic analysis revealed that the number of PCR attempts before a successful sequence was an important negative predictor across all three responses (success of species identification, success of species identification from the first sequence and PCR amplification success), whereas the relative importance of the other three predictors (sample condition, season, and distance from forest) varied between the three responses. Nuclear microsatellite amplification of DNA from jaguar faeces had lower success rates (15–44%) compared with those of the mtDNA marker. Our results show that DNA identification of carnivore species from faecal samples works efficiently in the Amazon forest and can provide data on species occurrence as well as a valuable tool for genetic, ecological and conservation studies

PApops-DRYAD

Microsatellite data from Pantanal Jaguar populations. Each population is named after original collection site. The file is in genepop format. To analyse at genepop user should change population name for "Pop"

Michalski_etal_files

Michalski_etal_file