Non invasive methods for genetic analysis applied to ecological and behavioral studies in Latino-America

Documenting the presence and abundance of the neotropical mammals is the first step for understanding their population ecology, behavior and genetic dynamics in designing conservation plans. The combination of field research with molecular genetics techniques are new tools that provide valuable biological information avoiding the disturbance in the ecosystems, trying to minimize the human impact in the process to gather biological information. The objective of this paper is to review the available non invasive sampling techniques that have been used in Neotropical mammal studies to apply to determine the presence and abundance, population structure, sex ratio, taxonomic diagnostic using mitochondrial markers, and assessing genetic variability using nuclear markers. There are a wide range of non invasive sampling techniques used to determine the species identification that inhabit an area such as searching for tracks, feces, and carcasses. Other useful equipment is the camera traps that can generate an image bank that can be valuable to assess species presence and abundance by morphology. With recent advances in molecular biology, it is now possible to use the trace amounts of DNA in feces and amplify it to analyze the species diversity in an area, and the genetic variability at intraspecific level. This is particularly helpful in cases of sympatric and cryptic species in which morphology failed to diagnose the taxonomic status of several species of brocket deer of the genus Mazama.

Spoligotypes of Mycobacterium tuberculosis complex isolates from patients residents of 11 states of Brazil

One of the high tuberculosis (TB) incidence countries in the world, Brazil is characterized by considerable differences in TB incidence on regional and state level. In the present study, we describe Brazilian spoligotypes of 1991 Mycobacterium tuberculosis complex (MTC) clinical isolates from patients residents of 11 states from different regions of the country, diagnosed between 1996 and 2005. By performing spoligotyping on a large number of M. tuberculosis clinical isolates, one of the main objectives of this study was to determine the major genotype families causing TB in Brazil and to verify the region-associated genotype distribution. We observed a total of 577 distinct spoligopatterns, 12.6% of these corresponded to orphan patterns while 87.4% belonged to 326 shared-types (SITs). Among the latter, 86 SITs (isolated from 178 patients) had been observed for the first time in this study, the most frequent being SIT2517 which belonged to the T3-ETH lineage and was exclusively found among patients residents of Belem, the capital of the state of Para (n = 8 isolates). Irrespective of shared-type labeling, a total of 19.5% strains were unique (unclustered) in our study as opposed to 80.5% clustered isolates (189 clusters, size range from 2 to 205 isolates). The three largest clusters were SIT42 of the Latin-America & Mediterranean (LAM) 9 clade (10.3%), SIT53 of the T clade (7.6%), and SIT50 of the Haarlem clade (5.4%). The predominant MTC lineages in Brazil in decreasing order belonged to the LAM (46%); the ill-defined T (18.6%); the Haarlem (12.2%), the X (4.7%), the S (1.9%), and the East African Indian (EAI) (0.85%) families. The rest of clades grouped together as Mycobacterium africanum, Mycobacterium bovis, Beijing, Central Asian (CAS), and the Manu types, represented less than 1% of the strains. Finally, about 15% of the isolates showed spoligotype signatures that were not yet classified among well-defined lineages. In conclusion, we provide hereby a first insight into the population structure of MTC isolates in Brazil, showing the predominance of both LAM and T family and the existence of region-associated genotypes. (C) 2011 Elsevier B.V. All rights reserved.

Estrutura genética de Chromis multilineata (Guichenot, 1853) (Perciformes Pomacentridae) na costa NE do Brasil e ilhas oceânicas: evidências de um passado evolutivo instável.

The fauna of Brazilian reef fishes comprises approximately 320 species distributed along the coast of the mainland and islands ocean. Little is known about the levels of connectivity between their populations, but has been given the interest in the relations between the offshore and the islands of the Brazil, in a biogeographical perspective. The oceanic islands Brazilian hosting a considerable number of endemic species, which are locally abundant, and divide a substantial portion of its reef fish fauna with the Western Atlantic. Among the richest families of reef fish in species are Pomacentridae. This study analyzed through analysis of sequences of the mitochondrial DNA control region (D-loop), the standards-breeding population of C. Multilineata in different areas of the NE coast of Brazil, involving both oceanic islands (Fernando de Noronha Archipelago and of St. Peter and St. Paul) and continental shelf (RN and BA). To this aim, partial sequences were used in the region HVR1 of mtDNA (312pb). The population structure and parameters for the estimates of genetic variability, molecular variance (AMOVA), estimation of the index for fixing (FST) and number of migrants were determined. The phylogenetic relationships between the populations were estimated using neighbor-joining (NJ) method. A group of Bayesian analysis was used to verify population structure, according to haplotype frequency of each individual. The genetic variability of populations was extremely high. The populations sampled show moderate genetic structure, with a higher degree of genetic divergence being observed for the sample of the Archipelago of St. Peter and St. Paul. At smaller geographical scale, the sample of Rio Grande do Norte and the Archipelago of Fernando de Noronha do not have genetic differentiation. Three moderately differentiated population groups were identified: a population group (I), formed by the Rio Grande do Norte (I') and the archipelago of Fernando de Noronha (I''), and two other different groups formed by the island population of the archipelago of Saint Peter and St. Paul (II) and Bahia (III). The genetic patterns found suggest that the species has suffered a relatively recent radiation favoring the absence of shared haplotypes. C. multilineata seems to constitute a relatively homogenous population along the West Atlantic coast, with evidence of a moderate population genetic structure in relation to the Archipelago of St. Peter and St. Paul. These data supports the importance of the dispersal larvae by marine current and the interpopulation similarity this species.

Caracterização da resistência do algodoeiro a Ramularia areola e variabilidade molecular do patógeno

This research was conducted with the aim to study the genetic and pathogenic structure of Ramularia areola isolates collected in Brazil and to characterize the resistance response in cotton plants to ramularia spot. The genetic variability of 28 isolates of R. areola was studied using RAPD markers. The pathogenicity evaluation was realized by the inoculation of 6 isolates on cotton varieties Guazuncho-2 (Gossypium hirsutum) and VH8-4602 (Gossypium barbadense). The inheritance of disease resistance was studied using an artificially inoculated population of F2 individuals derived from the intercross of Guazuncho-2 (susceptible variety) end VH8-4602 (resistant variety), and also the parents and F1 individuals. Molecular polymorphism between the G. hisutum varieties DeltaOpal (suscetible) and CNPA CO-11612 (resistant) was estimated by 118 SSR and 24 AFLP markers. The parental genotypes Guazuncho-2 and VH8-4602 were selected for mapping, and then Recombinant Inbred Lines (RIL´s) derived from this crossing were evaluated with SSR 12 markers. The analysis of population structure of R. areola revealed that the three subpopulations were genetically simillar (Gst=0.18), and the isolates from Goiás and Minas Gerais were more similar to each other (0,92). This probability can be related to the relatively high gene flow among the three subpopulations (Nm=2.20). The isolates R. areola 9.1, from Minas Gerais State and 8.1 and 8.3 from Goiás State were the most aggressive ones to the susceptible variety Guazuncho-2. The variety VH8-4602 presented high level of resistance to ramularia spot. No differential interaction was observed between the pathogens and the analyzed varieties, and the resistance was classified as horizontal. The quantification of disease by number of necrotic lesions and number of spores in individual plants of F1 and F2 generations from the crossing between the varieties Guazuncho-2 and VH8-4602 presented continuous distribution, suggesting polygenic resistance. The resistance is probabilly recessive, since necrotic lesions and sporulation were observed on F1 plants. The molecular polymorphism between DeltaOpal e CNPA CO-11612 lineages was low (6%), then would be difficult to accomplish molecular mapping of disease resistance using this intercross. With the genotyping of the RIL s it was verified that 25% of the markers segregated in the proportions proposed by Mendel s Law and 75% of the studied markers presented segregation distortion in favor to the parental G. hirsutum. Both the low genetic variability of the pathogen and the number of resistance genes suggest that durable genetic resitance may be achieved

Estratégia reprodutiva do peixe-voador, Hirundichthys affinis e do peixe agulha preta, Hemiramphus brasiliensis no litoral de Caiçara do Norte, Rio Grande do Norte, Brasil

The flyingfish, Hirundichthys affinis (Günther, 1866) (Exocoetidae) and ballyhoo half beak, Hemiramphus brasiliensis (Linnaeus, 1758) (Hemiramphidae) are marine fish species of commercial value, which contribute to artisanal fishery production of Rio Grande do Norte, Brazil. Besides the economic importance, these fish are important from an ecological point of view, being components in pelagic food chain, where they are the preferred prey of larger predators of high commercial value. This study aimed to determine the reproductive strategies of H. affinis and H. brasiliensis and the fishery production of H. affinis in the northern coast of Rio Grande do Norte. The results are presented in the form of six cientific articles and a review paper. The first article presents the morphometric measurements and meristic counts which confirmed the taxonomic status, population structure in length-weight and the gonad development of H. affinis through macroscopic observations of the ovaries and testes. Females of this species were bigger and heavier than males. The second article describes the reproductive tactics, such as, sex ratio, length at first sexual maturity, histological aspects of gonads, fecundity and spawning season, that indicate the reproductive strategy of H. affinis. The third article shows annual changes in the fishery production of H. affinis in Caiçara do Norte, during the period of 1993 to 2010, emphasizing the relevance of this fish in total fishery production of Rio Grande do Norte, besides registering the fall in production in the years 2008 to 2010. The fourth article describes the population structure, with respect to the length and weight, the length-weight relationship, growth type and sex ratio of Hemiramphus brasiliensis. The fifth article describes the reproductive biology of H. brasiliensis, with details about sex ratio, length at first sexual maturity, fecundity, type of breeding and spawning season. The sixth article deals with the reproductive strategy of H. brasiliensis. The review paper presents the topic of age determination of tropical fish using analysis of otoliths. Both species use the coastal waters of Caiçara do Norte for reproductive purposes. The flying fish, H. affinis migrates from the oceanic waters to the coastal waters to reproduce, coinciding with the rainy season. H. affinis presents total spawning and a seasonal reproductive strategy. However, H. brasiliensis lives and reproduces in the coastal waters displaying partial spawning and an equilibrium reproductive strategy

Highly polymorphic microsatellite loci in the rice- and maize-infecting fungal pathogen Rhizoctonia solani anastomosis group 1 IA

Ten polymorphic microsatellite loci were isolated and characterized from the rice- and maize-infecting Basidiomycete fungus Rhizoctonia solani anastomosis group AG-1 IA. All loci were polymorphic in two populations from Louisiana in USA and Venezuela. The total number of alleles per locus ranged from four to eight. All 10 loci were also useful for genotyping soybean-infecting R. solani AG-1 isolates from Brazil and USA. One locus, TC06, amplified across two other AG groups representing different species, showing species-specific repeat length polymorphism. This marker suite will be used to determine the global population structure of this important pathogenic fungus.

High levels of genetic differentiation and selfing in the Brazilian cerrado fruit tree Dipteryx alata Vog. (Fabaceae)

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Melhoramento e estrutura populacional em bubalinos da raça Mediterrâneo no Brasil

O objetivo deste trabalho foi avaliar a estrutura populacional e os progressos genéticos, fenotípicos e ambientais de características de desenvolvimento ponderal, em bubalinos da raça Mediterrâneo. Foram utilizadas informações dos pesos ajustados aos 205, 365 e 550 dias de idade, de 6.243 bubalinos nascidos no período de 1974 a 2003, provenientes de quatro fazendas. As estimativas dos coeficientes de herdabilidade foram altas para os pesos ajustados nas três idades. Os rebanhos apresentaram ganho genético positivo quanto a essas três características, porém, aquém do possível, provavelmente em razão da seleção baseada somente no fenótipo, realizada pelos produtores. Para aumento nos ganhos genéticos, são necessários a redução do intervalo de geração, o aumento do tamanho efetivo, o uso de reprodutores avaliados com base nos valores genéticos preditos pelo BLUP e o controle dos acasalamentos de animais aparentados.

Identification and characterization of polymorphic microsatellite loci in the blue shark Prionace glauca, and cross-amplification in other shark species

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Genetic variability of two populations of Pseudoplatystoma reticulatum from the Upper Paraguay River Basin

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Influence of cage fish farming on the diet of dominant fish species of a Brazilian reservoir (Tiete River, High Parana River basin)

The cage farming of aquatic organisms was initiated 50 years ago, and was introduced to Brazil in the 1990's. In these systems, there is an input of organic matter from ration that is not totally used by the cage fishes, becoming available for the organisms of adjacent biota, including fish fauna. The aim of this work is to evaluate the interference in the diet of three dominant fish species (Plagioscion squamosissimus Heckel, 1840, Astyanax altiparanae Garutti and Britski, 2000 and Metynnis maculatus Kner, 1858) associated with ish cage farming. For determination of the diet, the Alimentary Index (AI) was used. In both stretches (around cage farm and control), P. squamosissimus selected aquatic insects, while A. altiparanae preferred terrestrial insects and M. maculatus eats ration remains. Diferences in abundance of these feeding resources found of the stomach content were observed among the two stretches. Thus, the small alterations in the diets of P. squamosissimus and A. altiparanae, indicate that cage farming can change the diet of resident species in reservoirs. This practice also influences the population structure of fish species, since higher middle standard lengths were found in A. altiparanae and P. squamosissimus populations resident around cage farms, in relation to the control stretch.

Populations analysis of the Brazilian Sharpnose Shark Rhizoprionodon lalandii (Chondrichthyes: Carcharhinidae) on the São Paulo coast, Southern Brazil: inferences from mt DNA sequences

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Characterization of eight single nucleotide polymorphism markers in Aedes aegypti

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Reproductive period and size at the onset of sexual maturity of mottled purse crab, Persephona mediterranea (Herbst, 1794) (Brachyura, Leucosioidea) on the southeastern Brazilian coast

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Development of 22 Polymorphic Microsatellite Loci for the Critically Endangered Morato's Digger Toad, Proceratophrys moratoi

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)