Genetic variation and population structuring in two brooding coral species (Siderastrea stellata and Siderastrea radians) from Brazil

Siderastrea stellata and S. radians are scleractinian coral species that present a remarkable overlap of diagnostic characteristics and sympatric distribution. Moreover, both are viviparous with similar reproductive strategies and with a gregarious larval behavior. Samples of both species from the Brazilian coast were analyzed using 18 isozymic loci to quantify their genetic variability and populational structure. Results confirmed species identity, high intrapopulational variability and revealed moderate genetic structuring among all samples (S. stellata: F(ST) = 0.070; S. radians: F(ST) = 0.092). Based on genotypic diversity analysis, there was evidence that local recruitment may have a minor role in the populations (mean, G(o) :G(e) = 1.00 +/- 0.0003 SD for S. stellata and 0.99 +/- 0.0023 SD for S. radians). Deviations towards heterozygote deficiencies found in both Siderastrea species could be explained by the Wahlund effect, since there was evidence that populations might be composed of colonies of different ages. In S. radians it is also likely that there is some inbreeding occurring in the studied populations. Despite the brooding pattern and the gregarious larval behavior, our data suggest the occurrence of gene flow along the Brazilian coast. This is the first study on population genetics of Brazilian reef corals.

Evolution of Dendrocolaptes platyrostris (Aves: Furnariidae) between the South American open vegetation corridor and the Atlantic forest

The open vegetation corridor of South America is a region dominated by savanna biomes. It contains forests (i.e. riverine forests) that may act as corridors for rainforest specialists between the open vegetation corridor and its neighbouring biomes (i.e. the Amazonian and Atlantic forests). A prediction for this scenario is that populations of rainforest specialists in the open vegetation corridor and in the forested biomes show no significant genetic divergence. We addressed this hypothesis by studying plumage and genetic variation of the Planalto woodcreeper Dendrocolaptes platyrostris Spix (1824) (Aves: Furnariidae), a forest specialist that occurs in both open habitat and in the Atlantic forest. The study questions were: (1) is there any evidence of genetic continuity between populations of the open habitat and the Atlantic forest and (2) is plumage variation congruent with patterns of neutral genetic structure or with ecological factors related to habitat type? We used cytochrome b and mitochondrial DNA control region sequences to show that D. platyrostris is monophyletic and presents substantial intraspecific differentiation. We found two areas of plumage stability: one associated with Cerrado and the other associated with southern Atlantic Forest. Multiple Mantel tests showed that most of the plumage variation followed the transition of habitats but not phylogeographical gaps, suggesting that selection may be related to the evolution of the plumage of the species. The results were not compatible with the idea that forest specialists in the open vegetation corridor and in the Atlantic forest are linked at the population level because birds from each region were not part of the same genetic unit. Divergence in the presence of gene flow across the ecotone between both regions might explain our results. Also, our findings indicate that the southern Atlantic forest may have been significantly affected by Pleistocene climatic alteration, although such events did not cause local extinction of most taxa, as occurred in other regions of the globe where forests were significantly affected by global glaciations. Finally, our results neither support plumage stability areas, nor subspecies as full species. (C) 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 103, 801-820.

Genetic differentiation between sympatric populations of Bacillus cereus and Bacillus thuringiensis

Little is known about genetic exchanges in natural populations of bacteria of the spore-forming Bacillus cereus group, because no population genetics studies have been performed with local sympatric populations. We isolated strains of Bacillus thuringiensis and B. cereus from small samples of soil collected at the same time from two separate geographical sites, one within the forest and the other at the edge of the forest. A total of 100 B. cercus and 98 B. thuringiensis strains were isolated and characterized by electrophoresis to determine allelic composition at nine enzymatic loci. We observed genetic differentiation between populations of B. cereus and B. thuringiensis. Populations of a given Bacillus species-B. thuringiensis or B. cereus-were genetically more similar to each other than to populations of the other Bacillus species. Hemolytic activity provided further evidence of this genetic divergence, which remained evident even if putative clones were removed from the data set. Our results suggest that the rate of gene flow was higher between strains of the same species, but that exchanges between B. cereus and B. thuringiensis were nonetheless possible. Linkage disequilibrium analysis revealed sufficient recombination for B. cereus populations to be considered panmictic units. In B. thuringiensis, the balance between clonal proliferation and recombination seemed to depend on location. Overall, our data indicate that it is not important for risk assessment purposes to determine whether B. cereus and B. thuringiensis belong to a single or two species. Assessment of the biosafety of pest control based on B. thuringiensis requires evaluation of the extent of genetic exchange between strains in realistic natural conditions.

RAPD analysis of genetic variability in a multiprovenance base population of Eucalyptus grandis hill ex maiden

Este estudo visou avaliar a variabilidade e distância genética dentro de uma população-base de melhoramento genético de Eucalyptus grandis. A avaliação da variabilidade genética tem como objetivos principais analisar a base genética da população-base e montar um banco de dados marcadores moleculares da população em análise. Essa população é formada por 327 indivíduos, principalmente das procedências de Coff's Harbour, Atherton e Rio Claro. Devido à heterozigosidade natural dessa população, ela pode ser dividida em diversas subpopulações, de acordo com a latitude e longitude de origem; e dentro de subpopulações, em função do grau de melhoramento genético já realizado do material analisado no Brasil. Isso permitiu avaliar quanto da variabilidade detectada dentro da população-base foi devido a esses fatores: procedência e grau de melhoramento. A aplicação da técnica RAPD permitiu avaliar 70 locos polimórficos, que foram analisados utilizando-se o coeficiente de Jaccard, o que resultou em matrizes de similaridade genética entre os indivíduos. Os dados de similaridade genética posteriormente foram submetidos à análise estatística. Osdados indicaram que a população-base apresenta ampla base genética, com média de similaridade genética de 0,328. O subgrupo denominado Região 3, composto por material selvagem da macrorregião de Atherton, juntamente com material de APS da macrorregião de Coff's Harbour, foi um dos que mais contribuíram para a ampla base genética da população-base. Foi possível detectar diferença estatística entre as populações selvagens das procedências de Atherton e Coff's Harbour, assim como entre essas procedências e a de Rio Claro.

Seasonal population dynamics and the genetic structure of the mosquito vector Aedes aegypti in São Paulo, Brazil

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

Exploitation of mitochondrial nad6 as a complementary marker for studying population variability in Lepidoptera

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Genetic structure of Blastocerus dichotomus populations in the Parana River basin (Brazil) based on protein variability

The population structure of 147 marsh deer (Blastocerus dichotomus) from three areas in the Parana River basin, Brazil, was studied by observing protein polymorphism at 17 loci. Six loci were polymorphic and 11 monomorphic. The proportion of polymorphic loci (P) was 35.29% and the average heterozygosity (H) was 6.31%. Wright's F-ST indicated that only 4.9% of the total variation in allelic frequencies was due to genetic differences between the three groups. The high value of F-IS (0.246) indicated inbreeding in the marsh deer. Genetic distance values (D = 0.014-0.051) showed little divergence between the three areas. We suggest that probable mechanisms accounting for the genetic structure are female phylopatry and polygyny and also that inbreeding has resulted from decreasing areas of wetland leading to isolation, overhunting, and diseases transmitted by cattle.

Strong selection against hybrids at a hybrid zone in the Ensatina ring species complex and its evolutionary implications

The analysis of interactions between lineages at varying levels of genetic divergence can provide insights into the process of speciation through the accumulation of incompatible mutations. Ring species, and especially the Ensatina eschscholtzii system exemplify this approach. The plethodontid salamanders E. eschscholtzii xanthoptica and E. eschscholtzii platensis hybridize in the central Sierran foothills of California. We compared the genetic structure across two transects (southern and northern Calaveras Co.), one of which was resampled over 20 years, and examined diagnostic molecular markers (eight allozyme loci and mitochondrial DNA) and a diagnostic quantitative trait (color pattern). Key results across all studies were: (1) cline centers for all markers were coincident and the zones were narrow, with width estimates of 730 m to 2000 m; (2) cline centers at the northern Calaveras transect were coincident between 1981 and 2001, demonstrating repeatability over five generations; (3) there were very few if any putative F1s, but a relatively high number of backcrossed individuals in the central portion of transects: and (4) we found substantial linkage disequilibrium in all three studies and strong heterozygote deficit both in northern Calaveras, in 2001, and southern Calaveras. Both linkage disequilibrium and heterozygote deficit showed maximum values near the center of the zones. Using estimates of cline width and dispersal, we infer strong selection against hybrids. This is sufficient to promote accumulation of differences at loci that are neutral or under divergent selection, but would still allow for introgression of adaptive alleles. The evidence for strong but incomplete isolation across this centrally located contact is consistent with theory suggesting a gradual increase in postzygotic incompatibility between allopatric populations subject to divergent selection and reinforces the value of Ensatina as a system for the study of divergence and speciation at multiple stages. © 2005 The Society for the Study of Evolution. All rights reserved.

Internal genetic structure and outcrossing rate in a natural population of Araucaria angustifolia (Bert.) O. Kuntze

The internal genetic structure and outcrossing rate of a population of Araucaria angustifolia (Bert.) O. Kuntze were investigated using 16 allozyme loci. Estimates of the mean number of alleles per loci (1.6), percentage of polymorphic loci (43.8%), and expected genetic diversity (0.170) were similar to those obtained for other gymnosperms. The analysis of spatial autocorrelation demonstrated the presence of internal structure in the first distance classes (up to 70 m), suggesting the presence of family structure. The outcrossing rate was high (0.956), as expected for a dioecious species. However, it was different from unity, indicating outcrossings between related individuals and corroborating the presence of internal genetic structure. The results of this study have implications for the methodologies used in conservation collections and for the use or analysis of this forest species. © The American Genetic Association. 2006. All rights reserved.

Population genetic data of five X-chromosomal loci in Bauru (São Paulo, Brazil)

Genetic population data for five X-STR (DXS6854, DXS7424, DXS101, DXS6808 and DXS7132) were obtained from Bauru population (São Paulo, Brazil). No deviations from the Hardy-Weinberg equilibrium were observed, with the exception of DXS101. The combined powers of discrimination in males and females were 0.99897253 and 0.99999120, respectively. These high values show the potential of this system in human identification and paternity testing. © 2008 Elsevier B.V. All rights reserved.

Influence of δβ-thalassemia or regulatory elements in individuals with increased fetal Hb levels in the São Paulo northwest population

Fetal hemoglobin (Hb F), formed by two alpha globin chains (α) and two gamma chains (γ) (α2 γ2), has reduced expression in adults, ranging from 0 to 1% of total hemoglobin. Increased levels of Hb F are due to mutations in the β-globin family, which cause hereditary persistence of fetal hemoglobin (HPFH) and delta-beta thalassemia (δβ-thalassemia).The control of the production takes place by the regulatory region and regions outside the β-globin family, among them 2q16, 6q23, 8q, and Xp22.2.The aims of this study were to determine the presence and frequency of two mutations for δβ-thalassemia, the XmnI polymorphism and β-globin haplotypes in healthy individuals with increased Hb F in the State of São Paulo. We analyzed 60 samples of peripheral blood of healthy adults, without complaints of anemia. The samples were separated into two groups according to Hb F level: group I - 34 samples with Hb F ranging from 2 to 15% and group II - 26 samples with Hb F over 15%. In relation to the polymorphisms examined, we found three heterozygous individuals (5%) for Spanish δβ-thalassemia, belonging to group I, whose Hb F levels were within the normal range.The Sicilian δβ-thalassemia mutation was not found, indicating the need to study other polymorphisms related to the increase of Hb F in adult life.The frequency of XmnI polymorphism was 33.3% and the mean Hb F levels were 15.48 ± 11.69%.The frequency observed in our study for this polymorphic site is higher than that found in the literature for healthy subjects.This polymorphism was more prevalent in individuals with Hb F levels below 15%. For four samples positive for this polymorphism, the Hb F levels were explained by the presence of HPFH and Spanish δβ-thalassemia mutations, so that the presence of the XmnI polymorphic site was not a determinant in the overexpression of γ-globin genes. Regarding β-globin haplotypes, 18 alleles and 27 distinct genotypic patterns were found.The pattern Atp1/Atp2 was the mostfrequent genotype (13.72%).Of the 18 alleles, 13 showed atypical patterns.The results show that the haplotype V was the most frequent (27.45%), followed by atypical Atp2 (13.72%) and Atp1 (11.76%), and that there was a higher correlation with the presence of HPFH and XmnI polymorphism.The high frequency of haplotype V in our samples and high frequency of atypical haplotypes may reflect a high rate of miscegenation in this population, suggesting an ethnic characteristic for the Brazilian population, requiring the evaluation of population genetic markers to corroborate this hypothesis. © FUNPEC-RP.

Population genetic evidence that basidiospores play an important role in the disease cycle of rice-infecting populations of Rhizoctonia solani AG-1 IA in Iran

The fungus Rhizoctonia solani AG-1 IA causes sheath blight, one of the most important rice diseases worldwide. The first objective of this study was to analyse the genetic structure of R. solani AG-1 IA populations from three locations in the Iranian Caspian Sea rice agroecosystem. Three population samples of R. solani AG-1 IA isolates were obtained in 2006 from infected rice fields separated by 126-263km. Each field was sampled twice during the season: at the early booting stage and 45days later at the early mature grain stage. The genetic structure of these three populations was analysed using nine microsatellite loci. While the population genetic structure from Tonekabon and Amol indicated high gene flow, they were both differentiated from Rasht. The high gene flow between Tonekabon and Amol was probably due mainly to human-mediated movement of infested seeds. The second objective was to determine the importance of recombination. All three populations exhibited a mixed reproductive mode, including both sexual and asexual reproduction. No inbreeding was detected, suggesting that the pathogen is random mating. The third objective was to determine if genetic structure within a field changes over the course of a growing season. A decrease in the proportion of admixed genotypes from the early to the late season was detected. There was also a significant (P=0·002) increase in the proportion of loci under Hardy-Weinberg equilibrium. These two lines of evidence support the hypothesis that basidiospores can be a source of secondary inoculum. © 2012 BSPP.

Global sampling reveals low genetic diversity within Compsopogon (Compsopogonales, Rhodophyta)

Twenty-five specimens of the freshwater red alga Compsopogon were collected from locations in North America, South America, Europe, Asia, Australasia and Oceania, and from an aquarium, with the goal of determining genetic diversity among specimens and ascertaining the number of phylogenetic species. Specimens were morphologically identified as having either the 'caeruleus' morphology, with regular polyhedral cortical cells, or the 'leptoclados' morphology, with irregular cortical cells with rhizoidal outgrowths. The 'leptoclados' morphology has been used by some researchers to distinguish the genus Compsopogonopsis from Compsopogon, or at least to distinguish C. leptoclados from other Compsopogon species. Sequence data for the rbcL gene and cox1 barcoding region were obtained for most specimens. In addition, SSU and partial LSU (barcode) rDNA were explored for a few specimens, but all sequences were identical. For the 25 newly generated and eight previously published rbcL gene data, there were seven unique haplotypes, but the sequence divergence was very low (≤7 bp, ≤ 0.7%). One haplotype was widespread, represented by 21 specimens from diverse locations in all regions sampled. Likewise, the 22 new and one previously published cox1 barcode region sequences yielded seven unique haplotypes with little sequence divergence (≤13 bp, ≤ 2.0%). One haplotype was widespread, being shared among 16 specimens from all regions. The combined molecular and morphological data showed no genetic differentiation between the 'caeruleus' and 'leptoclados' morphologies. The ubiquitous distribution of Compsopogon in tropical/subtropical regions and its low genetic variation are probably facilitated by the alga's ability to tolerate a wide range of stream conditions and its propagation via asexual spores. Given the findings of previous culture-based studies, morphometric research and field observations, coupled with the results of our study, we conclude there is only a single monospecific genus worldwide and that the species is correctly called C. caeruleus, since this is the oldest validly published name; all other previously described species of Compsopogon and Compsopogonopsis are synonyms. © 2013 British Phycological Society.

The population genetic structure of Rhizoctonia solani AG-3PT from potato in the Colombian Andes

The soilborne fungus Rhizoctonia solani anastomosis group 3 (AG-3PT) is a globally important potato pathogen. However, little is known about the population genetic processes affecting field populations of R. solani AG-3PT, especially in the South American Colombian Andes, which is near the center of diversity of the two most common groups of cultivated potato, Solanum tuberosum and S. phureja. We analyzed the genetic structure of 15 populations of R. solani AG-3PT infecting potato in Colombia using 11 simple-sequence repeat (SSR) markers. In total, 288 different multilocus genotypes were identified among 349 fungal isolates. Clonal fractions within field populations were 7 to 33%. R ST statistics indicated a very low level of population differentiation overall, consistent with high contemporary gene flow, though moderate differentiation was found for the most distant southern populations. Genotype flow was also detected, with the most common genotype found widely distributed among field populations. All populations showed evidence of a mixed reproductive mode, including both asexual and sexual reproduction, but two populations displayed evidence of inbreeding. © 2013 The American Phytopathological Society.

Epigenetic alterations in human brain tumors in a Brazilian population

Aberrant methylation of CpG islands located in promoter regions represents one of the major mechanisms for silencing cancer-related genes in tumor cells. We determined the frequency of aberrant CpG island methylation for several tumor-associated genes: DAPK, MGMT, p14^ARF, p16^INK4a, TP73, RB1 and TIMP-3 in 55 brain tumors, consisting of 26 neuroepithelial tumors, 6 peripheral nerve tumors, 13 meningeal tumors and 10 metastatic brain tumors. Aberrant methylation of at least one of the seven genes studied was detected in 83.6% of the cases. The frequencies of aberrant methylation were: 40% for p14^ARF, 38.2% for MGMT, 30.9% for, p16^INK4a, 14.6% for TP73 and for TIMP-3, 12.7% for DAPK and 1.8% for RB1. These data suggest that the hypermethylation observed in the genes p14^ARF, MGMT and p16^INK4a is a very important event in the formation or progression of brain tumors, since the inactivation of these genes directly interferes with the cell cycle or DNA repair. The altered methylation rate of the other genes has already been reported to be related to tumorigenesis, but the low methylation rate of RB1 found in tumors in our sample is different from that so far reported in the literature, suggesting that perhaps hypermethylation of the promoter is not the main event in the inactivation of this gene. Our results suggest that hypermethylation of the promoter region is a very common event in nervous system tumors.