The GHEP-EMPOP collaboration on mtDNA population data-A new resource for forensic casework

Mitochondrial DNA (mtDNA) population data for forensic purposes are still scarce for some populations, which may limit the evaluation of forensic evidence especially when the rarity of a haplotype needs to be determined in a database search. In order to improve the collection of mtDNA lineages from the Iberian and South American subcontinents, we here report the results of a collaborative study involving nine laboratories from the Spanish and Portuguese Speaking Working Group of the International Society for Forensic Genetics (GHEP-ISFG) and EMPOP. The individual laboratories contributed population data that were generated throughout the past 10 years, but in the majority of cases have not been made available to the scientific community. A total of 1019 haplotypes from Iberia (Basque Country, 2 general Spanish populations, 2 North and 1 Central Portugal populations), and Latin America (3 populations from São Paulo) were collected, reviewed and harmonized according to defined EMPOP criteria. The majority of data ambiguities that were found during the reviewing process (41 in total) were transcription errors confirming that the documentation process is still the most error-prone stage in reporting mtDNA population data, especially when performed manually. This GHEP-EMPOP collaboration has significantly improved the quality of the individual mtDNA datasets and adds mtDNA population data as valuable resource to the EMPOP database (www.empop.org). (C) 2010 Elsevier B.V. All rights reserved.

Isolation and characterization of ten novel microsatellite loci in the red-winged tinamou (Rhynchotus rufescens, Tinamiformes, Aves) and cross-amplification in other tinamous

We describe the isolation and characterization of ten microsatellite loci from the red-winged tinamou (Rhynchotus rufescens) and also evaluated the cross-amplification of these loci and other ten loci previously developed for the great tinamou (Tinamus major) in other tinamous. Genetic variability was assessed using 24 individuals. Six loci were polymorphic with moderate to high number of alleles per locus (2-12 alleles) and showed expected heterozygosity (HE) ranging from 0.267 to 0.860. All loci conformed to the Hardy-Weinberg expectation and linkage disequilibrium was not significant for any pair of loci. This battery of polymorphic loci showed high paternity exclusion probability (0.986) and low genetic identity probability (4.95 x 10(-5)), proving to be helpful for parentage tests and population analyses in the red-winged tinamou. The cross-amplification was moderate where of the 160 locus/taxon combinations, 46 (28.75%) successfully amplified.

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)

The evolutionary dynamics of the Helena retrotransposon revealed by sequenced Drosophila genomes

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

Estimates of genetic parameters, and cluster and principal components analyses of breeding values related to egg production traits in a White Leghorn population

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

Atlantic forest fragmentation and genetic diversity of an isolated population of the Blue-manakin, Chiroxiphia caudata (Pipridae), assessed by microsatellite analyses

Habitat fragmentation is predicted to restrict gene flow, which can result in the loss of genetic variation and inbreeding depression. The Brazilian Atlantic forest has experienced extensive loss of habitats since European settlement five centuries ago, and many bird populations and species are vanishing. Genetic variability analysis in fragmented populations could be important in determining their long-term viability and for guiding management plans. Here we analyzed genetic diversity of a small understory bird, the Blue-manakins Chiroxiphia caudata (Pipridae), from an Atlantic forest fragment (112 ha) isolated 73 years ago, and from a 10,000 ha continuous forest tract (control), using orthologous microsatellite loci. Three of the nine loci tested were polymorphic. No statistically significant heterozygote loss was detected for the fragment population. Although genetic diversity, which was estimated by expected heterozygosity and allelic richness, has been lower in the fragment population in relation to the control, it was not statistically significant, suggesting that this 112 ha fragment can be sufficient to maintain a blue-manakin population large enough to avoid stochastic effects, such as inbreeding and/or genetic drift. Alternatively, it is possible that 73 years of isolation did not accumulate sufficient generations for these effects to be detected. However, some alleles have been likely lost, specially the rare ones, what is expected from genetic drift for such a small and isolated population. A high genetic differentiation was detected between populations by comparing both allelic and genotypic distributions. Only future studies in continuous areas are likely to answer if such a structure was caused by the isolation resulted from the forest fragmentation or by natural population structure.

Initial description of the phylogeography, population structure and genetic diversity of Atlantic spotted dolphins from Brazil and the Caribbean, inferred from analyses of mitochondrial and nuclear DNA

We provide initial information regarding the population structure and genetic diversity of Stenella frontalis from the Caribbean and southeastern Brazil from analyses of mitochondrial control region sequences and sequences from the first intron of the α-lactalbumin gene. Comparisons with previously described S. frontalis sequences showed a high number of haplotypes shared between populations throughout their distribution range. High diversity was found for southeastern Brazil and Caribbean samples, and population structure analyses indicate significant differentiation among population units at the FST level, but not at the ΦST level. Significant differentiation at the FST level was found between the Caribbean population unit and all other populations units. These results suggest historical or present connectivity between the Azores and Madeira and the southeastern Brazil groups and population differentiation between the Caribbean and southeastern Brazil, supporting the notion of two separate stocks in the waters around the Atlantic coast of South America. © 2013 Elsevier Ltd.

Cryptic lineages and Pleistocene population expansion in a Brazilian Cerrado frog

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Random regression analyses using B-splines functions to model growth from birth to adult age in Canchim cattle

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Distribution of paracoccidioidomycosis: determination of ecologic correlates through spatial analyses

Paracoccidioidomycosis (PCM) is endemic in Latin America and in countries like Brazil it carries a high mortality rate. The fungus' habitat has not been precisely determined. The present study aims to identify ecologic correlates based on PCM distribution in a hyper-endemic area in southeastern Brazil. The Geographic Information System (GIS) and spatial statistics were used to associate environmental attributes, human population density and, PCM distribution. By means of the Pearson r correlation coefficient, the highest statistically significant associations with prevalence density were the percent area (by county) of: basaltic rocks (r = 0.63; P < 0.0001), Podzolic soils (r = - 0.48; P < 0.001), Latosol soils (r = 0.40; P < 0.01), mean annual precipitation between 1500 and 1600 mm (r = 0.46; P < 0.001) and, mean precipitation during the wet season between 940 and 1040 mm (r = - 0.44; P < 0.01). Soil texture and precipitation analyzed together reached r = 0.61 (P < 0.000002) for fine-textured soils with annual precipitation above 1400 mm. Environmental correlates indicate that moisture availability plays an important role in PCM distribution.

Pixel intensity and fractal analyses: detecting osteoporosis in perimenopausal and postmenopausal women by using digital panoramic images

Objective. Pixel intensity values (PI) and fractal dimensions (FD) were compared in selected mandibular regions on digital panoramic images of normal, osteopenic, and osteoporotic perimenopausal and postmenopausal women to evaluate their relative efficacies in detecting osteoporotic-associated bone density changes.Study design. Standardized mandibular angle, body, and canine/premolar (C/PM) regions on 54 charge-coupied device (CCD) digital panoramic images of normal and potentially osteoporotic postmenopausal women were analyzed for PI and FD. Lumbar spine and femoral neck dual-energy x-ray absorptiometry QXA) on each patient served as the reference standard examination. Pearson correlation coefficients and analysis of variance (ANOVA) were performed.Results. There was significant correlation among PI measurements (P < 0.01), and no significant correlation between FD. C/PM had significantly lower PI than control C/PM (P = 0.049).Conclusions. Osteoporotic changes in mandibular C/PM cancellous bone were detected in our study population on CCD digital panoramic images by using a robust image analysis paradigm. Future automated application of such image analysis could enable widespread, cost effective screening for osteoporosis in dental settings.

Phylogeography and genetic population structure of Caribbean sharpnose shark Rhizoprionodon porosus

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

Population structure and reproductive period of whitebelly prawn Nematopalaemon schmitti (Holthuis 1950) (Decapoda: Caridea: Palaemonidae) on the southeastern coast of Brazil

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

Population dynamic of Sesarma rectum (Crustacea, Brachyura, Sesarmidae) from a muddy flat under human impact, Paraty, Rio de Janeiro, Brazil

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

Astylus variegatus (Coleoptera, Melyridae): Cytogenetic study of a population exposed to agrochemical products

In this work we describe the cytogenetic analyses performed in specimens of Astylus variegatus (Germar, 1824) collected in two localities: one area of natural vegetation and one of agricultural crops, where agrochemical products were used. Astylus variegatus had karyotypes with 2n(male) = 16+Xy p and 2n (female) = 16+XXp, with exclusively metacentric chromosomes. Pachytene spermatocytes showed synapsed autosomal bivalents and non-associated sex chromosomes. In diplotene, the autosomal bivalents exhibited one or two terminal chiasmata and the Xy p had a typical parachute configuration. In meiotic cells of some specimens, an extra chromosome, interpreted as a B chromosome, was observed. C-banding showed constitutive heterochromatin in the pericentromeric region of all chromosomes, with the exception of the y p. Silver nitrate staining revealed one nucleolus organizer region (NOR) on the terminal region of the short arm of the second autosome pair. Silver staining of meiotic cells confirmed the NOR pattern detected in mitotic cells and revealed an argentophilous material on the Xy p. A cytogenetic comparison between the two populations of A. variegatus showed a statistically significant divergence (chi2 = 117.10; df = 1) in the number of aneuploid cells and a higher frequency of B chromosome in the population exposed to agrochemicals.