Population genetic structure and morphological diversity of Cruzia tentaculata (Nematoda: Ascaridida), a parasite of marsupials (Didelphinae), along the Atlantic Forest on the eastern coast of South America.

Cruzia tentaculata is a helminth parasite of marsupials and has a wide geographic distribution from Mexico to Argentina. The aim of this study was to analyse the genetic population structure of this nematode along the Atlantic Forest biome. Cruzia tentaculata specimens were recovered from Didelphis aurita, Didelphis albiventris and Philander quica in 9 localities. Morphological and morphometric data were investigated for phenotypic diversity among localities and hosts using multivariate discriminant analysis of principal components. Phylogenetic relationships of C. tentaculata were determined using maximum likelihood and Bayesian inference. The population structure was analysed by fixation indices, molecular variance analysis, Tajima's D and Fu's Fs neutrality tests, Mantel tests and Bayesian clustering analysis. A higher significant morphometric difference for males was observed between localities. In the haplogroup networks, 2 groups were recovered, separating locations from the north and from the south/southeast. The morphometric variation in C. tentaculata between different localities was compatible with this north and southeast/south pattern, suggesting adaptation to different ecological conditions. Population genetic analyses suggested a pattern of evolutionary processes driven by Pleistocene glacial refugia in the northeast and southeast of the Atlantic Forest based on the distribution of genetic diversity.

Population genetic structure and phenotypic diversity of Aspidodera raillieti (Nematoda: Heterakoidea), a parasite of Didelphini marsupials in Brazil's South and Southeast Atlantic Forest.

BACKGROUND: The population genetics of parasites may be influenced by host specificity, life cycle, host geographical range, evolutionary history, and host population structure. The nematode Aspidodera raillieti infects different marsupial and rodent hosts in the Nearctic and Neotropical regions, implying a gene flow among populations. However, niche diversification of the main hosts of A. raillieti in superimposed areas may provide conditions for population genetic structuring within this parasite species. We examined the genetic structuring of A. raillieti infecting three marsupial species co-occurring along the South and Southeast Brazilian Atlantic Forest, a hotspot of biodiversity. METHODS: We employed morphometric analyses and partial mitochondrial cytochrome c oxidase I gene sequences (MT-CO1) to characterize populations via phylogenetic and phylogeographic analyses. RESULTS: Among 175 A. raillieti specimens recovered from the marsupial hosts Didelphis aurita, D. albiventris, and Philander quica, we identified 99 MT-CO1 haplotypes forming four haplogroups and four clades in networks and phylogenetic trees, respectively. Clades I and II encompassed parasites of D. albiventris from the South region, clade III comprised parasites of D. aurita from the South and Southeast regions, and clade IV encompassed parasites of D. aurita and D. albiventris from the South and Southeast regions and parasites of P. quica from the South region. High genetic differentiation between clades, with a high fixation index and greater genetic variation in the analysis of molecular variance (AMOVA), indicated low gene flow between clades. Haplotypes shared among host species revealed a lack of host specificity. A significant correlation in the Mantel test suggested parasite isolation by distance, while there was no evidence of geographical structure between populations. Negative neutrality test values for clades III and IV suggested recent population expansion. Morphometric differentiation between A. raillieti specimens recovered from different host species, as well as from different localities, was more evident in males. CONCLUSION: The genetic structure of A. raillieti populations in the South and Southeast Atlantic Forest resulted from historical events rather than from current geographical distribution or host specificity. We also demonstrate morphometric variation associated with host species and localities, suggesting phenotypic plasticity to host attributes and to spatial variables.

Pharmacogenetic differentiation across Latin America.

Aim: To explore the pharmacogenetic differentiation across Latin American populations, using the fixation index statistics (FST). Materials & methods: FST analyses were applied to 1519 pharmacogenetic markers in the 1000 Genomes admixed American superpopulation (1KG_AMR) and an admixed Brazilian sample. Results: Allele-specific FST values for the overall cohort point to little overall pharmacogenetic differentiation (average FST = 0.017); however, moderate differentiation (FST = 0.05-0.15) was observed for 83 markers, while large differentiation (FST = 0.15-0.25) was restricted to three markers. Pairwise FST analysis identified three markers with very large differentiation (FST >0.25). Conclusion: The present study verifies and extends previous reports of little overall pharmacogenetic divergence across Latin America, although a number of markers display substantial differentiation.

Diversity and Genetic Structure of Dioon holmgrenii (Cycadales: Zamiaceae) in the Mexican Pacific Coast Biogeographic Province: Implications for Conservation.

Dioon holmgrenii De Luca, Sabato et Vázq.Torres is an endangered species; it is endemic and its distribution is restricted to the biogeographic province of the Mexican Pacific Coast. The aim of this work was to determine the diversity and genetic structure of nine populations. The genetic diversity parameters and Wright's F statistics were determined with six microsatellite loci. The genetic structure was determined by using the Structure software and by a discriminant analysis. The genetic diversity of the populations was high. The proportion of polymorphic loci was 0.89, the observed heterogeneity was higher (Ho = 0.62 to 0.98) than expected (He = 0.48 to 0.78), and the fixation index was negative (IF = -0.091 to -0.601). Heterozygous deficiency (FIT = 0.071) was found at the species level and heterozygotes excess (FIS = -0.287) at the population level. The genetic differentiation between populations was high (FST = 0.287), with the number of migrants less than one. Three groups of populations were differentiated, and the variation within populations, between populations, and between groups was: 65.5, 26.3, and 8.2%, respectively. Multiple factors explain the high genetic diversity, while the genetic structure is due to geographic barriers. Community reserves are urgent in at least one most diverse population of each group.

Identification of selection signatures involved in performance traits in a paternal broiler line.

BACKGROUND: Natural and artificial selection leads to changes in certain regions of the genome resulting in selection signatures that can reveal genes associated with the selected traits. Selection signatures may be identified using different methodologies, of which some are based on detecting contiguous sequences of homozygous identical-by-descent haplotypes, called runs of homozygosity (ROH), or estimating fixation index (FST) of genomic windows that indicates genetic differentiation. This study aimed to identify selection signatures in a paternal broiler TT line at generations 7th and 16th of selection and to investigate the genes annotated in these regions as well as the biological pathways involved. For such purpose, ROH and FST-based analysis were performed using whole genome sequence of twenty-eight chickens from two different generations. RESULTS: ROH analysis identified homozygous regions of short and moderate size. Analysis of ROH patterns revealed regions commonly shared among animals and changes in ROH abundance and size between the two generations. Results also suggest that whole genome sequencing (WGS) outperforms SNPchip data avoiding overestimation of ROH size and underestimation of ROH number; however, sequencing costs can limited the number of animals analyzed. FST-based analysis revealed genetic differentiation in several genomic windows. Annotation of the consensus regions of ROH and FST windows revealed new and previously identified genes associated with traits of economic interest, such as APOB, IGF1, IGFBP2, POMC, PPARG, and ZNF423. Over-representation analysis of the genes resulted in biological terms of skeletal muscle, matrilin proteins, adipose tissue, hyperglycemia, diabetes, Salmonella infections and tyrosine. CONCLUSIONS: Identification of ROH and FST-based analyses revealed selection signatures in TT line and genes that have important role in traits of economic interest. Changes in the genome of the chickens were observed between the 7th and 16th generations showing that ancient and recent selection in TT line may have acted over genomic regions affecting diseases and performance traits.

Genetic variability in a population of Astyanax scabripinnis: recent bottleneck and the possible influence of individuals with B chromosomes

Access the genetic variability of endangered and isolated populations has become an important conservation tool. Astyanax scabripinnis is a well-known fish model for genetic studies, forming very isolated populations in headwaters. Besides that, this species frequently presents supernumerary chromosomes, which elevates the interest on genetic studies. Genetic diversity of an Astyanax scabripinnispopulation from the Atlantic Forest (Serra da Mantiqueira region, Brazil) was assessed with microsatellite markers for the first time. Since microsatellite markers are not described for this species, we tested markers described for a related species for transferability to A. scabripinnis. Six polymorphic loci were sufficiently reliable for population genetic analysis. We found that this population passed through a recent bottleneck because of the presence of an excess of heterozygotes, low allelic diversity, heterozygosity excess, and small effective population size. Individuals with and without B chromosomes were previously identified in this population and our study found private alleles in the individuals without B chromosomes. Furthermore, when individuals without B chromosomes were removed from the analysis, the population did not present heterozygosity excess, suggesting that the bottleneck event was driven by individuals with B chromosomes. Our results provide an insight into the value of microsatellite markers as molecular tools and is the first genetic study using molecular data of A. scabripinnis from this area.

Genomic variation and population structure detected by single nucleotide polymorphism arrays in Corriedale, Merino and Creole sheep.

THE AIM OF THIS STUDY WAS TO INVESTIGATE THE GENETIC DIVERSITY WITHIN AND AMONG THREE BREEDS OF SHEEP: Corriedale, Merino and Creole. Sheep from the three breeds (Merino n = 110, Corriedale n = 108 and Creole n = 10) were genotyped using the Illumina Ovine SNP50 beadchip(®). Genetic diversity was evaluated by comparing the minor allele frequency (MAF) among breeds. Population structure and genetic differentiation were assessed using STRUCTURE software, principal component analysis (PCA) and fixation index (FST). Fixed markers (MAF = 0) that were different among breeds were identified as specific breed markers. Using a subset of 18,181 single nucleotide polymorphisms (SNPs), PCA and STUCTURE analysis were able to explain population stratification within breeds. Merino and Corriedale divergent lines showed high levels of polymorphism (89.4% and 86% of polymorphic SNPs, respectively) and moderate genetic differentiation (FST = 0.08) between them. In contrast, Creole had only 69% polymorphic SNPs and showed greater genetic differentiation from the other two breeds (FST = 0.17 for both breeds). Hence, a subset of molecular markers present in the OvineSNP50 is informative enough for breed assignment and population structure analysis of commercial and Creole breeds.

Genética poblacional para el sistema sanguíneo ABO en una población con malaria endémica / Population Genetics for the ABO Blood System in a Population with Endemic Malaria

Introducción: el sistema sanguíneo ABO es un factor de riesgo para la malaria. Esta asociación afecta la estructura genética de poblaciones donde la malaria es endémica. Se desconoce la estructura genética para el sistema ABO en pacientes de Gambia. Objetivo: caracterizar la estructura genética para el sistema ABO de la población gambiana. Métodos: se realizó un estudio transversal en una muestra de 739 individuos admitidos en el Hospital Docente Reina Victoria, Gambia, desde diciembre de 2011 hasta septiembre de 2012. Los grupos del sistema ABO fueron determinados con el uso de antisueros comerciales. Los datos fueron digitalizados en forma de archivos Excel y procesados con el software SPSS y GDA. Resultados: las frecuencias para la grupos A, AB, B y O fueron: 0,24; 0,06; 0,22 y 0,48, respectivamente. Se asumió un equilibrio de Hardy-Weinberg, las frecuencias alélicas estimadas fueron de 0,16; 0,15 y 0,69 para los alelos I A, I B e I O, respectivamente. Esta distribución no mostró desviación significativa del equilibrio genético (p=0,9978). La heterocigocidad observada (H O=0,4804) mostró un ligero incremento respecto a la esperada (H E=0,4796). El mayor valor para el índice de fijación global correspondió al alelo I O (F ST=-0,002594). Conclusiones: existió un ligero incremento en la diversidad genética para el sistema ABO en pacientes de Gambia, que favoreció la transmisión del alelo I O y que sugirió la ocurrencia de cambios micro-evolutivos en respuesta a la presión selectiva impuesta por la malaria endémica, que significó el grupo O protector frente a la infección por el Plasmodium falciparum.

Introduction: the ABO blood system is a risk factor for malaria. This association affects the genetic structure of populations where malaria is endemic. Genetic structure for the ABO system in Gambia is unknown. Objective: to characterize the genetic structure for the ABO system of the Gambian population. Methods: a cross-sectional study was performed in a sample of 739 individuals admitted to the Reina Victoria Teaching Hospital , Gambia , from December 2011 to September 2012. ABO groups were determined using commercial antiserum The data were digitized in the form of Excel files and processed with SPSS software and GDA. Results: frequencies for groups A, AB, B and O were 0.24, 0.06, 0.22 and 0.48, respectively. A balance of Hardy -Weinberg equilibrium was assumed, estimated allele frequencies were 0.16, 0.15 and 0.69 for I A, I B and I O, respectively alleles. This distribution showed no significant deviation from genetic equilibrium (p = 0.9978). The observed heterozygosity (H O = 0.4804) showed a slight increase from the expected one (H E = 0.4796). The highest value for the overall index corresponded to first allele fixation (F ST = -0.002594). Conclusions: there was a slight increase in genetic diversity for the ABO system in Gambia, favoring transmission first allele and suggested the occurrence of micro - evolution changes in response to selective pressure imposed by endemic malaria, which represented the group O protector against infection by Plasmodium falciparum.

Effect of a GFOD2 variant on responses in total and LDL cholesterol in Mexican subjects with hypercholesterolemia after soy protein and soluble fiber supplementation.

BACKGROUND: Although dietary treatments can successfully reduce blood lipids in hypercholesterolemic subjects, individual variation in that response has on occasion been linked to allelic differences. SNP rs12449157 has shown association with HDL-C concentrations in GWAS and falls in the glucose-fructose oxidoreductase domain containing 2 (GFOD2) locus. Of interest, previous data suggest that this SNP may be under environmentally driven selection. Thus, the aim of this study was to assess if rs12449157 may mediate the response of lipid traits to a dietary supplementation (DS) with soy protein and soluble fiber in a Mexican population with hypercholesterolemia. METHODS: Forty-one subjects with hypercholesterolemia were given a low saturated fat diet (LSFD) for 1 month, followed by a LSFD+DS that included 25 g of soy protein and 15 g of soluble fiber (S/SF) daily for 2 months. Anthropometric, clinical, biochemical and dietary variables were determined. We analyzed the gene-diet interaction between the GFOD2 genotype, with the minor allele frequency of 0.24, and the DS on total cholesterol (TC) and LDL-C concentrations. RESULTS: Hypercholesterolemic subjects with GFOD2 rs12449157 G allele had higher serum TC and LDL-C at the baseline and showed a greater response to the LSCD+S/SF (-83.9 and -57.5mg/dl, respectively) than those with GFOD2 AA genotype (-40.1 and -21.8 mg/dl, respectively) (P=0.006 for TC, 0.025 for LDL-C, respectively). CONCLUSION: The observed differences in allele-driven, diet-induced changes in blood lipids may be the result of a recent environmentally driven selection on the rs12449157 minor allele. Variation in the GFOD2 gene contributes to the genetic basis for a differential response to a cholesterol- or lipid-lowering diet.