Complete Chloroplast Genomes of Vogel and Benth: Comparative and Phylogenetic Analyses.

Background: The species and , popularly known as white sucupira or faveira, are native to the Cerrado biome and have the potential for medicinal use and reforestation. They are sister species with evolutionary proximity.

Objective: Considering that the chloroplast genome exhibits a conserved structure and genes, the analysis of its sequences can contribute to the understanding of evolutionary, phylogenetic, and diversity issues.

Forecasting effects of climate changes on the population genetic structure of Anacardium occidentale in the Cerrado biome, Brazil.

There has been a continuous interest in understanding the patterns of genetic diversity in natural populations because of the role of intraspecific genetic diversity as the basis of all evolutionary change and thus, its potential effects on population persistence when facing environmental changes. Here, we provided the first description of genetic diversity distribution and population structure of Anacardium occidentale L. (cashew) from the Brazilian Cerrado, one of the most economically important tropical crops in the world.

Diversity of eukaryotic and prokaryotic microbiota revealed by metabarcoding in Neotropical floodplain lakes.

The diversity of eukaryotic and prokaryotic communities has been assessed by morphological and genetic approaches, which are used to characterize the microbiota in different environments. Here, planktonic prokaryotic and eukaryotic communities of the Araguaia River, located in the Central region of Brazil, were analyzed based on metabarcoding analysis of rRNA genes to evaluate the diversity of these groups in tropical floodplain lakes. Also, we tested their spatial concordance throughout the Araguaia river.

A Pipeline for the Development of Microsatellite Markers using Next Generation Sequencing Data.

Also known as Simple Sequence Repetitions (SSRs), microsatellites are profoundly informative molecular markers and powerful tools in genetics and ecology studies on plants. This research presents a workflow for developing microsatellite markers using genome skimming. The pipeline was proposed in several stages that must be performed sequentially: obtaining DNA sequences, identifying microsatellite regions, designing primers, and selecting candidate microsatellite regions to develop the markers.

Complete chloroplast genome sequence of Caryocar brasiliense Camb. (Caryocaraceae) and comparative analysis brings new insights into the plastome evolution of Malpighiales.

Caryocar brasiliense (Caryocaraceae) is a Neotropical tree species widely distributed in Brazilian Savannas. This species is very popular in central Brazil mainly by the use of its fruits in the local cuisine, and indeed it is one of the candidates, among Brazilian native plants, for fast track incorporation into cropping systems. Here we sequenced the complete chloroplast genome of C.

The importance of understanding the distribution of GSTM1 and GSTT1 genotypes and haplotypes in a region with intense agriculture activity.

Brazil is one of the largest pesticide consumers in the world, mainly due to its intense agricultural activity. The State of Goias, situated in Central Brazil, is a region recognized as an essential producer of soy, corn, beans, sorghum, sugar cane, and cotton. In this study, we evaluated 602 unrelated individuals, distributed in central and southern regions in Goias, presenting combined frequencies (haplotypes) of the and genes.

Evaluating the OGG1 rs1052133 and rs293795 polymorphisms in a sample of rural workers from Central Brazil population: a comparative approach with the 1000 Genomes Project.

Brazilian population is one of the largest consumers of pesticides in the world, especially the Central Brazil population. Thus, the aim of this study was to evaluate the frequency of genotypes, alleles, haplotypes, and the linkage disequilibrium (DL) of the OGG1 gene in rural workers from Central Brazil, comparing with the populations of the 1000 genome. Three hundred thirty healthy individuals not related and randomly selected were included in this study.

Unraveling CYP2E1 haplotypes in alcoholics from Central Brazil: A comparative study with 1000 genomes population.

We evaluated genetic variability of single nucleotide polymorphisms (SNPs) situated in the CYP2E1 gene promoter in alcoholics. We also compared 1000 Genomes Project of CYP2E1 polymorphisms with frequencies of genotypes and haplotypes. Eight variation points were exclusively found in Brazilians.

Morphological characteristics and genetic evidence reveals a new species of (Euphorbiaceae, Crotonoideae) from Goiás, Brazil.

During botanical expeditions between 2010 and 2015, as part of a taxonomic study of in the Midwest region of Brazil, approximately 500 specimens of the genus were collected. Some of these specimens presented similarities to . However, after careful morphological analyses, associated with genetic evidence, we propose here as a new species.

DNA damage in peripheral blood lymphocytes and association with polymorphisms in the promoter region of the CYP2E1 gene in alcoholics from Central Brazil.

DNA damage caused by the accumulation of bio-products generated in the biotransformation of ethanol to acetaldehyde mediated by the CYP2E1 enzyme has been studied. To evaluate DNA damage in peripheral blood lymphocytes and the possible association with polymorphisms in the promoter region of the CYP2E1 gene, we performed a case-control study including 75 alcoholics and 59 individuals who consume alcohol socially. Alcoholics were previously diagnosed by the Psychosocial Care Center - Alcohol and Drugs (CAPS A/D) in the city of Goiania, Goias state, Central Brazil.

Geographically weighted regression as a generalized Wombling to detect barriers to gene flow.

Barriers to gene flow play an important role in structuring populations, especially in human-modified landscapes, and several methods have been proposed to detect such barriers. However, most applications of these methods require a relative large number of individuals or populations distributed in space, connected by vertices from Delaunay or Gabriel networks. Here we show, using both simulated and empirical data, a new application of geographically weighted regression (GWR) to detect such barriers, modeling the genetic variation as a "local" linear function of geographic coordinates (latitude and longitude).

Correlation between genetic diversity and environmental suitability: taking uncertainty from ecological niche models into account.

The hindcast of shifts in the geographical ranges of species as estimated by ecological niche modelling (ENM) has been coupled with phylogeographical patterns, allowing the inference of past processes that drove population differentiation and genetic variability. However, more recently, some studies have suggested that maps of environmental suitability estimated by ENM may be correlated to species' abundance, raising the possibility of using environmental suitability to infer processes related to population demographic dynamics and genetic variability. In both cases, one of the main problems is that there is a wide variation in ENM development methods and climatic models.

Mantel test in population genetics.

The comparison of genetic divergence or genetic distances, estimated by pairwise FST and related statistics, with geographical distances by Mantel test is one of the most popular approaches to evaluate spatial processes driving population structure. There have been, however, recent criticisms and discussions on the statistical performance of the Mantel test. Simultaneously, alternative frameworks for data analyses are being proposed.

A new eigenfunction spatial analysis describing population genetic structure.

Several methods of spatial analyses have been proposed to infer the relative importance of evolutionary processes on genetic population structure. Here we show how a new eigenfunction spatial analysis can be used to model spatial patterns in genetic data. Considering a sample of n local populations, the method starts by modeling the response variable (allele frequencies or phenotypic variation) against the eigenvectors sequentially extracted from a geographic distance matrix (n × n).

Geographical patterns of turnover and nestedness-resultant components of allelic diversity among populations.

The analysis of geographical patterns in population divergence has always been a powerful way to infer microevolutionary processes involved in population differentiation, and several approaches have been used to investigate such patterns. Most frequently, multivariate spatial patterns of population differentiation are analyzed by computing pairwise genetic distances or F(ST) (or related statistics, such as ϕ(ST) from AMOVA), which are then correlated with geographical distances or landscape features. However, when calculating distances, especially based on presence-absence of alleles in local populations, there would be a confounding effect of allelic richness differences in the population differentiation.

Development of microsatellite markers for the neotropical tree species Dipteryx alata (Fabaceae).

Premise Of The Study: Microsatellite markers were developed for the population genetic analyses of the neotropical tree Dipteryx alata (Fabaceae).

Methods And Results: Microsatellites were developed from a genomic shotgun library. Polymorphism at each microsatellite loci was analyzed based on 94 individuals from three populations.

A review of techniques for spatial modeling in geographical, conservation and landscape genetics.

Most evolutionary processes occur in a spatial context and several spatial analysis techniques have been employed in an exploratory context. However, the existence of autocorrelation can also perturb significance tests when data is analyzed using standard correlation and regression techniques on modeling genetic data as a function of explanatory variables. In this case, more complex models incorporating the effects of autocorrelation must be used.

Landscape conservation genetics of Dipteryx alata ("baru" tree: Fabaceae) from Cerrado region of central Brazil.

In this paper random amplified polymorphic DNA (RAPD) was used to evaluate the degree of among-population differentiation and associated spatial patterns of genetic divergence for Dipteryx alata Vogel populations from Cerrado region of central Brazil, furnishing support for future programs of conservation of this species. We analyzed patterns of genetic and spatial population structure using 45 RAPD loci scored for 309 trees, sampled from five different regions with two populations each. Genetic structure analysis suggested that panmixia null hypothesis can be rejected, with significant among-population components of 15%.

RAPD variation and population genetic structure of Physalaemus cuvieri (Anura: Leptodactylidae) in Central Brazil.

Studies about the organization of the genetic variability and population structure in natural populations are used either to understand microevolutionary processes or the effects of isolation by human-inducted landscape modifications. In this paper, we analyzed patterns of genetic population structure using 126 RAPD loci scored for 214 individuals of Physalaemus cuvieri, sampled from 18 local populations. Around 97% of these loci were polymorphic.