Mitochondrion genomes of seven species of the endangered genus Sporophila (Passeriformes: Thraupidae).

We announce the mitochondrial genomes of seven species of the genus Sporophila (S. bouvreuil, S. iberaensis, S.

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.

Chloroplast genome characterization of Uncaria guianensis and Uncaria tomentosa and evolutive dynamics of the Cinchonoideae subfamily.

Uncaria species are used in traditional medicine and are considered of high therapeutic value and economic importance. This work describes the assembly and annotation of the chloroplast genomes of U. guianensis and U.

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.

Large-scale Degradation of the Tocantins-Araguaia River Basin.

The Tocantins-Araguaia Basin is one of the largest river systems in South America, located entirely within Brazilian territory. In the last decades, capital-concentrating activities such as agribusiness, mining, and hydropower promoted extensive changes in land cover, hydrology, and environmental conditions. These changes are jeopardizing the basin's biodiversity and ecosystem services.

The complete mitochondrial genome of the aquatic coralsnake (Reptilia, Serpentes, Elapidae).

In this study, we report the first complete mitochondrial genome sequence of the Aquatic Coralsnake . The mitochondrial genome lengthis 17,375 bp, comprising 13 protein-coding genes, 2 rRNA (12S and 16S) and 22 tRNA, as well as two typical control regions. Phylogenetic analysis based upon 13 protein-coding genes showed clusters based on terrestrial and marine species.

Development and characterization of microsatellite markers in (Leguminosae).

In this study, we report the development and characterization of 15 new microsatellite markers for (Leguminosae) in order to support future analyses of genetic diversity in populations of this species. In screening with 48 individuals from three different populations of , we tested the amplification of 20 microsatellite loci, of which five are not useful for population genetic studies due to the lack of polymorphisms or amplification failures. For the final set of 15 loci, the number of alleles ranged from 2 to 15, with a total of 116 alleles.

BarcodingGO: A problem-based approach to teach concepts related to environmental-DNA and bioinformatics.

In this paper, we propose and describe a new approach, named BarcodingGO, to teach environmental DNA and bioinformatics concepts to undergraduate or graduate students in molecular biology-related fields. The learning pipeline proposed here aims to solve a simulated environmental monitoring problem, in which a biodiversity survey of a particular region is needed to assess the impact of an environmental disaster. Biological surveys, in the context of environmental DNA studies, are performed by analyzing the DNA released by organisms living in a specific environment.

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.

Genetic diversity in populations of African mahogany (Khaya grandioliola C. DC.) introduced in Brazil.

Given its high-valued wood, the African mahogany (Khaya grandifoliola) has been envisaged as a renewable source of tropical hardwoods in Brazil. However, there are concerns about the hypothesized low diversity among the few K. grandifoliola germplasm sources introduced in the country.

Data on the draft genome sequence of Camb. (Caryocaraceae): An important genetic resource from Brazilian savannas.

(Caryocaraceae) is a Neotropical tree species widely distributed in Brazilian savannas. This species is very popular in central Brazil mainly due to the use of its fruits in the local cuisine and their anti-inflammatory proprieties, and indeed it is one of the candidates, among Brazilian native plants, for fast track incorporation into cropping systems. Considering the importance of , little is known about its genetics and genomics, and determination of a reference genome sequence could improve the understanding of its evolution, as well as the development of tools for domestication.

The complete chloroplast genome of Stryphnodendron adstringens (Leguminosae - Caesalpinioideae): comparative analysis with related Mimosoid species.

Stryphnodendron adstringens is a medicinal plant belonging to the Leguminosae family, and it is commonly found in the southeastern savannas, endemic to the Cerrado biome. The goal of this study was to assemble and annotate the chloroplast genome of S. adstringens and to compare it with previously known genomes of the mimosoid clade within Leguminosae.

Genetic variability and effective population size in Hymenaea stigonocarpa (Fabaceae) germplasm collection: tools for breeding programs and genetic conservation.

The conservation of plant genetic resources is essential for breeding programs. Regarding the native species of the Brazilian Cerrado biome, many studies have demonstrated their high potential for use in both medicines and foods. Hymenaea stigonocarpa, a tree with wide occurrence in the Cerrado, has economic importance, and due its extractive use, the establishment of a breeding program is relevant for sustainable use and conservation.

Cytogenetics of two hylid frogs from Brazilian Cerrado.

Cytogenetic data can be useful for taxonomic and phylogenetic studies, as well as to provide information about chromosome evolution. Therefore, it may help design conservation priorities for some threatened species, such as anurans. Herein, we describe the karyotypes of Scinax constrictus and Ololygon centralis, native endemic species from the Brazilian Cerrado.

The Cerrado (Brazil) plant cytogenetics database.

Cerrado is a biodiversity hotspot that has lost ca. 50% of its original vegetation cover and hosts ca. 11,000 species belonging to 1,423 genera of phanerogams.

Coralsnake Venomics: Analyses of Venom Gland Transcriptomes and Proteomes of Six Brazilian Taxa.

Venom gland transcriptomes and proteomes of six taxa (, , , , , and ) were investigated, providing the most comprehensive, quantitative data on venom composition to date, and more than tripling the number of venom protein sequences previously available. The six venomes differ dramatically. All are dominated by 2-6 toxin classes that account for 91-99% of the toxin transcripts.

Genetic and chemical diversity of Uncaria tomentosa (Willd. ex. Schult.) DC. in the Brazilian Amazon.

Uncaria tomentosa (Willd. ex Schult.) DC.

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).

Conservation biogeography of the Cerrado's wild edible plants under climate change: Linking biotic stability with agricultural expansion.

Unlabelled: REMISE OF THE STUDY: Wild edible plants (WEPs) have an important cultural and economic role in human population worldwide. Human impacts are quickly converting natural habitats in agricultural, cattle ranch, and urbanized lands, putting native species on peril of risk of extinction, including some WEPs. Moreover, global climate changes also can pose another threat to species persistency.

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.

Isolation and characterization of microsatellite loci in Byrsonima cydoniifolia (Malpighiaceae) and cross-amplification in B. crassifolia.

Premise Of The Study: Microsatellite markers were developed and characterized in Byrsonima cydoniifolia (Malpighiaceae) to allow further investigation of genetic variation in natural populations. Cross-amplification was tested in the related species B. crassifolia.

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.