Abstract We announce the mitochondrial genomes of seven species of the genus Sporophila (S. bouvreuil, S. iberaensis, S. melanogaster, S. minuta, S. nigrorufa, S. pileata, and S. ruficollis) which were validated by comparative genomic and phylogenetic analysis with related species. The mitochondrial genomes of seven passerines of the genus Sporophila were assembled (three complete and four nearly complete genomes) and were validated by reconstructing phylogenetic relations within Thraupidae. The complete mitogenomes ranged from 16,781 bp in S. ruficollis to 16,791 bp in S. minuta. We identified a conserved genome composition within all mitogenomes with 13 protein-coding genes, 22 tRNAs and two rRNAs. We observed a bias in the nucleotide composition and six mutational hotspots in Sporophila mitogenomes. Our mitogenome-based phylogenetic tree has S. minuta, S. maximiliani and S. nigricollis as sister species of the remaining species in the genus. We present new mitogenome sequences for seven Sporophila species, providing new genomic resources that may be useful for research on the evolution, comparative genetics, and conservation of this threatened group. S (S bouvreuil iberaensis melanogaster minuta nigrorufa pileata three Thraupidae 16781 16 781 16,78 16791 791 16,79 1 proteincoding protein coding genes 2 rRNAs mitogenomebased based evolution genetics group 1678 78 16,7 1679 79 167 7 16,

Resumo O objetivo deste trabalho foi descrever e comparar os padrões de variação genética em 19 populações de Anacardium humile do bioma Cerrado da região Centro-Oeste brasileira. A coleção ex situ de germoplasma da Universidade Federal de Jataí, no estado de Goiás, Brasil, foi utilizada para o estudo. Para quantificar a variabilidade genética de A. humile, 529 plantas oriundas de 17 populações de Goiás e de 2 do estado de Mato Grosso foram estudadas, das quais nove loci microssatélites foram genotipados por eletroforese capilar. As populações apresentaram altos níveis de diversidade genética, com valor médio de 0,830, e altos valores de endogamia, o que sugere um déficit de heterozigotos. O valor de diferenciação genética entre as populações foi de 0,065. Já a maior variabilidade, estruturada de forma moderada, foi observada dentro das populações. Há endogamia significativa na população de A. humile no bioma Cerrado da região Centro-Oeste brasileira. As populações de A. humile estão divididas em dois grupos. 1 CentroOeste Centro Oeste brasileira Jataí Brasil estudo 52 estudadas capilar 0830 0 830 0,830 heterozigotos 0065 065 0,065 moderada grupos 5 083 83 0,83 006 06 0,06 08 8 0,8 00 0,0 0,

Abstract The objective of this work was to describe and compare the patterns of genetic variation in 19 populations of Anacardium humile from the Cerrado biome of the Brazilian Midwestern region. The ex situ germplasm collection of Universidade Federal de Jataí, in the state of Goiás, Brazil, was used for the study. To quantify the genetic variability of A. humile, 529 plants from 17 populations in Goiás from 2 in the state of Mato Grosso were studied, from which nine microsatellite loci were genotyped by capillary electrophoresis. The populations showed high levels of genetic diversity, with an average value of 0.830, and high inbreeding values, which suggests a deficit of heterozygotes. The genetic differentiation value between populations was 0.065. The greatest variability, which is moderately structured, was observed within populations. There is a significant inbreeding within the A. humile population in the Cerrado biome of the Brazilian Midwestern region. The A. humile populations are divided into two groups. 1 region Jataí Brazil study A 52 studied electrophoresis diversity 0830 0 830 0.830 values heterozygotes 0065 065 0.065 structured groups 5 083 83 0.83 006 06 0.06 08 8 0.8 00 0.0 0.

RESUMO Hymenaea stigonocarpa (Mart. Ex Hayne), popularmente conhecida como jatobá-do-cerrado, é uma árvore frutífera amplamente distribuída no Cerrado, a qual possui múltiplos usos e é um recurso genético promissor. Objetivou-se caracterizar fisicamente frutos e sementes de H. stigonocarpa, bem como estimar a variabilidade fenotípica em três níveis hierárquicos: populações, matrizes dentro de populações e frutos/sementes dentro de matrizes. Frutos de seis matrizes foram amostrados de cada uma das 25 populações naturais encontradas no Cerrado. A caracterização morfométrica de 742 frutos foi realizada avaliando-se 10 caracteres quantitativos em frutos e sementes. Além disso, foram realizadas análises comparativas entre os valores médios de H. stigonocarpa e a variedade botânica H. stigonocarpa var. brevipetiolata. Variações fenotípicas significativas ocorreram em todos os níveis hierárquicos. Observou-se alta diferenciação fenotípica entre as populações para caracteres quantitativos (massa e tamanho do fruto, massa da polpa e da semente), a qual foi ainda maior quando H. stigonocarpa var. brevipetiolata foi incluída na análise

ABSTRACT Hymenaea stigonocarpa (Mart. Ex Hayne), popularly known as jatobá-do-cerrado, is a fruit tree widely distributed in the Brazilian Savanna, has multiple uses and is a promising genetic resource. This study aimed to physically characterize fruits and seeds of H. stigonocarpa, as well as to estimate the phenotypic variability at three hierarchical levels: populations, mother trees within populations, and fruits/seeds within mother trees. Fruits from six mother trees were sampled from each of the 25 natural populations found in the Brazilian Savanna. The morphometric characterization of 742 fruits was carried out by evaluating 10 quantitative traits in fruits and seeds. In addition, comparative analyses were performed between the average values of H. stigonocarpa and the botanical variety H. stigonocarpa var. brevipetiolata. Significant phenotypic variations were noticed at all hierarchical levels. A high phenotypic differentiation among the populations was observed for quantitative traits (fruit mass and size, pulp mass and seed mass), being higher when H. stigonocarpa var. brevipetiolata was included in the analysis.

RESUMO Eugenia dysenterica DC. é uma árvore nativa do Cerrado conhecida como recurso genético por seus frutos e potencial culinário. O conhecimento da variabilidade genética de características agronômicas é importante para subsidiar pesquisas sobre a sua conservação e domesticação. Objetivou-se estimar os parâmetros genéticos quantitativos das características iniciais de crescimento entre e dentro de subpopulações de E. dysenterica, em teste de procedências e progênies, e estabelecer uma coleção de germoplasma representativa da distribuição da espécie. Para isso, 25 subpopulações naturais foram amostradas e, dentro de cada subpopulação, 6 árvores matrizes. As progênies foram semeadas em viveiro, em delineamento de blocos ao acaso constituído de 150 progênies, quatro repetições e cinco plantas por parcela. A análise de variância de caracteres do desenvolvimento inicial revelou maior variabilidade entre progênies dentro da subpopulação do que a observada entre as subpopulações. A biomassa acima do solo representou apenas 15 % da biomassa total, característica recorrente em espécies do Cerrado. A herdabilidade estimada e os coeficientes de variação genética apresentaram potencial de seleção para os caracteres de desenvolvimento inicial, importantes para a produção comercial de mudas. Uma coleção de germoplasma in vivo ex situ foi estabelecida para fins de conservação e melhoramento, utilizando-se uma amostra de quatro plantas de cada progênie.

ABSTRACT Eugenia dysenterica DC. is a native tree from the Brazilian Savanna known as a genetic resource for its fruits and culinary potential. The knowledge on the genetic variability of agronomic traits is important to support studies on its conservation and domestication. This study aimed to estimate the quantitative genetic parameters of initial growth traits among and within E. dysenterica subpopulations, in provenance and progeny testing, and establish a germplasm collection representative of the species distribution. For that, 25 natural subpopulations were sampled and, within each subpopulation, six mother trees. The progenies were sown in a nursery, in a randomized complete blocks design consisting of 150 progenies, four replications and five plants per plot. The analysis of variance of the initial development traits revealed a greater variability among the progenies within the subpopulation than that observed among the subpopulations. The aboveground biomass represented only 15 % of the total biomass, a recurrent characteristic in Brazilian Savanna species. The estimated heritability and coefficients of genetic variation presented selection potential for the initial development traits, which are important for commercial seedlings production. An in vivo ex situ germplasm collection was established for conservation and breeding purposes, using a sample of four plants from each progeny.

ABSTRACT The genus Manihot Mill. contains about 120 species of which about 104 occur in Brazil. We tested the cross-amplification of ten microsatellite markers developed for Manihot esculenta in 15 species of Manihot endemic to the Brazilian Cerrado. We also evaluated the genetic diversity of Manihot irwinii, M. orbicularis, and M. purpureocostata. Ten pairs of primers were amplified among 14 species of Manihot. The percentage of polymorphic loci per species varied from 70 to 100 %. Nine markers showed amplification and polymorphism when evaluated on polyacrylamide gel. The markers were combined to form three sets for multiplex genotyping for genetic diversity analysis, and showed 51, 75, and 75 alleles in M. irwinii, M. orbicularis, and M. purpureocostata, respectively. The levels of genetic diversity for the transferred markers were high for the three species and proved to be useful for population genetics studies of species of Manihot endemic to the Cerrado. The results of this study will help to better understand the genetic diversity, taxonomy and relationships among species Manihot, and to develop conservation programs for the genus.

Abstract 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. brasiliense and used the data to access its genomic resources using high-throughput sequencing. The chloroplast exhibits a genome length of 165,793 bp and the typical angiosperm quadripartite structure with two copies of an inverted repeat sequence (IRa and IRb) of 34,902 bp each, separating a small single copy (SSC) region of 11,852 bp and a large single copy (LSC) region of 84,137 bp. The annotation analysis identified 136 genes being 87 protein-coding, eight rRNA and 37 tRNA genes. We identified 49 repetitive DNA elements and 85 microsatellites. A bayesian phylogenetic analysis helped to understand previously unresolved relationships in Malpighiales, placing Caryocaraceae as a separated group in the order, with high supported nodes. This study synthetizes valuable information for further studies allowing a better understanding of evolutionary patterns in the group and providing resources for future breeding programs.

Abstract 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. Using eight microsatellite markers, we evaluated the genetic diversity and divergence among 53 superior trees selected from three provenances of K. grandifoliola located in the state of Para. These populations are among the oldest plantations (>15 years) in Brazil and, therefore, the country's main seed sources. The average number of alleles per locus was 5.9, expected heterozygosity was moderate (^=0.56) and lower than the high observed heterozygosity (HO=0.74). Therefore, the intrapopulation fixation index was negative (f=-0.31) indicating the possibility that selection of superior trees might have favored heterozygous plants with heterosis. No genetic structure was observed between provenances. The genetic diversity observed within selected trees, with an effective population size (Ne) of 30.4, is comparable to that of natural populations of African and Brazilian mahoganies. Therefore, our results contradict the idea that the genetic diversity of K. grandifoliola introduced in Brazil is low and show that our germplasm can be exploited for breeding purposes.

Abstract Dipteryx alata Vogel (Leguminosae) is a native Neotropical tree with a wide distribution in the Brazilian Cerrado that is commonly known as the baru tree. The genetic diversity of 150 D. alata progeny from a germplasm collection was characterized using nine microsatellite markers. Genetic diversity analysis detected 50 alleles ranging from 2 to 14 alleles per locus. The genetic differentiation among populations (θ p = 0.097) suggests moderate genetic structuring and high genetic differentiation among progenies (θ s = 0.169). The intrapopulation index (f = 0.122) indicates the presence of low endogamy. The effective population size (Ne = 96) shows that the germplasm collection has sufficient representativeness for use as a base population for breeding programmes. These results are useful for the exploitation of the genetic resources of D. alata for future conservation efforts and breeding programmes.

Abstract 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. Chromosome preparations for both species were stained with Giemsa for morphological analyses and then impregnated by the Ag-NOR method for localization of the nucleolar organizer region (NOR). Both species had 24 chromosomes, as confirmed by meiotic analyses, which showed 12 bivalents. Chromosome morphologies presented the same pattern for Scinax and Ololygon compared to species already karyotyped in both genera. The NOR was interstitially located in the long arm of pair 7 in S. constrictus, whereas in O. centralis it was found near the centromere in the long arm of pair 1, thus diverging from what is commonly found for other Ololygon species. Therefore, we provide the first description of the karyotype of O. centralis and the first report of the localization of the NOR for the karyotype of both species. Our study increases the cytogenetic knowledge in species of the genera Scinax and Ololygon, and provide support for further studies on the taxonomy, ecology, and evolution of hylid anurans.

Resumo Eugenia dysenterica DC. (cagaiteira) é uma árvore frutífera nativa do Cerrado brasileiro. É uma espécie promissora para cultivo, mas que carece de informações básicas sobre diversidade fenotípica e variação quantitativa de seus frutos e sementes em escala populacional. Neste contexto, o presente estudo propõe estimar parâmetros fenotípicos de frutos e de sementes da espécie, a partir da variabilidade entre matrizes e subpopulações, visando a ampliar o conhecimento para o melhoramento e a conservação da espécie. Para isso, foram amostradas 25 subpopulações (populações locais) naturais, em cinco estados brasileiros. Dentro de cada subpopulação, foram coletados 20 frutos de cada uma das seis matrizes amostradas. Dados de massa, comprimento transversal e longitudinal dos frutos e sementes foram submetidos à análise descritiva, correlações e análise de variância, por um modelo hierárquico. Houve variação significativa entre matrizes dentro de subpopulações e entre subpopulações, com altos níveis de variação fenotípica. As altas variações e a formação de grupos divergentes fenotipicamente são importantes elementos para o pré-melhoramento da cagaiteira, cujas matrizes já podem ser selecionadas para os caracteres estudados. A divergência fenotípica entre populações (PST) pode ser utilizada como um indicador da estruturação da variação fenotípica da espécie em sua área natural de ocorrência.

Abstract Eugenia dysenterica DC. (cagaita tree) is a fruit tree native to the Brazilian Cerrado. It is a promising species for cultivation, but little basic information exists on the phenotypic diversity and quantitative variation of its fruits and seeds at a population scale. Thus, the present study proposes to estimate the phenotypic parameters of the species’ fruits and seeds based on the variability among mother plants and among subpopulations, thereby aiming to increase knowledge for breeding and conservation of the species. For this, 25 natural subpopulations (local populations) were sampled in five Brazilian states. Within each subpopulation, 20 fruits were collected from each of six sampled mother plants. Data for biomass, transverse and longitudinal lengths of the fruits and seeds were subjected to estimates of descriptive parameters, correlation and hierarchical analysis of variance (ANOVA). Significant variation, including high levels of phenotypic variation, was observed among mother plants within the subpopulations and between the subpopulations. The high variation and the formation of phenotypically divergent groups are important elements for the breeding of cagaita tree, whose mother plants can now be selected for the traits studied. Phenotypic divergence between populations (PST) can be used as an indicator of the structuring of the phenotypic variation of the species in its natural area of occurrence.

RESUMO O Cerrado é considerado um dos "hotspots" mundiais de biodiversidade, em função da grande extensão de vegetação natural que vem sendo continuamente perdida e do elevado número de espécies endêmicas de plantas, que muitas vezes têm sido listadas como prioridades em programas de conservação e para estudos de genética de populações. A fim de verificar tendências nos estudos de genética de populações das espécies de plantas deste bioma, uma avaliação cienciométrica dos artigos publicados e disponíveis em diferentes bases de dados foi realizada. Um total de 171 publicações provenientes de 48 periódicos foi encontrada, entre os anos de 1999 a 2014, com o número de publicações aumentando significativamente nesse período. Noventa e uma espécies com diferentes formas de vida foram estudadas, usando diferentes tipos de marcadores moleculares. A análise cienciometrica dos artigos encontrados permitiu uma melhor compreensão do conhecimento atual sobre a genética de populações de plantas do bioma Cerrado.

ABSTRACT The Cerrado biome is considered one of the biodiversity hotspots in the world, due to both the large extent of natural vegetation that has been continually lost and the high number of endemic plant species. It has often been listed as a priority in conservation programs and in population genetic studies. In order to determine trends in plant population genetic studies in this biome, a scientometric evaluation of published and available articles in different databases was performed. A total of 171 publications from 48 journals was found between the years 1999 and 2014, with the number of publications increasing significantly during this period. Ninety-one species with different life forms were studied, using different types of molecular markers. These analyses confer a better understanding of the current knowledge of plant population genetics in the Cerrado biome.

The comparison of genetic divergence or genetic distances, estimated by pairwise F ST 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. Here, we review the Mantel test and its variations, including Mantel correlograms and partial correlations and regressions. For illustrative purposes, we studied spatial genetic divergence among 25 populations of Dipteryx alata ("Baru"), a tree species endemic to the Cerrado, the Brazilian savannas, based on 8 microsatellite loci. We also applied alternative methods to analyze spatial patterns in this dataset, especially a multivariate generalization of Spatial Eigenfunction Analysis based on redundancy analysis. The different approaches resulted in similar estimates of the magnitude of spatial structure in the genetic data. Furthermore, the results were expected based on previous knowledge of the ecological and evolutionary processes underlying genetic variation in this species. Our review shows that a careful application and interpretation of Mantel tests, especially Mantel correlograms, can overcome some potential statistical problems and provide a simple and useful tool for multivariate analysis of spatial patterns of genetic divergence.

O presente trabalho teve como objetivo utilizar marcadores RAPD para conhecer a variabilidade genética de populações de Tibouchina papyrus (Pohl) Toledo, provenientes da região de Serra Dourada e Serra dos Pirineus, no Estado de Goiás. Os seis iniciadores RAPD produziram um total de 147 locos, variando entre 23 e 26 por iniciador. A avaliação hierárquica da estruturação da variabilidade genética, realizada pela a AMOVA, considerando a existência de duas regiões (Serra dos Pirineus e Serra Dourada) apresentou uma estimativa de F ST = 0,3439. O valor do componente entre regiões (F CT) foi igual a 18,96% e a variação entre populações dentro de regiões igual a 15,43%. As estimativas de fluxo gênico sugerem a existência de uma baixa proporção de migrantes entre populações. As análises multivariadas (UPGMA e NMDS) indicam que existe uma relação entre distância genética e espaço geográfico, hipótese esta que foi confirmada por uma análise de padrão espacial utilizando o teste de Mantel (r = 0,71; P = 0,015 com 1000 permutações aleatórias). Os resultados indicam assim que esta estrutura tenha se originado seguindo um modelo de diferenciação estocástica (neutro), ou seja, por um balanço entre fluxo gênico a curtas distâncias e deriva genética nas populações. Os valores de diversidade genética obtidos apóiam a hipótese de que a espécie T. papyrus é uma espécie xenógama facultativa e o fato de não serem encontrados altos níveis de homozigose, indica que devem existir mecanismos relacionados à biologia reprodutiva da espécie, que previnem, de alguma maneira, a ocorrência de elevadas taxas de endogamia, que poderia ter um efeito deletério em médio e longo prazo.

This paper has the aim of using RAPD markers to describe the genetic of variability of Tibouchina papyrus (Pohl) Toledo local populations, from the regions of Serra Dourada and Serra de Pirineus, in Goiás State, Central Brazil. The six RAPD primers generated a total of 147 loci, varying from 23 to 26 per primer. The hierarchical evaluation of genetic variability, performed using an Analysis of Molecular Variance (AMOVA) considering the local populations within the two regions (i.e., Serra Dourada and Serra de Pirineus), showed an estimate of overall diversity among populations equal to F ST = 0.3439. The value of divergence between regions (F CT) was equal to 18.96% so that the variation among local populations within regions was equal to 15.43%. Estimates of gene flow suggest a small number of migrants among local populations per generation. Multivariate analyses (UPGMA and NMDS) indicated that a relationship between genetic and geographical distances exists, which was confirmed by a spatial pattern analysis using Mantel test (r = 0.71; P < 0.015 with 1000 random permutations). Thus, this structure was originated from a stochastic neutral model of population differentiation, in which drift within populations is counteracted by short distance gene flow. Despite strong levels of population structure (i.e., high divergence among populations within regions), the diversity observed support the hypothesis that T. papyrus is a facultative xenogamous species. The lack of high levels of homozigosity indicates that ecological mechanisms related to species' reproductive biology prevent, someway, a high level of endogamy within local structured populations, which could cause deleterious effects in a long run.

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. Here we review those models and compared their relative performances in a simple simulation, in which spatial patterns in allele frequencies were generated by a balance between random variation within populations and spatially-structured gene flow. Notwithstanding the somewhat idiosyncratic behavior of the techniques evaluated, it is clear that spatial autocorrelation affects Type I errors and that standard linear regression does not provide minimum variance estimators. Due to its flexibility, we stress that principal coordinate of neighbor matrices (PCNM) and related eigenvector mapping techniques seem to be the best approaches to spatial regression. In general, we hope that our review of commonly used spatial regression techniques in biology and ecology may aid population geneticists towards providing better explanations for population structures dealing with more complex regression problems throughout geographic space.

O objetivo deste trabalho foi avaliar o padrão espacial da variabilidade genética entre plantas, dentro de três populações naturais de barueiro (Dipteryx alata Vogel), pela genotipagem por RAPD e técnicas de autocorrelação espacial. Os cinco iniciadores RAPD permitiram a codificação de 45 locos, utilizados nas análises de diversidade, estrutura e distribuição espacial da variabilidade genética entre populações. As populações apresentaram diversidade genética (Hs) com valor médio 0,314. Verificou-se que 12% da variação total se encontra entre as populações, o que indica que estas mantêm um considerável nível de variabilidade genética. Foi observada tendência de autocorrelação espacial positiva nas primeiras classes de distâncias, nas três populações, o que indica a formação de grupos de vizinhança com estruturação familiar, dentro das populações de barueiro. Entretanto, o tamanho desses grupos de vizinhança varia entre as populações; isso mostra que outros processos ecológicos influenciaram a distribuição espacial da variabilidade genética. As populações naturais de barueiro apresentam consideráveis níveis de diversidade genética, com base nos 45 locos RAPD avaliados.

The aim of this paper was to evaluate the spatial pattern of the genetic variability among plants, within local populations of "barueiro" (Dipteryx alata Vogel), using RAPD markers and spatial autocorrelation analyses. The five RAPD primers used allowed the coding of 45 loci used for standard analyses of diversity, structure and spatial distribution of genetic variability within each local population. These populations showed considerable amount of genetic diversity, with an average Hs of 0.314. From the total genetic variation 12% occur among the three local populations studied, indicating that each of these contains a significant amount of variation. Within each population, this variability is structured with significant and positive spatial autocorrelation in the first three distance classes, suggesting the existence of neighbor groups of genetically similar individuals. The size of these neighbor groups, however, varies among local populations; this shows that other ecological components affected the spatial structure of genetic diversity. Natural populations of "barueiro" present considerable levels of genetic diversity, based on 45 RAPD loci analysed.