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.

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.

Eigenfunction analyses have been widely used to model patterns of autocorrelation in time, space and phylogeny. In a phylogenetic context, Diniz-Filho et al. (1998) proposed what they called Phylogenetic Eigenvector Regression (PVR), in which pairwise phylogenetic distances among species are submitted to a Principal Coordinate Analysis, and eigenvectors are then used as explanatory variables in regression, correlation or ANOVAs. More recently, a new approach called Phylogenetic Eigenvector Mapping (PEM) was proposed, with the main advantage of explicitly incorporating a model-based warping in phylogenetic distance in which an Ornstein-Uhlenbeck (O-U) process is fitted to data before eigenvector extraction. Here we compared PVR and PEM in respect to estimated phylogenetic signal, correlated evolution under alternative evolutionary models and phylogenetic imputation, using simulated data. Despite similarity between the two approaches, PEM has a slightly higher prediction ability and is more general than the original PVR. Even so, in a conceptual sense, PEM may provide a technique in the best of both worlds, combining the flexibility of data-driven and empirical eigenfunction analyses and the sounding insights provided by evolutionary models well known in comparative analyses.

Neste trabalho, diferentes modelos climáticos, métodos de modelagem e cenários de emissão de carbono foram utilizados para avaliar os efeitos das mudanças climáticas sobre a distribuição geográfica de espécies de importância econômica e cultural das regiões abrangidas pelo bioma Cerrado. Assim como os resultados de vários trabalhos têm evidenciado ao longo dos anos, ainda há muitas incertezas relacionadas a essas projeções, apesar de os modelos bioclimáticos ainda serem a metodologia mais utilizada e eficaz para avaliar as consequências dessas mudanças climáticas para a biodiversidade. Neste artigo, foi possível observar que 90% dessas incertezas estão relacionadas aos métodos de modelagem. Contudo, independente disso, os resultados revelaram que as espécies estudadas reduzirão, em média, 78% de sua distribuição geográfica no Cerrado. Para que haja trabalho eficaz sobre a conservação dessas espécies, muitos estudos ainda precisam ser executados, apesar de já ser possível prever que as mudanças climáticas terão forte influência no padrão de distribuição dessas espécies.

Different climate models, modeling methods and carbon emission scenarios were used in this paper to evaluate the effects of future climate changes on geographical distribution of species of economic and cultural importance across the Cerrado biome. As the results of several studies have shown, there are still many uncertainties associated with these projections, although bioclimatic models are still widely used and effective method to evaluate the consequences for biodiversity of these climate changes. In this article, it was found that 90% of these uncertainties are related to methods of modeling, although, regardless of the uncertainties, the results revealed that the studied species will reduce about 78% of their geographic distribution in Cerrado. For an effective work on the conservation of these species, many studies still need to be carried out, although it is already possible to observe that climate change will have a strong influence on the pattern of distribution of these species.

A distribuição geográfica das espécies tem sido considerada como a unidade básica em macroecologia e biogeografia, mas ainda há dificuldades em mensurá-la de forma adequada, por diferentes razões. Há cerca de 20 anos atrás, os pesquisadores começaram a utilizar dados locais da ocorrência das espécies para estimar essas distribuições utilizando modelos de nicho ecológico. Entretanto, ainda há uma série de problemas na avaliação dos modelos e em suas aplicações, e uma das soluções é utilizar um consenso de diferentes modelos, projeções climáticas, cenários de emissão e combinação de variáveis, que são fontes de incerteza durante o processo de modelagem de nicho. Neste artigo nós discutimos essa abordagem de consenso e a dividimos em três fases, com níveis crescentes de complexidade. A Fase I é simplesmente a combinação de mapas e a obtenção e interpretação de um único mapa de consenso. A Fase II envolve a descrição das diferenças entre os mapas utilizando técnicas de análise multidimensional, enquanto que a Fase III consiste em analisar quantitativamente e mapear a magnitude relativa das diferentes fontes de incerteza. A fim de ilustrar essa abordagem, nós analisamos dados de ocorrência de Utetheisa ornatrix (Lepidoptera, Arctiidae), uma mariposa distribuída na região Neotropical, modelando sua distribuição geográfica com base em dados climáticos atuais e projeções de mudança climática.

Species' geographic ranges are usually considered as basic units in macroecology and biogeography, yet it is still difficult to measure them accurately for many reasons. About 20 years ago, researchers started using local data on species' occurrences to estimate broad scale ranges, thereby establishing the niche modeling approach. However, there are still many problems in model evaluation and application, and one of the solutions is to find a consensus solution among models derived from different mathematical and statistical models for niche modeling, climatic projections and variable combination, all of which are sources of uncertainty during niche modeling. In this paper, we discuss this approach of ensemble forecasting and propose that it can be divided into three phases with increasing levels of complexity. Phase I is the simple combination of maps to achieve a consensual and hopefully conservative solution. In Phase II, differences among the maps used are described by multivariate analyses, and Phase III consists of the quantitative evaluation of the relative magnitude of uncertainties from different sources and their mapping. To illustrate these developments, we analyzed the occurrence data of the tiger moth, Utetheisa ornatrix (Lepidoptera, Arctiidae), a Neotropical moth species, and modeled its geographic range in current and future climates.

O bioma Cerrado é o segundo maior da região Neotropical e é formado por mosaico de diferentes tipos de hábitats, desde campos abertos até florestas densas. Um recente e intensivo processo de ocupação humana tem transformado essa eco-região em uma das mais importantes regiões para agropecuária no Brasil. Uma abordagem macroecológica foi utilizada para elucidar padrões em amplas escalas espaciais de perdas de hábitat no Cerrado brasileiro, implementando técnicas de autocorrelação espacial e análises de regressão parcial para entender como a proporção de remanescentes de vegetação natural está correlacionada com variáveis socioeconômicas, expressando diferentes dimensões de ocupação humana e com variações climáticas. Em média, 59% da área é ocupada por remanescentes de vegetação, na escala da análise, mesmo que os padrões de perda de hábitat estejam fortemente estruturados no espaço, com o coeficiente de autocorrelação espacial de I de Moran igual a 0,825 ± 0,055 (p < 0 ,001). As análises de regressão parcial explicaram 89% da variação no percentual de remanescente de vegetação. A maior proporção da variância é explicada pela sobreposição múltipla entre a ocupação humana, variação climática e a estrutura geográfica (67%), bem como pelo componente estruturado climaticamente da ocupação humana (8%). Baseado no processo interativo no tempo e no espaço da ocupação humana no bioma, cenários futuros devem ser mais pessimistas. Se o movimento de ocupação continuar em direção a região Norte do bioma, como esperado, nós podemos predizer que as proporções de remanescente de vegetação natural irão declinar rapidamente, indicando assim uma forte perda da biodiversidade nas escalas do bioma.

The Cerrado biome, the second largest biome in Neotropical region, consists of a mosaic of different habitat types, ranging from open grasslands to dense woodlands and dry forests. An intensive recent occupation process has transformed it into the most important region for cattle ranching and intensive commodity crops in Brazil. In this study, a macroecological approach was used to evaluate broad-scale spatial patterns of habitat loss in the Brazilian Cerrado, applying a series of spatial autocorrelation and partial regression analyses to understand how the proportion of remaining natural habitats is correlated with socio-economic variables, expressing different dimensions of human occupation and climatic variation. On average, 59% of the area is occupied by natural remnants at the spatial scale analyzed, although patterns of habitat loss are strongly spatially structured, with a Moran's I spatial autocorrelation coefficient equal to 0.825 ± 0.055 (p < 0.001). The partial regression analysis explains 89% of variation in percentage of natural remnants. The highest proportion of variance is explained by the multiple overlap between human occupation, climatic variation and geographic structure (67%), as well as by the climatically structured component of human occupation (8%). Based on the space-time interactive process of human occupation in the biome, future scenarios should be rather pessimistic. If the wave of human occupation continues towards the northern parts of the biome, as expected, we can predict that percentages will decline rapidly including even stronger losses of habitat at the biome scale.

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.

The use of phylogenetic comparative methods in ecological research has advanced during the last twenty years, mainly due to accurate phylogenetic reconstructions based on molecular data and computational and statistical advances. We used phylogenetic correlograms and phylogenetic eigenvector regression (PVR) to model body size evolution in 35 worldwide Felidae (Mammalia, Carnivora) species using two alternative phylogenies and published body size data. The purpose was not to contrast the phylogenetic hypotheses but to evaluate how analyses of body size evolution patterns can be affected by the phylogeny used for comparative analyses (CA). Both phylogenies produced a strong phylogenetic pattern, with closely related species having similar body sizes and the similarity decreasing with increasing distances in time. The PVR explained 65% to 67% of body size variation and all Moran's I values for the PVR residuals were non-significant, indicating that both these models explained phylogenetic structures in trait variation. Even though our results did not suggest that any phylogeny can be used for CA with the same power, or that “good” phylogenies are unnecessary for the correct interpretation of the evolutionary dynamics of ecological, biogeographical, physiological or behavioral patterns, it does suggest that developments in CA can, and indeed should, proceed without waiting for perfect and fully resolved phylogenies.

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.

Embora os índices de vegetação MODIS estejam sendo extensivamente investigados quanto ao seu potencial para o mapeamento e monitoramento biofísico do bioma Cerrado, em particular no que diz respeito à sazonalidade e fenologia da cobertura vegetal, pouco se sabe sobre o comportamento espacial desses índices em escalas regionais. Assim, neste estudo foram avaliados, à escala adotada em estudos de macroecologia (Resolução de 1º x 1º), os padrões de autocorrelação espacial do EVI (índice de vegetação realçado) e NDVI (índice de vegetação da diferença normalizada), utilizando-se índices I de Moran obtidos em diferentes classes de distância geográfica (correlogramas espaciais). Em média, os valores apresentados por esses índices são autocorrelacionados até uma distância aproximada de 800 km, que pode revelar um padrão de manchas afetado por variação ambiental e conversão da vegetação nativa. No entanto, esses padrões de similaridade espacial são principalmente influenciados pelo contraste sazonal encontrado no bioma Cerrado, bem como em função dos padrões de cobertura da terra e do tipo de índice considerado (i.e., EVI ou NDVI).

While the MODIS vegetation indices have been extensively investigated regarding their potential for mapping and biophysical monitoring of the Cerrado biome, particularly with respect to the seasonality and phenology of the vegetative cover, very little is known about the spatial behavior of these indices. Thus, this study assessed, at the "macroecology" scale (1º x 1º spatial resolution), the autocorrelation patterns of both the EVI (enhanced vegetation index) and NDVI (normalized difference vegetation index), using Moran's I coefficients obtained for several geographic distance classes (spatial correlogram). On average, the values presented by these two indices are correlated up to a distance of about 800 km, possibly revealing a patch pattern affected by environmental variables and native vegetation conversion. On the other hand, these spatial similarity patterns are mainly influenced by the marked seasonal contrast of the cerrado biome, as well as by the land cover classes and the vegetation index considered (i.e. EVI or NDVI).

Despite methodological and theoretical advances in conservation genetics, data on genetic variation on broad regional spatial scales are still scarce, leading conservation planners to use general heuristic or simulation models for an integrated analysis of genetic, demographic and landscape parameters. Here, we extended previous results by evaluating spatial patterns of extinction by inbreeding depression under stochastic variation of environments for mammalian populations in 31 conservation units of the Brazilian Cerrado. We observed a large spatial variation of times to extinction, for different conservation units and body-size classes of species. For small-bodied species (500 g), the population times to extinction in the conservation units were usually longer than 200 years, whereas for medium-bodied (5 kg) and large-bodied (50 kg) species this time was considerably shorter, and only a few units would maintain viable populations for more than 100 years. These figures are consistent with the current status of mammalian conservation in Brazil, and hopefully the simulated scenarios can be integrated to patterns of human occupation and habitat loss in the biome, in order to furnish overall guidelines for biodiversity conservation.

A frequently addressed question in conservation biology is what is the chance of survival for a population for a given number of years under certain conditions of habitat loss and human activities. This can be estimated through an integrated analysis of genetic, demographic and landscape processes, which allows the prediction of more realistic and precise models of population persistence. In this study, we modeled extinction in stochastic environments under inbreeding depression for two canid species, the maned wolf (Chrysocyon brachiurus) and the crab-eating fox (Cerdocyon thous), in southwest Goiás State. Genetic parameters were obtained from six microsattelite loci (Short Tandem Repeats - STR), which allowed estimates of inbreeding levels and of the effective population size under a stepwise mutation model based on heterozygosis. The simulations included twelve alternative scenarios with varying rates of habitat loss, magnitude of population fluctuation and initial inbreeding levels. ANOVA analyses of the simulation results showed that times to extinction were better explained by demographic parameters. Times to extinction ranged from 352 to 844, in the worst and best scenario, respectively, for the large-bodied maned wolf. For the small-bodied crab-eating fox, these same estimates were 422 and 974 years. Simulations results are within the expectation based on knowledge about species' life history, genetics and demography. They suggest that populations can persist through a reasonable time (i.e., more than 200 years) even under the worst demographic scenario. Our analyses are a starting point for a more focused evaluation of persistence in these populations. Our results can be used in future research aiming at obtaining better estimates of parameters that may, in turn, be used to achieve more appropriate and realist population viability models at a regional scale.

This study reports on 156 specimens of the amphibian Eupemphix nattereri, a widely distributed leiuperid, obtained from 11 municipalities of central Brazil. The extent of genetic variation was quantified by determining the mean number of alleles per locus and the proportion of polymorphic loci. An analysis of molecular variance (AMOVA) was performed on the random amplified polymorphic DNA (RAPD) haplotypes. The genetic distances obtained by calculating pairwise phist among local samples were used to determine population relationships using the unweighted pair-group method (UPGMA) and non-metric multidimensional scaling (NMDS). The cophenetic correlation was calculated to confirm agreement between the genetic matrix and the unweighted pair group method with averages (UPGMA) dendrogram. To determine if genetic distances were correlated to geographical distances we constructed pairwise genetic distance and geographical distance matrices and compared them using the Mantel test. The AMOVA results indicated significant genetic differences (p < 0.001) between E. nattereri populations, representing 69.5% of the within population genetic diversity. The Mantel test showed no significant correlation (r = 0.03; p = 0.45) between the genetic and geographical distance matrices. Our findings indicate that the genetic variation of E. nattereri populations was randomly distributed in geographic space and that gene flow for this species is probably structured at spatial scales smaller than those between our samples

As anemias hereditárias, em especial as talassemias e hemoglobinas (Hb) variantes, são as mais comuns das alterações genéticas humanas; sua freqüência na população brasileira é muito variável, dependendo dos grupos raciais formadores de cada região. O povoamento de Goiás, que teve início logo após o seu descobrimento, em 1726, motivado pela procura de ouro, foi composto principalmente por portugueses e escravos africanos, contexto que favoreceu a mestiçagem entre eles. Considerando que esses povos apresentam genes para as hemoglobinas anormais com freqüências variadas, é esperado que se encontrem essas alterações genéticas na nossa população. O objetivo deste trabalho foi avaliar a prevalência de talassemias e hemoglobinas variantes na população de Goiás. Para isso a casuística foi composta por 404 alunos participantes dos diversos cursos da Universidade Católica de Goiás (UCG), oriundos de 55 cidades do estado de Goiás. A prevalência de anemia hereditária por talassemias e hemoglobinas variantes em Goiás foi de 10,1%, cuja ordem decrescente foi a seguinte: talassemia alfa heterozigótica (5,2%), heterozigose para hemoglobina S (Hb AS) (2,2%), heterozigose para hemoglobina C (Hb AC) (1%), talassemia beta menor (0,7%), associação entre talassemia alfa e heterozigose para Hb S (0,5%), associação entre talassemia alfa e heterozigose para Hb C (0,3%) e heterozigose para hemoglobina D (Hb AD) (0,3%). Nenhum caso de homozigose foi encontrado no presente estudo. Este trabalho demonstrou a dispersão dos genes para Hb S, Hb C e Hb D, bem como de talassemias alfa e beta em uma população do estado de Goiás. Por essa razão, concluímos que é importante realizar programas com maior abrangência da população para estudo da epidemiologia das talassemias e hemoglobinas variantes no estado de Goiás.

The hereditary anemias, especially the thalassemies and hemoglobinopathies are the most common human genetic abnormalities. Their frequency in the Brazilian population is very variable depending on the racial groups typical of each region. The settlement of Goiás, that had its beginning after discovery in 1726 owing to the search for gold, was composed basically by Portuguese and African slaves, a context that favored the racial mixing among them. Considering that these groups present genes for abnormal hemoglobins with varied frequencies it is expected the finding of these genetic abnormalities within our population. The objective of this study was to evaluate the prevalence of thalassemies and variant hemoglobins in the population of Goiás. For this purpose the sample was composed by 404 participating students from several graduate courses of the Catholic University of Goiás originally from 55 cities of the state of Goiás. Laboratory tests were used taking into account the historical and demographic factors of the population. The prevalence of hereditary anemias by thalassemias and variant hemoglobins in Goiás was 10.1%, in which the decreasing order of these abnormalities was: alfa heterozygous thalassemy (5.2%); heterozygous hemoglobin S (Hb AS) (2.2%); heterozygous hemoglobin C (Hb AC) (1%); beta short thalassemy (0.7%); association between alpha thalassemy and heterozygous for hemoglobin S (0.5%); association between alpha thalassemy and heterozygous for hemoglobin C (0.3%); and heterozygous for hemoglobin D (0.3%). No homozygosity was found in the study group. This study demonstrates the need for large scale screening in human populations for epidemiological studies of the thalassemies and variant hemoglobins in the state of Goiás.