Search

Background: Also known as Simple Sequence Repetitions (SSRs), microsatellites are profoundly informative molecular markers and powerful tools in genetics and ecology studies on plants. Objective: This research presents a workflow for developing microsatellite markers using genome skimming. Methods: 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. Our pipeline efficiency was analyzed using Illumina sequencing data from the non-model tree species Pterodon emarginatus Vog. Results: The pipeline revealed 4,382 microsatellite regions and drew 7,411 pairs of primers for P. emarginatus. However, a much larger number of microsatellite regions with the potential to develop markers were discovered from our pipeline. We selected 50 microsatellite regions with high potential for developing markers and organized 29 microsatellite regions in sets for multiplex PCR. Conclusions: The proposed pipeline is a powerful tool for fast and efficient development of microsatellite markers on a large scale in several species, especially nonmodel plant species.

Dipteryx alata Vog. (Fabaceae) is a species of tree native to the Brazilian Cerrado that has economic potential due to its use for food, forage, medicinal, recovery of degraded areas, landscaping and wood extraction. The objective of the present study was to sequence, assemble and annotate the chloroplast genome sequence (cp genome) of D. alata and perform comparative analysis with the cp genome of other species of Fabaceae. The chloroplast is 158,647 bp in length and exhibits a quadripartite structure, with a pair of inverted repeats (IRs: 24,948 bp) separated by the large single copy (LSC: 88,769 bp) and small single copy (SSC: 19,982 bp) regions. It contains 125 genes, of which 109 are unique, including 76 protein-coding genes (CDS), 29 transporter RNA genes (tRNA) and four ribosomal RNA genes (rRNA). Comparative analysis of the cp genome of D. alata with the genome of other Fabaceae indicated similarity to the gene content, but gene losses and rearrangements have been identified. Comparative analysis indicated that the genes located in the IR regions were the most conserved, with average values of nucleotide diversity (Pi) of 0.03 followed by SSC (Pi-0.08) and LSC (Pi-0.09). Some non-coding regions exhibited relatively high divergence of sequences. The chloroplast genome contains also 131 simple sequence repeats (SSRs) of which 121 are located in intergenic regions and ten in protein-coding regions. The most frequent SSR repetition was A/T and AT/TA. The complete cp genome sequence of D. alata reported in this paper represents a valuable addition to the scarce available genomic resources for this Brazilian Cerrado species. This work shows the first complete plastoma of a species belonging to the ADA clade, within the Papilionoideae subfamily, and contributes to improve studies of phylogeny and plastoma evolution of the Fabaceae family. In addition, it provides new genetic information on plastid sequences useful for designing conservation and breeding strategies. Chloroplast sequences will be useful in phylogenetic studies, population genetics, phylogeography and molecular systematics.

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.

16 pages, 7 figures, 3 tables, supplementary data https://doi.org/10.1093/plankt/fbz019, The aquatic microbiota plays key roles in ecosystem processes; however, the mechanisms that influence their biogeographic patterns are not yet fully understood. Using high-throughput 18S rDNA gene sequencing, we investigated the composition of planktonic microeukaryotes (organisms sampled using a 68-μm plankton net) in 27 floodplain lakes of the Araguaia River, central Brazil and explored the influence of environmental and spatial factors for communities considering taxonomic and trophic groups. Of the 807 operational taxonomic units (OTUs) observed, Chlorophyta and Charophyta were the groups with greater abundance. Beta diversity was high, and the similarity of communities decreased as the geographic distance increased. We found a shared explanation between environmental and spatial predictors for total and autotrophic microbiota. Environmental variables influence only mixotrophic microbiota. These results suggest an OTU turnover along the floodplain and a spatially structured composition. This spatial pattern can be derived from the association with extrinsic factors, such as spatially structured environmental variables, that generate spatial dependence. However, the relationship between the composition of microbiota and environmental conditions is still unclear, Conselho Nacional de Desenvolvimento Científico e Tecnológico and research productivity grant (project nos. 473730/2013-8; 563834/2010-2; 563839/2010-4 to T.N.S., M.P.C.T., V.L.M.H. and J.C.N.); Fundação de Amparo a Pesquisa do Estado de Goiás (FAPEG; project no. 201212267001071); National Institutes for Science and Technology in Ecology, Evolution and Biodiversity Conservation, supported by MCTIC/CNPq (proc. 465610/2014–5) and FAPEG for the PhD scholarship to K.B.M. and Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (R.L., as a visiting researcher in the Science without Borders Program)

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.

[Aim]: The Island Rule—that is, the tendency for body size to decrease in large mammals and increase in small mammals on islands has been commonly evaluated through mac-roecological or macroevolutionary, pattern-orientated approaches, which generally fail to model the microevolutionary processes driving either dwarfing or gigantism. Here, we seek to identify which microevolutionary process could have driven extreme insular dwarfism in the extinct dwarf red deer population on the island of Jersey., [Location]: Jersey, UK (Channel Islands)., [Taxon]: Red deer (Cervus elaphus)., [Methods]: We applied an individual-based quantitative genetics model parameterized with red deer life-history data to study the evolution of dwarfism in Jersey's deer, con-sidering variations in island area and isolation through time due to sea level changes., [Results]: The body size of red deer on Jersey decreased fast early on, due to pheno-typic plasticity, then kept decreasing almost linearly over time down to the actual body size of the Jersey deer (36kg on average). Only 1% of 10,000 replicates failed to reach that size in our simulations. The distribution of time to adaptation in these simulations was right skewed, with a median of 395 generations (equivalent to roughly 4kyr), with complete dwarfism effectively occurring in less than 6kyr 84.6% of times. About 72% of the variation in the time to adaptation between simulations was col-lectively explained by higher mutational variance, the number of immigrants from the continent after isolation, available genetic variance, heritability, and phenotypic plasticity., [Main Conclusions]: The extreme dwarfing of red deer on Jersey is an expected out-come of high mutational variance, high immigration rate, a wide adaptive landscape, low levels of inbreeding, and high phenotypic plasticity (in the early phase of dwarfing), all occurring within a time window of around 6kyr. Our model reveals how extreme dwarfism is a plausible outcome of common, well-known evolutionary processes., This study is a contribution of the INCT in Ecology, Evolution and Biodiversity Conservation founded by MCTIC/CNPq/FAPEG (grant 465610/2014-5), arising from the workshop “Fast Evolution on Islands”, organized by AMCS and JAFD-F. Authors EB, FN, WS, KSS, RSS, and ZASV are supported by CAPES MsC or Doctoral fellowships. JAFD-F, RT, TFR, and RD are supported by CNPq Productivity Fellowships and grants, and LJ and EB received CNPq/DTI-A Fellowships from INCT. JH was supported by the project ‘Predicting diversity variations across scales through process-based models linking community ecology and biogeography’ (CNPq PVE 314523/2014-6), and AMCS by a Spanish MICIU Juan de la Cierva-Incorporación (IJCI-2014-19502) fellowship.

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. The allelic distributions of the rs3813867, rs2031920 and rs2031921 polymorphisms in the CYP2E1 showed that the wild alleles (G, C, T, respectively) had higher frequencies in both groups, alcoholic (96%, 96%, 96%) and a control group (95.8%, 94.9%, 94.9%), when compared to the mutated allele (C, T, C, respectively). The variation points, rs3813867, rs2031920 and rs2031921 showed strong linkage disequilibrium (LOD ≥ 2, D ' = 1). South Asian populations presented larger LD blocks compared to the other populations. Our results showed that the allelic frequencies were markedly different among ethnicities and have contributed to the knowledge regarding the distribution among ethnic groups, being associated to alcohol consumption worldwide.

Annona crassiflora (Annonaceae) is a protogynous beetle-pollinated savannah tree species, widely distributed in the savannahs of the Cerrado biome. Studies on the mating system and pollen dispersal of protogynous species are very scarce. Here, we used six microsatellite loci to assess the mating system and pollen dispersal of A. crassiflora in a savannah remnant in Central Brazil. We mapped and sampled leaves of 112 adult trees and collected 74 fruits from 20 mother trees (1–4 fruits per plant) to obtain the seeds used (460) for mating system and parentage analyses. Annona crassiflora has predominantly allogamous mating systems, with a high multilocus outcrossing rate (tm = 0.974, SE = 0.011) that did not differ among mother trees (F = 1.32, p = 0.165). However, tm–ts was variable among seed trees, indicating that some seeds were produced by mating among relatives. Our results also showed multiple paternity within fruits. Multilocus correlation of outcrossed paternity was high (rp = 0.302, SE = 0.045), indicating that for each mother tree, the probability that the same pollen donor sired two random sibs was 30.2%, and the mean number of pollen donors per mother tree was high (6.3). We detected a maximum pollen dispersal distance of 360.7 m and an average of 124.3 m (SD = 80 m), but most pollination events (73%) occurred at shorter distances (

We studied the genetic diversity and spatial genetic structure (SGS) of adult and juvenile individuals in a population of Hancornia speciosa in Central-West Brazil. For this, we sampled and mapped 113 adults and 100 juveniles in an area of 2.5 ha. Genomic DNA was obtained from leaves and seven microsatellite loci were used to genotype all individuals. The studied population showed high genetic diversity ( H e ) but with significant inbreeding ( f ) for both life stages most likely due to biparental inbreeding. Spatial genetic structure was weak for both life stages and the values of S P were low and neighborhoods ( Nb ) was high for both generations showing a potential long-distance gene dispersal.

During botanical expeditions between 2010 and 2015, as part of a taxonomic study of Manihot in the Midwest region of Brazil, approximately 500 specimens of the genus were collected. Some of these specimens presented similarities to Manihot irwinii. However, after careful morphological analyses, associated with genetic evidence, we propose here Manihot pulchrifolius as a new species. The new species is described, illustrated, and compared to Manihot irwinii, its most similar species. Furthermore, geographic distribution, conservation status, and period of flowering and fruiting of the novel species are also provided.

There are several approaches to understand how a landscape, with its several components, affects the genetic population structure by imposing resistance to gene flow. Here we propose the creation of resistance surfaces using a Pattern-Oriented Modeling approach to explain genetic differentiation, estimated by pairwise FST, among “Baruzeiro” populations (Dipteryx alata), a tree species widely distributed in Brazilian Cerrado. To establish the resistance surface, we used land use layers from the area in which the 25 “Baruzeiro” populations were sampled, generating 10000 resistance surfaces. To establish the resistance surface, we used land use layers from the area in which the 25 “Baru” populations were sampled, generating 10000 resistance surfaces. We randomized the cost values for each landscape component between 0 and 100. We use these surfaces to calculate pairwise matrices of the effective resistance among populations. Mantel test revealed a correlation of pairwise FST with a geographical distance equal to r = 0.48 (P < 0.001), whereas the Mantel correlations between pairwise FST and the generated resistance matrices ranged between r = −0.2019 and r= 0.6736. Partial regression on distance matrices was used to select the resistance matrix that provided the highest correlation with pairwise FST, based on the AIC criterion. The selected models suggest that the areas with lower resistance are characterized as natural savanna habitats of different forms, mainly arboreal dense savannas. In contrast, roads, big rivers, and agricultural lands cause higher resistance to gene flow.

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 GSTT1 and GSTM1 genes. In all municipalities, the frequency of the GSTT1 null genotype was 38.2% and of the GSTM1 null genotype was 50.3%. Goiania, the capital of Goias, presented the highest frequencies of GSTT1 and GSTM1 null genotypes, probably due to a founder effect of non-representative colonizing ancestors. So, the ancestral population adapted to the environment, with the frequencies observed in Goiania. However, nowadays, as there is excessive use of pesticides, the community becomes susceptible to the harmful effects of xenobiotics exposure, mainly due to the high frequency of GSTT1 and GSTM1 null genotypes. As in Goias, the consumption of pesticides has shown considerable growth, haplotypes with null alleles are of high risk for the population. Our results indicated that it is essential to understand the frequencies of the GSTT1 and GSTM1 genes for the monitoring of risk groups, like farmers, who have contact with pesticides, directly or indirectly, as well as assisting in the development of preventive medicine practices., Agricultural Science; Environmental Health; Environmental Pollution; Environmental Science; Environmental Toxicology; Genetics; Public Health; Toxicology; pesticides; susceptible; population; exposure; haplotypes; frequencies.

We experimentally evaluated how different temperatures affect germination of individual seedlings of Dipteryx alata, and estimated the impact of climate change on the species using ecological niche modeling. A total of 240 seeds were randomly distributed among three different temperature treatments (32 oC, 36 oC, and 40 oC), and monitored for 35 days. We measured seven seed traits and estimated the ecological niche of D. alata using a consensus of four methods. The treatment with the highest temperature produced smaller and lighter seedlings. The consensus of ecological niche modeling indicated that are expected to reduce the areas with climates favorable for D. alata in future scenarios. Thus, our two results (experiment and ecological niche modeling) are concordant, and both indicate the impact of global warming on germination (initial stage of the plant) and potential geographic distribution. Moreover, in geographic context, our experiment and ecological niche modeling indicated that north, northwest and central regions of the “Cerrado” are predicted to have lower morphological traits of germination and loss climate favorable area, since these regions are predicted to have higher temperatures (nearly 40 oC) in future climatic scenarios.

Dipteryx alata is a Neotropical tree widely distributed throughout the Brazilian Cerrado biome and is popularly known as baru. In this study, we evaluated the mating system of D. alata and compared pollen dispersal patterns between the in situ and ex situ conditions. For this, we used 515 genotypes of adults, juveniles, and progeny from a natural population (in situ) in Orizona-GO, Brazil. In addition, we used 488 genotypes of adults and progeny from a germplasm collection (ex situ) located at the Federal University of Goias. Both locations are situated in central Brazil. The genetic diversity, cross-pollination rates, and pollen dispersal distance under both conditions were estimated. Genetic diversity and polymorphism differed between the in situ and ex situ conditions. The average number of alleles found in situ (5.2) and ex situ (6.2) showed that the germplasm collection stores greater genetic diversity than the in situ condition. Cross-pollination detected among mother trees under both the in situ and ex situ conditions were high (tm = 0.815 and tm = 0.934, respectively), indicating that the species has a mixed reproductive system that was predominantly allogamous. The difference between tm and ts indicated that the in situ condition shows greater biparental inbreeding. Our results showed that, across generations, the ex situ condition preserved a larger number of alleles, confirming that the D. alata germplasm collection plays a role in conserving genetic diversity. The presence of self-fertilization suggests self-compatibility. Paternity correlation and the dispersal distance of the pollen donors were higher in the in situ condition, a maximum distance of 2.9 km of pollen flow. This can be explained by the number of pollinators and tree spatial distribution.

Nesta proposta apresentamos, em um contexto de Genética da conservação, um método simples para o estabelecimento de áreas prioritárias para conservação da variabilidade genética, possibilitando aos estudantes de graduação ou pós-graduação perceber a importância de utilizar métodos matemáticos e computacionais para delinear estratégias de conservação da biodiversidade. O exemplo utilizado para o exercício diz respeito à utilização de métodos para o estabelecimento de populações prioritárias para a conservação, de uma espécie hipotética de plantas no Cerrado, levando-se em consideração também o nível de antropização em diferentes regiões do bioma. Para estudantes mais avançados ou em cursos nos quais seja possível uma integração entre Genética e Bioestatística, foi proposto um script na plataforma computacional “R” para realizar os procedimentos apresentados.

The aquatic microbiota is involved in crucial ecosystem functions. Thus, investigating the effects of global warming on these organisms is highly relevant, especially given the numerous climatic changes expected by the end of the century. In this study, we used an experimental approach and high-throughput sequencing to evaluate the shortterm effect of warming predicted by different future scenarios in the composition of the planktonic freshwater bacteria and microeukaryotes, and to verify if the same effects occur for each trophic level separately (autotrophic, heterotrophic and mixotrophic). Our experiment demonstrated that the composition for eukaryotes and prokaryotes based on DNA metabarcoding is affected by the increase in temperature and these have a similar pattern of response to warming. This highlights the temperature importance in structuring the communities of different groups. Modifications in the communities were observed through the substitution of specific taxa, which occurred mainly in warmer levels. Changes in community composition were also identified when trophic levels were assessed separately. Mixotrophic eukaryotes organisms are more sensitive to warming, modifying the patterns of composition with an increase in temperature of 2 °C. Microeukaryotes and heterotrophic bacteria were more resistant, with alterations in the communities composition visualized only in higher warming levels. The composition of autotrophic organisms was not affected by the increase in water temperature in any of the biological classifications evaluated, although the richness of eukaryotic autotrophic has decreased with warming. Our results contribute to predict how different biological levels and trophic groups of the aquatic microbiota respond to global warming. This approach is relevant because warming leads to changes in community composition and affects ecosystem processes essentials to the aquatic environment.

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. We obtained genomic DNA from peripheral blood lymphocytes. The 748-bp OGG1 gene was amplified by PCR and sequenced. Of the 330 individuals, 215 (65%) were males and 115 (35%) were females. There were no differences in the distribution of the rs1052133 and rs293795 with age and sexes. Haplotypes containing only conserved T/C alleles were the most common in our population. The frequency of the mutant alleles of rs1052133 and rs293795, in our population, was 20% and 30%, respectively, and it is noteworthy, worldwide, that mutant alleles are commonly associated to an increased risk for the development of cancer, specially due to direct or indirect contact to pesticides, as occurs in rural workers of Central Brazil population.

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. In this study, we analyse the relationship between heterozygosity (He) and environmental suitability from multiple ENMs for 25 population estimates for Dipteryx alata, a widely distributed, endemic tree species of the Cerrado region of central Brazil. We propose a new approach for generating a statistical distribution of correlations under randomly generated ENM. The confidence intervals from these distributions indicate how model selection with different properties affects the ability to detect a correlation of interest (e.g. the correlation between He and suitability). Additionally, our approach allows us to explore which particular ensemble of ENMs produces the better result for finding an association between environmental suitability and He. Caution is necessary when choosing a method or a climatic data set for modelling geographical distributions, but the new approach proposed here provides a conservative way to evaluate the ability of ensembles to detect patterns of interest.

Biodiversity crises have led scientists to develop strategies for achieving conservation goals. The underlying principle of these strategies lies in systematic conservation planning (SCP), in which there are at least 2 conflicting objectives, making it a good candidate for multi-objective optimization. Although SCP is typically applied at the species level (or hierarchically higher), it can be used at lower hierarchical levels, such as using alleles as basic units for analysis, for conservation genetics. Here, we propose a method of SCP using a multi-objective approach. We used non-dominated sorting genetic algorithm II in order to identify the smallest set of local populations of Dipteryx alata (baru) (a Brazilian Cerrado species) for conservation, representing the known genetic diversity and using allele frequency information associated with heterozygosity and Hardy-Weinberg equilibrium. We worked in 3 variations for the problem. First, we reproduced a previous experiment, but using a multi-objective approach. We found that the smallest set of populations needed to represent all alleles under study was 7, corroborating the results of the previous study, but with more distinct solutions. In the 2nd and 3rd variations, we performed simultaneous optimization of 4 and 5 objectives, respectively. We found similar but refined results for 7 populations, and a larger portfolio considering intra-specific diversity and persistence with populations ranging from 8-22. This is the first study to apply multi-objective algorithms to an SCP problem using alleles at the population level as basic units for analysis.

The use of next-generation sequencing (NGS) technologies provides a great volume of genome sequence data even for non-model species. The development of microsatellite markers using these data is a relatively quick and easy process. Dipteryx alata Vogel (Fabaceae) is an arboreal species from the Cerrado biome and is considered an important plant genetic resource. Here, we report the development of microsatellite markers for D. alata using NGS data. DNA samples from four individuals were sequenced using the Illumina MiSeq platform and high-quality reads were assembled into contigs of the D. alata genome sequence. Microsatellite regions were identified using the IMEX webserver and primer pairs were designed using the Primer3 software. The amplification settings for each locus were optimized. Fluorescent-labeled primers were developed and used to genotype individuals derived from three natural populations of D. alata. Fifty-four microsatellite regions were identified, from which 27 were elected to primer design. Among the amplified loci, 11 were polymorphic, with the number of alleles ranging from 2 to 10. The expected heterozygosity under Hardy-Weinberg Equilibrium (HWE) per locus varied from 0.191 to 0.807. Genotype and allele frequencies for all loci agreed with those expected under HWE and linkage disequilibrium was not significant for all pairs of loci. The probabilities of exclusion of paternity and of combined identity were equal to 0.993 and 5.65 x 10-8, respectively. The markers developed in this study are useful to several types of population genetic studies with D. alata and, eventually, for closely related species.

This study tested whether genetic parameters in Dipteryx alata populations, estimated from genomic and chloroplastidial microsatellite markers, were distributed according to a central-peripheral model, inferring which factors drive this spatial distribution of genetic variability within populations. For each of the 23 populations sampled throughout the species’ range, the mean number of alleles per locus, expected heterozygosity and intrapopulation fixation indices were calculated using a rarefaction approach based on 54 alleles from 8 nuclear microsatellites. Explanatory variables were grouped into three subsets: the ecological suitability estimated by combining different techniques of ecological niche modeling, variables expressing human occupation, and a historical variable represented by the first eigenvector from the pairwise F ST matrix based on cpDNA microsatellites. Each response variable was modeled using first (linear) and second (quadratic) order trend surface analysis (TSA). Multiple regressions were then used to evaluate the relative effects of the explanatory variables, based on AIC multi-model selection. In general, the genetic parameters did not follow a classical central-periphery model. Ecological suitability had a significance influence in all genetic parameters, so more suitable regions have higher genetic diversity and low endogamy. There was also a relationship between fixation indices and human impacts. The high genetic diversity in the southwestern region of Cerrado suggested that recent range expansion (after the Last Glacial Maximum) may also influenced the observed intrapopulation genetic patterns. Thus, complex combinations of both historical and ecological drivers, as well as contemporary human occupation, seem to drive current genetic composition within D. alata populations throughout its geographic range.

Spatial genetic structure (SGS) is the non-random distribution of genotypes in space, which is usually correlated with life history traits and is driven by ecological and demographic processes. This study aimed to use spatial statistical analysis methods to assess genetic diversity and spatial genetic structure in three known disjunct localities where Tibouchina papyrus occurs, varying in aggregation and density of individuals and in landscape characteristics. This small tree species is endemic to the “Cerrado” (savannas) region of Central Brazil and is also restricted to elevation rock fields (“campo rupestre”). Therefore, it can be considered a model species to help guide studies on Cerrado endemic plants that are isolated with geographic distributions restricted to this highland habitat. The analyses were based on the polymorphisms at ten microsatellite loci. Our working hypothesis was that wind-dispersed species, such as T. papyrus, present no or low SGS because of the long distance seed gene flow. The spatial genetic structure was indeed weak for two of the three populations. The intensity and shape of the SGS are related to density and aggregation (defined by Ripley’s K statistic of spatial aggregation) of individuals in the three localities. Low SGS occurs in populations with aggregation patterns, corroborating the overall hypothesis, although in this species, this pattern depends on the landscape characteristics of each local population.

Although several statistical approaches can be used to describe patterns of genetic variation and infer stochastic differentiation, selective responses, or interruptions of gene flow due to physical or environmental barriers, it is worthwhile to note that similar processes, controlled by several parameters in theoretical models, frequently give rise to similar patterns. Here, we develop a Pattern-Oriented Modelling (POM) approach that allows us to determine how a complex set of parameters potentially driving empirical genetic differentiation among populations generate alternative scenarios that can be fitted to observed data. We generated 10 000 random combinations of parameters related to population size, gene flow and response to gradients (both driven by dispersal and selection) in a spatially explicit model, and analysed simulated patterns with FST statistics and mean correlograms using Moran's I spatial autocorrelation coefficients. These statistics were compared with observed patterns for a tree species endemic to the Brazilian Cerrado. For a best match with observed FST (equal to 0.182), the important parameters driving simulated scenario are mainly related to population structure, including low population size with closed populations (low Nm), strong distance decay of gene flow, in addition to a strong effect of the initial variance of allele frequencies. These scenarios present a low autocorrelation of allele frequencies. Best matching of correlograms, on the other hand, appears in simulations with a large population size, high Nm and low population differentiation and FST (as well as more gene flow). Thus, targeting the two statistics (correlograms and FST) shows that best matches with empirical data with two distinct sets of parameters in the simulations, because observed patterns involve both a relatively high FST and significant autocorrelation. This conflict can be resolved by assuming that initial variance in allele frequencies can be interpreted as reflecting deep-time historical variation and evolutionary dynamics of allele frequencies, creating a relatively high level of population differentiation, whereas current patterns in gene flow creates spatial autocorrelation. This make sense in terms of the previous knowledge on population differentiation in D. alata, especially if patterns are explained by a combination of isolation-by-distance and allelic surfing due to range expansion after the last glacial maximum. This reveals the potential for more complex applications of POM in population genetics. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 113, 1152–1161.

A cagaiteira é uma espécie frutífera comum no bioma Cerrado. A planta produz um fruto do tipo baga que é consumido in natura ou processado de várias formas. Em função do potencial produtivo da espécie, existe interesse na sua domesticação, para produção em larga escala. Para atender esse objetivo, a avaliação da variabilidade genética é fundamental para subsidiar programas de melhoramento e domesticação da espécie. Nesse sentido, o objetivo do trabalho foi estimar parâmetros genéticos quantitativos da coleção de germoplasma de Eugenia dysenterica DC., para disponibilizar informações que possam ser úteis em programas de melhoramento da espécie. O experimento foi montado no ano de 1998 em delineamento experimental de blocos completos ao acaso com 110 tratamentos e quatro repetições. Foram avaliadas as variáveis das plantas que incluem a altura (AP), altura da primeira bifurcação (AB), circunferência do caule a 10 cm do solo (CC), projeção média da copa (DC) e variáveis das folhas, que incluem o comprimento do limbo (CL), largura do limbo (LL), formato das folhas (FF) e comprimento do pecíolo (CP). Os coeficientes de herdabilidade ao nível das médias variaram entre 87,66% e 25,16% e os coeficientes de variação genética, entre 45% e 7%, valores próximos aos obtidos para outras espécies silvestres do Cerrado. As estimativas dos parâmetros sugerem respostas modestas à seleção para as variáveis das plantas e respostas expressivas para as variáveis das folhas. The cagaiteira is a common fruit species in the Cerrado. The plant produces a berry fruit eaten in natura or processed of several ways. Concerning the yield potential of the specie, there is interest in their domestication to large-scale production. To this aim, the evaluation of genetic variability is essential to support breeding and domestication programs for the species. Therefore, the aim of this study was to estimate genetic parameters of quantitative traits of germplasm collection of Eugenia dysenterica DC., to provide information that may be useful in breeding programs. The experiment was set up in 1998 in randomized block design, with 110 treatments and four replications. Variables of plants, which include height (AP), height of the first bifurcation (AB), the stem circumference (CC), average of crown projection (DC) and variable of leaves, which include leaf length (CL), leaf width (LL), leaf format (FF) and footstalk length (CP). The heritability coefficients ranged from 87.66 % to 25.16% and the coefficient of genetic variation ranged from 45% and 7%, similar values for other wild species of the Cerrado. Parameter estimates suggest modest responses of selection to variables of plants and expressive responses to the variables of leaves.

Geographical patterns of genetic variation and population structure and their relationship with habitat loss and fragmentation have been investigated at distinct scales and extents using spatially explicit statistics. Here, we analyzed population genetic structure of Dipteryx alata (Fabaceae; the “baru” tree), an economically important tree widely distributed in Central Brazil that is endemic to the “Cerrado” (savanna) biome, relating population genetic divergence with broad-scale landscape patterns. Genetic divergence among 25 populations, estimated based on eight microsatellite loci for a total of 644 individuals, was correlated with landscape features using several forms of Mantel tests (standard Mantel correlations, Mantel correlograms, partial correlations, and multiple regression). Patterns of genetic divergence are significantly correlated with human-driven landscape features of habitat loss and fragmentation, after taking into account isolation-by-distance and historical effects of range expansion after the last glacial maximum. Our findings present important implications for the conservation of this species, because interruption of gene flow by habitat loss and fragmentation jeopardize the persistence of population in the medium- and long term due to disruption of demographic patterns, increased endogamy, and recruitment problems. © 2014 Associacao Brasileira de Ciencia Ecologica e Conservacao. Published by Elsevier Editora Ltda

In continuous populations, fine-scale genetic structure tends to be stronger in species with restricted pollen and seed dispersal. However, habitat fragmentation and disturbances can affect genetic diversity and spatial genetic structure due to disruption in ecological processes, such as plant reproduction and seed dispersal. In this study, we compared the genetic diversity and fine-scale spatial genetic structure (SGS) in two populations of Annona crassiflora (Annonaceae) in a pristine savanna Reserve (ESECAE) and in a fragmented disturbed savanna area (PABE), both in Cerrado biome in Central Brazil. The analyses were based on the polymorphism at 10 microsatellite loci. Our working hypothesis was that SGS is stronger and genetic diversity is lower in population at fragmented area (PABE) than at pristine area (ESECAE). Both populations presented high levels of polymorphism and genetic diversity and showed no sign of bottleneck for both Wilcoxon sign-rank test for heterozygosity excess (p > 0.05) and coalescent analyses (growth parameter g not different from zero), but population at fragmented area showed higher fixation index and stronger SGS. Besides, populations are significantly differentiated (FST = 0.239, RST = 0.483, p < 0.001 for both). Coalescent analyses showed high historical effective population sizes for both populations, high gene flow between ESECAE and PABE and recent time to most recent common ancestor (~37 k year BP). Our results suggest that despite the high genetic diversity, fragmentation and disturbance may have been affecting populations of this species increasing mating between closely related individuals leading to high fixation index and strong SGS.

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). The relationship between the coefficient of determination (R 2) of the models and the cumulative eigenvalues, which we named the spatial signal-representation (SSR) curve, can be more efficient than Moran’s I correlograms in describing different patterns. The SSR curve was also applied to simulated data (under distinct scenarios of population differentiation) and to analyze spatial patterns in alleles from microsatellite data for 25 local populations of Dipteryx alata, a tree species endemic to the Brazilian Cerrado. The SSR curves are consistent with previous phylogeographical patterns of the species, revealing combined effects of isolation-by-distance and range expansion. Our analyses demonstrate that the SSR curve is a useful exploratory tool for describing spatial patterns of genetic variability and for selecting spatial eigenvectors for models aiming to explain spatial responses to environmental variables and landscape features.

Nesta atividade é apresentada uma abordagem para determinar a distância de dispersão de pólen em uma população de plantas, utilizando os princípios básicos da Genética. A determinação da distância de dispersão de pólen é realizada a partir da análise de paternidade de sementes com base no polimorfismo de marcadores moleculares do tipo microssatélites. A aplicação desta atividade proporciona a discussão e consolidação de alguns conceitos em genética, tais como os princípios de segregação e variabilidade genética em populações.