Mitochondrial DNA control region diversity in a population from Espirito Santo state,Brazil

Mitochondrial DNA (mtDNA) analysis has proved to be useful for forensic identification, especially in cases which nuclear DNA markers fail, as in degraded samples or in cases where the biological material has few traces or no nuclear DNA. Moreover, it can be applied in population genetics, inferring the origin of a population. In this work, the entire mtDNA control region of 97 individuals from the state of Espirito Santo, Brazil, was analyzed. We have found 94 different haplotypes yielding a high haplotype diversity of 0.9994 ± 0.0016. The probability of a random match calculated was 1.09. Haplogroup distribution analysis confirmed a highly admixed Latin American population: African lineages (43.3 %), European lineages (32.0 %), Native American lineages (23.7 %) and Asian lineages (1.0 %). We have concluded that this type of tool can be used both in forensic genetics to the study of different human populations, such as highly admixed populations, and in the study of migration’s history and colonization of different states and countries of the world.     

Espirito Santo virus: a new birnavirus that replicates in insect cells

Espirito Santo virus (ESV) is a newly discovered virus recovered as contamination in a sample of a virulent strain of dengue-2 virus (strain 44/2), which was recovered from a patient in the state of Espirito Santo, Brazil, and amplified in insect cells. ESV was found to be dependent upon coinfection with a virulent strain of dengue-2 virus and to replicate in C6/36 insect cells but not in mammalian Vero cells. A sequence of the genome has been produced by de novo assembly and was not found to match to any known viral sequence. An incomplete match to the nucleotide sequence of the RNA-dependent RNA polymerase from Drosophila X virus (DXV), another birnavirus, could be detected. Mass spectrometry analysis of ESV proteins found no matches in the protein data banks. However, peptides recovered by mass spectrometry corresponded to the de novo-assembled sequence by BLAST analysis. The composition and three-dimensional structure of ESV are presented, and its sequence is compared to those of other members of the birnavirus family. Although the virus was found to belong to the family Birnaviridae, biochemical and sequence information for ESV differed from that of DXV, the representative species of the genus Entomobirnavirus. Thus, significant differences underscore the uniqueness of this infectious agent, and its relationship to the coinfecting virus is discussed.     

Blue genes: genetic variation in our immune genes may be a mixed blessing

Today we know that almost all aspects of disease are affected in some way by our genes. The size of the genetic contribution towards each disease shows tremendous variation, but ultimately, the key to our survival of onslaught from environmental agents lies within our gene pool.     

Interdisciplinary assessment of the status quo of the marine fishery systems in the state of Espirito Santo, Brazil, using Rapfish

The aim of the present study was to carry out a comparative analysis of fishery systems in the state of Espírito Santo, Brazil (western coast of South America, between 18 and 22°S) using the Rapfish method – a rapid, innovative assessment model of fishery sustainability consisting of a multivariate ordination analysis of ecological, technological, social and economic data. The fisheries were divided into 26 fishery systems according to type of fleet, gear, target resource, ecosystem and environmental characteristics. A series of variables categorized in numeric scales from one to five were determined for each system. The attributes were compared through multivariate techniques. The comparison between fisheries in the state reflect the characteristic small-scale fisheries of the region, with minimal state intervention in management. The analysis of the social dimension revealed that the correlations between systems were mainly associated to the degree of isolation of the communities. The analysis of the ecological dimension revealed a clear coast/open ocean gradient and urbanized centers/isolated locations gradient related to the degree of commitment to the environment with regard to anthropogenic impact and the availability of resources. The economic and technological dimensions were arranged by variations in product destination, cost of fishing gear and degree of technology employed. The management dimension exhibited little sensitivity to the multivariate method employed. Few systems stood apart due to the few existing management measures that differentiated them. The pattern of sustainability found in the kite diagrams displays a balance between the dimensions in the perspective of maximum approximation to the optimum sustainability index. Either overfished and better socio-economic conditions, or marginalized people with use a more more sound strategy of resource exploitation.     

Genetic diversity and statistical parameters of 15 autosomal STR loci in the Pomeranian Subpopulation of Espirito Santo State,Brazil

Allelic frequencies and other population data analysis are reported for the 15 autosomal Short Tandem Repeats (STR) loci included in the PowerPlex^®16 kit (CSF1PO, D13S317, D16S539, D18S51, D21S11, D3S1358, D5S818, D7S820, D8S1179, FGA, Penta D, Penta E, TPOX, TH01 and vWA) in Pomeranian’s descendants from the Espirito Santo State (ES), Brazil, third largest population of Pomeranian’s descendants in the world. They chose the mountain region of the state for their preferred geographic location, and they have a very peculiar lifestyle with a selective mating behavior which has maintained their characteristics as a relatively pure subpopulation. Blood samples were obtained from 82 unrelated volunteers from 11 different cities of Espirito Santo State, where there are the Pomeranian’s descendants. All 15 loci analyzed showed Power of Discrimination (PD) values > 0.75. Except the TPOX locus, all analyzed loci were at Hardy–Weinberg equilibrium. This subpopulation has not yet been characterized for STR allelic frequencies used for forensic and genetic identification studies.     

The complexity of genetic variation in a simple immune system

Fruitflies derived from a wild population vary in their resistance to infection with the bacterial pathogen Serratia marcescens. A survey of nucleotide diversity in 21 genes involved in innate immunity concluded that 16 genes had polymorphisms associated with resistance to this specific pathogen. However, the effects of individual polymorphisms on the resistance phenotype were modest, and epistatic interactions appeared to be common. What might these findings tell us about genetic resistance to infection in humans?     

Participation of the dog in the cycle of transmission of cutaneous leishmaniasis in the municipality of Viana, State of Espirito Santo, Brazil

In an endemic area of cutaneous leishmaniasis in the Viana municipality, Espírito Santo state, an investigation was performed on natural hosts of Leishmania among domestic animals, trying to correlate the presence of infected animals with the occurrence of the disease in humans. Within a three weeks period 186 dogs were examined and 32 (17.2%) were found infected. Eleven new cases of cutaneous leishmaniasis were recorded during one year, among people living in the endemic area. A close relationship was observed between the presence of infected dogs and the occurrence of human leishmaniasis. In the area studied, the disease seems to behave as a zoonosis maintained by domestic dogs.     

Hyla ruschii n.sp., a New frog from the Atlantic Forest Domain in the state of Espirito Santo,Brazil (Amphibia,Hylidae)

Hyla ruschii n.sp., a small frog tentatively included into the "Hyla parviceps group”;, is described from the Atlantic Mountain Domain around Santa Teresa, State of Espirito Santo, Brasil.     

In silico study of transcriptome genetic variation in outbred populations

Dissecting the genetic architecture of regulatory elements on a genome-wide basis is now technically feasible. The potential medical and genetical implications of this kind of experiment being very large, it is paramount to assess the reliability and repeatability of the results. This is especially relevant in outbred populations, such as humans, where the genetic architecture is necessarily more complex than in crosses between inbred lines. Here we simulated a chromosome-wide SNP association study using real human microarray data. Our model predicted, as observed, a highly significant clustering of quantitative trait loci (QTL) for gene expression. Importantly, the estimates of QTL positions were often unstable, and a decrease in the number of individuals of 16% resulted in a loss of power of approximately 30% and a large shift in the position estimate in approximately 30-40% of the remaining significant QTL. We also found that the analysis of two repeated measures of the same mRNA can also result in two QTL that are located far apart. The intrinsic difficulties of analyzing outbred populations should not be underestimated. We anticipate that (many) conflicting results may be collected in the future if whole-genome association studies for mRNA levels are carried out in outbred populations.     

Population variation in tooth, jaw, and root size: a radiographic study of two populations in a high-attrition environment

Radiographs were taken of the jaws of skeletal remains of two populations of different-phenotype Prehistoric Australians from Roonka and Early New Zealanders (Maoris). On these radiographs crown, root, and corpus size were measured. Corpus height was subdivided into alveolar bone height, defined as the bone superior to the mandibular canal, and basal bone height, defined as that inferior to the mandibular canal. Both between and within the two populations there was a significant and negative correlation between crown size and corpus height. The differences between the two populations in corpus height were associated with differences in alveolar bone height rather than basal bone height and support hypotheses associating continued eruption of adult teeth with growth of the alveolar bone. The findings also support previous studies that have shown only a low correlation between crown size, root size, and corpus height.     

Polymorphic microsatellite loci in the sponge Crambe crambe (Porifera: Poecilosclerida) and their variation in two distant populations

Seven polymorphic microsatellite loci were characterized in the marine encrusting sponge Crambe crambe from a partial genomic DNA‐enriched library. Preliminary data on allelic variation of these loci in two distant populations of C. crambe are presented to assess their potential utility as high‐resolution genetic markers for this species. The number of alleles per locus ranged between three and 16 and the distributions of allele frequencies differed considerably between the two populations, indicating a marked genetic differentiation between them. These are the first microsatellite loci reported from any species in the phylum.     

A genetic study of two French Guiana Amerindian populations

Two Amerindian populations of French Guiana were investigated for plasma proteins and red-cell enzymes. In the Wayampi tribe, rare variants were identified in 4 systems. The corresponding alleles are designated AK1 3 Wayampi, PGM1 (4/10) Wayampi, PGM2 6 Wayampi, and TfD. In the Emerillon tribe, a variant allele of PGM2, designated PGM2 6 Emerillon, was identified. For three of the systems, PGM1, PGM2, Tf, similar isozymes have been described in other Amerindian populations. These findings suggest that the corresponding alleles may have the same origin.     

A genetic study of two French Guiana Amerindian populations

Summary Phenotypes and gene frequencies are presented for 20 serum and erythrocyte proteins in two Amerindian populations of inner French Guiana. No genetic variability was detected in 12 of these systems. Heterozygosity was calculated for the others and the reasons for its variation are discussed.     

Reproductive system and pattern of genetic variation in two Limnanthes species

Summary Several populations of two species of the genus Limnanthes, (L. alba, an outbreeder and L. floccosa, an inbreeder) were examined with respect to variability of fifteen quantitative characters, allozyme variation at 11 loci, and response to different pollination conditions and moisture stress. Nearly equal amounts of phenotypic variability were found in the two species. L. alba had higher within-family variability than L. floccosa, but this result was highly heterogeneous among characters. A study of between- and within-population variance estimates did not reject the null hypothesis that L. alba and L. floccosa are similar with regard to the partitioning and amount of variability for quantitative characters. However, allozyme variation at 11 loci in a large number of populations showed L. alba to be highly polymorphic in contrast to the virtual monomorphism within L. floccosa populations. The average number of alleles per locus in L. alba and L. floccosa was 1.97 and 1.02, respectively, and on an average, L. alba and L. floccosa populations had 63% and 3% loci with polymorphism, respectively. Three groups of allozyme allelic combinations emerged which correlated well with the taxonomic delineation of allogamous L. alba, three semi-autogamous L. floccosa forms and two autogamous L. floccosa forms.All taxa showed a significant reduction in the seed output per plant due to moisture stress. L. alba suffered a further loss of fecundity under the paucity of pollinators, L. floccosa ssp. floccosa showed no significant effect from this factor, whereas L. floccosa ssp. grandiflora exhibited a curvilinear response which peaked at partial pollination and decreased to a lower level at full pollination.The geographic distribution of the two species with regard to the temperature and rainfall distribution did not suggest L. floccosa to be living in drier marginal areas. Patterns of variation in flowering time showed L. alba to be less variable than L. floccosa. Overall, there seemed to be little direct support for the thesis that inbreeding species originated from outcrossing taxa in marginal environments as a direct adaptation to a shortened growing season of xeric environments and to the lack of pollinators. Alternative hypotheses suggest that autogamy in L. floccosa might have evolved as a reproductive isolating barrier acting through either cleistogamy or divergence in flowering times.     

Nucella lapillus: A possible model for the study of genetic variation in natural populations

The explanation of the maintenance of the large amount of genetic variation in natural populations is a major problem faced by evolutionary geneticists. It is proposed that Nucella lapillus would make a suitable model for the study of this problem. The presence of visible interpopulation variation in characteristics which can be utilised for such studies, is demonstrated at a particular geographic location. The importance of experimental design in studying genetic variation is emphasised.     

Patterns of genetic variation in anthropogenically impacted populations

Genetic variation is considered critical for allowing natural populations to adapt to their changing environment, and yet the effects of human disturbance on genetic variation in the wild are poorly understood. Different types of human disturbances may genetically impact natural populations in a predictable manner and so the aim of this study was to provide an overview of these changes using a quantitative literature review approach. I examined both allozyme and microsatellite estimates of genetic variation from peer-reviewed journals, using the mean number of alleles per locus and expected heterozygosity as standardized metrics. Populations within each study were categorized according to the type of human disturbance experienced (“hunting/harvest”, “habitat fragmentation”, or “pollution”), and taxon-specific, as well as time- and context-dependent disturbance effects were considered. I found that human disturbances are associated with weak, but consistent changes in neutral genetic variation within natural populations. The direction of change was dependent on the type of human disturbance experienced, with some forms of anthropogenic challenges consistently decreasing genetic variation from background patterns (e.g., habitat fragmentation), whereas others had no effect (e.g., hunting/harvest) or even slightly increased genetic variation (e.g., pollution). These same measures appeared sensitive to both the time of origin and duration of the disturbance as well. This suggests that the presence or absence, strength, type, as well as the spatial and temporal scale of human disturbance experienced may warrant careful consideration when conservation management plans are formulated for natural populations, with particular attention paid to the effects of habitat fragmentation.     

A preliminary study of genetic variation in populations of Monstera adansonii var. klotzschiana (Araceae) from North-East Brazil, estimated with AFLP molecular markers

BACKGROUND AND AIMS: This study sought genetic evidence of long-term isolation in populations of Monstera adansonii var. klotzschiana (Araceae), a herbaceous, probably outbreeding, humid forest hemi-epiphyte, in the brejo forests of Ceará (north-east Brazil), and clarification of their relationships with populations in Amazonia and the Atlantic forest of Brazil. METHODS: Within-population genetic diversity and between-population dissimilarity were estimated using AFLP molecular markers in 75 individuals from eight populations located in Ceará, the Brazilian Atlantic Forest and Amazonia. KEY RESULTS: The populations showed a clinal pattern of weak genetic differentiation over a large geographical region (F(ST) = 0.1896). A strong correlation between genetic and geographical distance (Mantel test: r = 0.6903, P = 0.002) suggests a historical pattern of isolation by distance. Genetic structure analysis revealed at least two distinct gene pools in the data. The two isolated Ceará populations are significantly different from each other (pairwise Phi(PT) = 0.137, P = 0.003) and as diverse (Nei's gene diversity, average H(e) = 0.1832, 0.1706) as those in the Atlantic and Amazon forest regions. The population in southern Brazil is less diverse (Nei's gene diversity, average H(e) = 0.127) than the rest. The Ceará populations are related to those of the Atlantic forest rather than those from Amazonia (AMOVA, among-groups variation = 11.95 %, P = 0.037). CONCLUSIONS: The gene pools detected within an overall pattern of clinal variation suggest distinct episodes of gene flow, possibly correlated with past humid forest expansions. The Ceará populations show no evidence of erosion of genetic diversity, although this was expected because of their isolation. Their genetic differentiation and relatively high diversity reinforce the importance of conserving the endangered brejo forests.     

Comparing G: multivariate analysis of genetic variation in multiple populations

The additive genetic variance–covariance matrix (G) summarizes themultivariate genetic relationships among a set of traits. The geometry of Gdescribes the distribution of multivariate genetic variance, and generates geneticconstraints that bias the direction of evolution. Determining if and how the multivariategenetic variance evolves has been limited by a number of analytical challenges incomparing G-matrices. Current methods for the comparison of G typically shareseveral drawbacks: metrics that lack a direct relationship to evolutionary theory, theinability to be applied in conjunction with complex experimental designs, difficultieswith determining statistical confidence in inferred differences and an inherentlypair-wise focus. Here, we present a cohesive and general analytical framework for thecomparative analysis of G that addresses these issues, and that incorporates andextends current methods with a strong geometrical basis. We describe the application ofrandom skewers, common subspace analysis, the 4th-order genetic covariance tensor and thedecomposition of the multivariate breeders equation, all within a Bayesian framework. Weillustrate these methods using data from an artificial selection experiment on eighttraits in Drosophila serrata, where a multi-generational pedigree was availableto estimate G in each of six populations. One method, the tensor, elegantlycaptures all of the variation in genetic variance among populations, and allows theidentification of the trait combinations that differ most in genetic variance. The tensorapproach is likely to be the most generally applicable method to the comparison ofG-matrices from any sampling or experimental design.