Indicadores de sustentabilidade para conservação genética de Erythrina velutina Willd., em área de mata ciliar

One of the greatest challenges for the agricultural system is to establish agricultural production combined with the conservation of genetic resources, mainly aiming to protect the Permanent Preservation Areas. In this context, mulungu ( Erythrina velutina Willd), among other native species, has been suffering with anthropogenic pressures in various ecosystems, causing reductions in its genetic basis. This work aims to identify ecological and genetic population parameters as indicators of sustainability in two natural populations of mulungu, located in riparian forest, in the state of Sergipe, and to assess the tendency to their sustainability, aiming genetic conservation of the species. The matrix of Pressure-State-Impact/Effect-Response (PEI/ER) was used with the selection of 13 indicators, from the use of RAPDmolecular markers and biochemical (enzymes) markers in populations, in order to present them as relevant information to measure progress as for sustainability and conservation ofmulungu. The studied populations presented low tendency to sustainability, requiring strategies to change this status.

New loci of Lychnophora ericoides and transferability to Lychnophora pinaster, endangered medicinal species from Brazil

Lychnophora ericoides and Lychnophora pinaster are species used in popular medicine as analgesic or anti-inflammatory agents to treat contusions, rheumatism, and insect bites. In this study, 21 simple sequence repeat loci of L. ericoides were developed and transferred to L. pinaster. Three populations of L. ericoides and 2 populations of L. pinaster were evaluated; they were collected in the State of Minas Gerais. Population parameters were estimated, and the mean values of observed and expected heterozygosity were 0.297 and 0.408 (L. ericoides) and 0.228 and 0.310 (L. pinaster), respectively. Greater genetic variability was observed within populations than between populations of L. ericoides (62 and 37%) and L. pinaster (97 and 2.8%). These results provide information for genetic conservation and taxonomic studies of these endangered species.

Estrutura populacional e parâmetros genéticos da característica classe de tempo em corridas de equinos da raça Quarto de Milha

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Crop, Native Vegetation, and Biofuels: Response of White- Tailed Deer to Changing Management Priorities

The expansion of the cellulosic biofuels industry throughout the United States has broad-scale implications for wildlife management on public and private lands. Knowledge is limited on the effects of reverting agriculture to native grass, and vice versa, on size of home range and habitat use of white-tailed deer (Odocoileus virginianus). We followed 68 radio-collared female deer from 1991 through 2004 that were residents of DeSoto National Wildlife Refuge (DNWR) in eastern Nebraska, USA. The refuge was undergoing conversion of vegetation out of row-crop agriculture and into native grass, forest, and emergent aquatic vegetation. Habitat in DNWR consisted of 30% crop in 1991 but removing crops to establish native grass and wetland habitat at DNWR resulted in a 44% reduction in crops by 2004. A decrease in the amount of crops on DNWR contributed to a decline in mean size of annual home range from 400 ha in 1991 to 200 ha in 2005 but percentage of crops in home ranges increased from 21% to 29%. Mean overlap for individuals was 77% between consecutive annual home ranges across 8 years, regardless of crop availability. Conversion of crop to native habitat will not likely result in home range abandonment but may impact disease transmission by increasing rates of contact between deer social groups that occupy adjacent areas. Future research on condition indices or changes in population parameters (e.g., recruitment) could be incorporated into the study design to assess impacts of habitat conversion for biofuel production.

Uric acid biorhythm, a feature of long-term variation in a clinical laboratory database

Background: The biorhythm of serum uric acid was evaluated in a large sample of a clinical laboratory database by spectral analysis and the influence of the gender and age on uric acid variability. Methods: Serum uric acid values were extracted from a large database of a clinical laboratory from May 2000 to August 2006. Outlier values were excluded from the analysis and the remaining data (n = 73,925) were grouped by gender and age ranges. Rhythm components were obtained by the Lomb Scargle method and Cosinor analysis. Results: Serum uric acid was higher in men than in women older than 13 years (p<0.05). Compared with 0-12 year group, uric acid increased in men but not in women older than 13 years (p<0.05). Circannual (12 months) and transyear (17 months) rhythm components were detected, but they were significant only in adult individuals (>26 years, p<0.05). Cosinor analysis showed that midline estimating statistic of rhythm (MESOR) values were higher in men (range: 353-368 mu mol/L) than in women (range: 240-278 mu mol/L; p<0.05), independent of the age and rhythm component. The extent of predictable change within a cycle, approximated by the double amplitude, represented up to 20% of the corresponding MESOR. Conclusions: Serum uric acid biorhythm is dependent on gender and age and it may have relevant influence on preanalytical variability of clinical laboratory results.

Estimating the mean and standard deviation of concentration distributions using censored samples

Environmental data sets of pollutant concentrations in air, water, and soil frequently include unquantified sample values reported only as being below the analytical method detection limit. These values, referred to as censored values, should be considered in the estimation of distribution parameters as each represents some value of pollutant concentration between zero and the detection limit. Most of the currently accepted methods for estimating the population parameters of environmental data sets containing censored values rely upon the assumption of an underlying normal (or transformed normal) distribution. This assumption can result in unacceptable levels of error in parameter estimation due to the unbounded left tail of the normal distribution. With the beta distribution, which is bounded by the same range of a distribution of concentrations, $\rm\lbrack0\le x\le1\rbrack,$ parameter estimation errors resulting from improper distribution bounds are avoided. This work developed a method that uses the beta distribution to estimate population parameters from censored environmental data sets and evaluated its performance in comparison to currently accepted methods that rely upon an underlying normal (or transformed normal) distribution. Data sets were generated assuming typical values encountered in environmental pollutant evaluation for mean, standard deviation, and number of variates. For each set of model values, data sets were generated assuming that the data was distributed either normally, lognormally, or according to a beta distribution. For varying levels of censoring, two established methods of parameter estimation, regression on normal ordered statistics, and regression on lognormal ordered statistics, were used to estimate the known mean and standard deviation of each data set. The method developed for this study, employing a beta distribution assumption, was also used to estimate parameters and the relative accuracy of all three methods were compared. For data sets of all three distribution types, and for censoring levels up to 50%, the performance of the new method equaled, if not exceeded, the performance of the two established methods. Because of its robustness in parameter estimation regardless of distribution type or censoring level, the method employing the beta distribution should be considered for full development in estimating parameters for censored environmental data sets. ^

Genetic analysis of white facial and leg markings in the Swiss Franches-Montagnes Horse Breed

White markings and spotting patterns in animal species are thought to be a result of the domestication process. They often serve for the identification of individuals but sometimes are accompanied by complex pathological syndromes. In the Swiss Franches-Montagnes horse population, white markings increased vastly in size and occurrence during the past 30 years, although the breeding goal demands a horse with as little depigmented areas as possible. In order to improve selection and avoid more excessive depigmentation on the population level, we estimated population parameters and breeding values for white head and anterior and posterior leg markings. Heritabilities and genetic correlations for the traits were high (h(2) > 0.5). A strong positive correlation was found between the chestnut allele at the melanocortin-1-receptor gene locus and the extent of white markings. Segregation analysis revealed that our data fit best to a model including a polygenic effect and a biallelic locus with a dominant-recessive mode of inheritance. The recessive allele was found to be the white trait-increasing allele. Multilocus linkage disequilibrium analysis allowed the mapping of the putative major locus to a chromosomal region on ECA3q harboring the KIT gene.

Parámetros biológicos y demograficos de áfidos (Hemiptera: aphididae) en variedades de colza canola (Brassica napus L.)

Myzus persicae (Sulz.), Brevicoryne brassicae L. y Lipaphis erysimi (Kalt.) constituyen plagas del cultivo de colza canola, Brassica napus L., y de otras crucíferas cultivadas. Los pulgones fueron colectados en un cultivo de canola y se multiplicaron en un insectario. Para el estudio se criaron 2 cohortes de 20 hembras neonatas, para cada especie de áfido y cultivar de colza, a 20 ± 1°C, 60-70% de humedad relativa y 14:10 horas de fotofase. Las principales diferencias entre especies de pulgones se observaron en la duración de los períodos reproductivo y post-reproductivo, la longevidad y la fecundidad. M. persicae fue el áfido más longevo y fecundo en Impact, mientras que en Teddy el más fecundo fue L. erysimi y el más longevo M. persicae. Con respecto a los parámetros poblacionales, la mayor tasa de incremento poblacional (R0) fue de 58,43 (♀/♀/generación) para M. persicae en Impact. En cambio en Teddy la mayor R0 (63,17) fue para L. erysimi. La tasa intrínseca de crecimiento natural (rm) más elevada fue para L. erysimi en Teddy (0,29 ♀/♀/día) y para M. persicae en Impact (0,24 ♀/♀/día). Estos estudios indican que, de acuerdo con el cultivar de colza empleado, teniendo en cuenta la tasa de crecimiento poblacional de las diferentes especies de pulgones, se podría inferir cuál será la especie dominante y el daño potencial que ocasionarían al cultivo.

Experimental assessment of sediment burial in eelgrass Zostera marina in Kiel Bight

Seagrass meadows, one of the world's most important and productive coastal habitats, are threatened by a range of anthropogenic actions. Burial of seagrass plants due to coastal activities is one important anthropogenic pressure leading to the decline of local populations. In our study, we assessed the response of eelgrass Zostera marina to sediment burial from physiological, morphological, and population parameters. In a full factorial field experiment, burial level (5-20cm) and burial duration (4-16 weeks) were manipulated. Negative effects were visible even at the lowest burial level (5 cm) and shortest duration (4 weeks), with increasing effects over time and burial level. Buried seagrasses showed higher shoot mortality, delayed growth and flowering and lower carbohydrate storage. The observed effects will likely have an impact on next year's survival of buried plants. Our results have implications for the management of this important coastal plant.

Mutation rates among RNA viruses

The rate of spontaneous mutation is a key parameter in modeling the genetic structure and evolution of populations. The impact of the accumulated load of mutations and the consequences of increasing the mutation rate are important in assessing the genetic health of populations. Mutation frequencies are among the more directly measurable population parameters, although the information needed to convert them into mutation rates is often lacking. A previous analysis of mutation rates in RNA viruses (specifically in riboviruses rather than retroviruses) was constrained by the quality and quantity of available measurements and by the lack of a specific theoretical framework for converting mutation frequencies into mutation rates in this group of organisms. Here, we describe a simple relation between ribovirus mutation frequencies and mutation rates, apply it to the best (albeit far from satisfactory) available data, and observe a central value for the mutation rate per genome per replication of μg ≈ 0.76. (The rate per round of cell infection is twice this value or about 1.5.) This value is so large, and ribovirus genomes are so informationally dense, that even a modest increase extinguishes the population.

Microsatellite variability and genetic distances.

We analyze the within- and between-population dynamics of the distribution of the number of repeats at multiple microsatellite DNA loci subject to stepwise mutation. Analytical expressions for moments up to the fourth order within a locus and the variance of between-locus variance at mutation-drift equilibrium have been obtained. These statistics may be used to test the appropriateness of the one-step mutation model and to detect between-locus variation in the mutation rate. Published data are compatible with the one-step mutation model, although they do not reject the two-step model. Using both multinomial sampling and diffusion approximations for the analysis of the genetic distance introduced by Goldstein et al. [Goldstein, D. B., Linares, A. R., Cavalli-Sforza, L. L. & Feldman, M. W. (1995) Proc. Natl. Acad. Sci. USA 92, 6723-6727], we show that this distance follows a chi 2 distribution with degrees of freedom equal to the number of loci when there is no variation in mutation rates among the loci. In the presence of such variation, the variance of the distance is obtained. We conclude that the number of microsatellite loci required for the construction of phylogenetic trees with reliable branch lengths may be several hundred. Also, mutations that change repeat scores by several units, even though extremely rare, may dramatically influence estimates of population parameters.

Protocols for listing threatened species can forecast extinction

Risk-ranking protocols are used widely to classify the conservation status of the world's species. Here we report on the first empirical assessment of their reliability by using a retrospective study of 18 pairs of bird and mammal species (one species extinct and the other extant) with eight different assessors. The performance of individual assessors varied substantially, but performance was improved by incorporating uncertainty in parameter estimates and consensus among the assessors. When this was done, the ranks from the protocols were consistent with the extinction outcome in 70-80% of pairs and there were mismatches in only 10-20% of cases. This performance was similar to the subjective judgements of the assessors after they had estimated the range and population parameters required by the protocols, and better than any single parameter. When used to inform subjective judgement, the protocols therefore offer a means of reducing unpredictable biases that may be associated with expert input and have the advantage of making the logic behind assessments explicit. We conclude that the protocols are useful for forecasting extinctions, although they are prone to some errors that have implications for conservation. Some level of error is to be expected, however, given the influence of chance on extinction. The performance of risk assessment protocols may be improved by providing training in the application of the protocols, incorporating uncertainty in parameter estimates and using consensus among multiple assessors, including some who are experts in the application of the protocols. Continued testing and refinement of the protocols may help to provide better absolute estimates of risk, particularly by re-evaluating how the protocols accommodate missing data.

Slowing down a pine invasion despite uncertainty in demography and dispersal

1. Management decisions regarding invasive plants often have to be made quickly and in the face of fragmentary knowledge of their population dynamics. However, recommendations are commonly made on the basis of only a restricted set of parameters. Without addressing uncertainty and variability in model parameters we risk ineffective management, resulting in wasted resources and an escalating problem if early chances to control spread are missed. 2. Using available data for Pinus nigra in ungrazed and grazed grassland and shrubland in New Zealand, we parameterized a stage-structured spread model to calculate invasion wave speed, population growth rate and their sensitivities and elasticities to population parameters. Uncertainty distributions of parameters were used with the model to generate confidence intervals (CI) about the model predictions. 3. Ungrazed grassland environments were most vulnerable to invasion and the highest elasticities and sensitivities of invasion speed were to long-distance dispersal parameters. However, there was overlap between the elasticity and sensitivity CI on juvenile survival, seedling establishment and long-distance dispersal parameters, indicating overlap in their effects on invasion speed. 4. While elasticity of invasion speed to long-distance dispersal was highest in shrubland environments, there was overlap with the CI of elasticity to juvenile survival. In shrubland invasion speed was most sensitive to the probability of establishment, especially when establishment was low. In the grazed environment elasticity and sensitivity of invasion speed to the severity of grazing were consistently highest. Management recommendations based on elasticities and sensitivities depend on the vulnerability of the habitat. 5. Synthesis and applications. Despite considerable uncertainty in demography and dispersal, robust management recommendations emerged from the model. Proportional or absolute reductions in long-distance dispersal, juvenile survival and seedling establishment parameters have the potential to reduce wave speed substantially. Plantations of wind-dispersed invasive conifers should not be sited on exposed sites vulnerable to long-distance dispersal events, and trees in these sites should be removed. Invasion speed can also be reduced by removing seedlings, establishing competitive shrubs and grazing. Incorporating uncertainty into the modelling process increases our confidence in the wide applicability of the management strategies recommended here.

Responses in carcass lean pH at 24 hours post-mortem in lines of Large White pigs selected for growth rate on a fixed ration over a set time

A restricted maximum likelihood analysis applied to an animal model showed no significant differences (P > 0.05) in pH value of the longissimus dorsi measured at 24 h post-mortem (pH24) between high and low lines of Large White pigs selected over 4 years for post-weaning growth rate on restricted feeding. Genetic and phenotypic correlations between pH24 and production and carcass traits were estimated using all performance testing records combined with the pH24 measurements (5.05–7.02) on slaughtered animals. The estimate of heritability for pH24 was moderate (0.29 ± 0.18). Genetic correlations between pH24 and production or carcass composition traits, except for ultrasonic backfat (UBF), were not significantly different from zero. UBF had a moderate, positive genetic correlation with pH24 (0.24 ± 0.33). These estimates of genetic correlations affirmed that selection for increased growth rate on restricted feeding is likely to result in limited changes in pH24 and pork quality since the selection does not put a high emphasis on reduced fatness.

Phenotypic effect of mutations in evolving populations of RNA molecules

Background. The secondary structure of folded RNA sequences is a good model to map phenotype onto genotype, as represented by the RNA sequence. Computational studies of the evolution of ensembles of RNA molecules towards target secondary structures yield valuable clues to the mechanisms behind adaptation of complex populations. The relationship between the space of sequences and structures, the organization of RNA ensembles at mutation-selection equilibrium, the time of adaptation as a function of the population parameters, the presence of collective effects in quasispecies, or the optimal mutation rates to promote adaptation all are issues that can be explored within this framework. Results. We investigate the effect of microscopic mutations on the phenotype of RNA molecules during their in silico evolution and adaptation. We calculate the distribution of the effects of mutations on fitness, the relative fractions of beneficial and deleterious mutations and the corresponding selection coefficients for populations evolving under different mutation rates. Three different situations are explored: the mutation-selection equilibrium (optimized population) in three different fitness landscapes, the dynamics during adaptation towards a goal structure (adapting population), and the behavior under periodic population bottlenecks (perturbed population). Conclusions. The ratio between the number of beneficial and deleterious mutations experienced by a population of RNA sequences increases with the value of the mutation rate µ at which evolution proceeds. In contrast, the selective value of mutations remains almost constant, independent of µ, indicating that adaptation occurs through an increase in the amount of beneficial mutations, with little variations in the average effect they have on fitness. Statistical analyses of the distribution of fitness effects reveal that small effects, either beneficial or deleterious, are well described by a Pareto distribution. These results are robust under changes in the fitness landscape, remarkably when, in addition to selecting a target secondary structure, specific subsequences or low-energy folds are required. A population perturbed by bottlenecks behaves similarly to an adapting population, struggling to return to the optimized state. Whether it can survive in the long run or whether it goes extinct depends critically on the length of the time interval between bottlenecks. © 2010 Stich et al; licensee BioMed Central Ltd.