Genetic diversity and selection in three plasmodium vivax merozoite surface protein 7 (pvmsp-7) genes in a colombian population

A completely effective vaccine for malaria (one of the major infectious diseases worldwide) is not yet available; different membrane proteins involved in parasite-host interactions have been proposed as candidates for designing it. It has been found that proteins encoded by the merozoite surface protein (msp)-7 multigene family are antibody targets in natural infection; the nucleotide diversity of three Pvmsp-7 genes was thus analyzed in a Colombian parasite population. By contrast with P. falciparum msp-7 loci and ancestral P. vivax msp-7 genes, specie-specific duplicates of the latter specie display high genetic variability, generated by single nucleotide polymorphisms, repeat regions, and recombination. At least three major allele types are present in Pvmsp-7C, Pvmsp-7H and Pvmsp-7I and positive selection seems to be operating on the central region of these msp-7 genes. Although this region has high genetic polymorphism, the C-terminus (Pfam domain ID: PF12948) is conserved and could be an important candidate when designing a subunit-based antimalarial vaccine.

Eficacia del diagnóstico prenatal no invasivo por células fetales libres en sangre materna 1990-2014. Revisión sistemática

ANTECEDENTES: El aislamiento de células fetales libres o ADN fetal en sangre materna abre una ventana de posibilidades diagnósticas no invasivas para patologías monogénicas y cromosómicas, además de permitir la identificación del sexo y del RH fetal. Actualmente existen múltiples estudios que evalúan la eficacia de estos métodos, mostrando resultados costo-efectivos y de menor riesgo que el estándar de oro. Este trabajo describe la evidencia encontrada acerca del diagnóstico prenatal no invasivo luego de realizar una revisión sistemática de la literatura. OBJETIVOS: El objetivo de este estudio fue reunir la evidencia que cumpla con los criterios de búsqueda, en el tema del diagnóstico fetal no invasivo por células fetales libres en sangre materna para determinar su utilidad diagnóstica.  MÉTODOS: Se realizó una revisión sistemática de la literatura con el fin de determinar si el diagnóstico prenatal no invasivo por células fetales libres en sangre materna es efectivo como método de diagnóstico.  RESULTADOS: Se encontraron 5,893 artículos que cumplían con los criterios de búsqueda; 67 cumplieron los criterios de inclusión: 49.3% (33/67) correspondieron a estudios de corte transversal, 38,8% (26/67) a estudios de cohortes y el 11.9% (8/67) a estudios casos y controles. Se obtuvieron resultados de sensibilidad, especificidad y tipo de prueba. CONCLUSIÓN: En la presente revisión sistemática, se evidencia como el diagnóstico prenatal no invasivo es una técnica feasible, reproducible y sensible para el diagnóstico fetal, evitando el riesgo de un diagnóstico invasivo.

Prevalencia de neumoconiosis y su relación con medidas de higiene y seguridad industrial y niveles ambientales de carbón en minería subterránea en el departamento de Cundinamarca - Colombia, 2015

Introducción: La exposición en minas subterráneas a altos niveles de polvo de carbón está relacionada con patologías pulmonares. Objetivo: Determinar la prevalencia de neumoconiosis, medidas de higiene y seguridad industrial y su relación con niveles ambientales de carbón en trabajadores de minas de socavón en Cundinamarca. Materiales y Métodos: Estudio de corte transversal, en 215 trabajadores seleccionados mediante muestreo probabilístico estratificado con asignación proporcional. Se realizaron monitoreos ambientales, radiografías de tórax y encuestas con variables sociodemográficas y laborales. Se emplearon medidas de tendencia central y dispersión y la prueba de independencia ji-cuadrado de Pearson o pruebas exactas, con el fin de establecer las asociaciones. Resultados: El 99,5% de la población perteneció al género masculino, el 36,7% tenía entre 41-50 años, con un promedio de años de trabajo de 21,70 ± 9,99. La prevalencia de neumoconiosis fue de 42,3% y la mediana de la concentración de polvo de carbón bituminoso fue de 2,329670 mg/m3. El índice de riesgo de polvo de carbón presentó diferencias significativas en las categorías de bajo (p=0,0001) y medio (p=0,0186) con la prevalencia de neumoconiosis. El 84,2% reporto no usar mascarilla. No se presentan diferencias entre los niveles de carbón (p=0,194) con la prevalencia de neumoconiosis. Conclusiones: Se encontró una prevalencia de neumoconiosis de 42,3% en Cundinamarca. Se requiere contar con medidas de higiene y seguridad industrial efectivas para controlar el riesgo al que están expuestos los mineros de carbón por la inhalación de polvo de carbón.

Zooplankton structure and dynamics in Mediterranean marshes (Empordà Wetlands): a size-based approach

Zooplankton community structure (composition, diversity, dynamics and trophic relationships) of Mediterranian marshes, has been analysed by means of a size based approach. In temporary basins the shape of the biomass-size spectra is related to the hydrological cycle. Linear shape spectra are more frequent in flooding situations when nutrient input causes population growth of small-sized organisms, more than compensating for the effect of competitive interactions. During confinement conditions the scarcity of food would decrease zooplankton growth and increase intra- and interspecific interactions between zooplankton organisms which favour the greatest sizes thus leading to the appearance of curved shape spectra. Temporary and permanent basins have similar taxonomic composition but the latter have higher species diversity, a more simplified temporal pattern and a size distribution dominated mainly by smaller sizes. In permanents basins zooplankton growth is not only conditioned by the availability of resources but by the variable predation of planktivorous fish, so that the temporal variability of the spectra may also be a result of temporal differences in fish predation. Size diversity seems to be a better indicator of the degree of this community structure than species diversity. The tendency of size diversity to increase during succession makes it useful to discriminate between different succession stages, fact that is not achieved by analysing only species diversity since it is low both under large and frequent or small and rare disturbances. Amino acid composition differences found among stages of copepod species indicate a gradual change in diet during the life cycle of these copepods, which provide evidence of food niche partitioning during ontogeny, whereas Daphnia species show a relatively constant amino acid composition. There is a relationship between the degree of trophic niche overlap among stages of the different species and nutrient concentration. Copepods, which have low trophic niche overlap among stages are dominant in food-limited environments, probably because trophic niche partitioning during development allow them to reduce intraspecific competition between adults, juveniles and nauplii. Daphnia species are only dominant in water bodies or periods with high productivity, probably due to the high trophic niche overlap between juveniles and adults. These findings suggest that, in addition to the effect of interspecific competition, predation and abiotic factors, the intraspecific competition might play also an important role in structuring zooplankton assemblages.

Lesser Scaup Population Dynamics: What Can Be Learned from Available Data?

Populations of Lesser Scaup (Aythya affinis) have declined markedly in North America since the early 1980s. When considering alternatives for achieving population recovery, it would be useful to understand how the rate of population growth is functionally related to the underlying vital rates and which vital rates affect population growth rate the most if changed (which need not be those that influenced historical population declines). To establish a more quantitative basis for learning about life history and population dynamics of Lesser Scaup, we summarized published and unpublished estimates of vital rates recorded between 1934 and 2005, and developed matrix life-cycle models with these data for females breeding in the boreal forest, prairie-parklands, and both regions combined. We then used perturbation analysis to evaluate the effect of changes in a variety of vital-rate statistics on finite population growth rate and abundance. Similar to Greater Scaup (Aythya marila), our modeled population growth rate for Lesser Scaup was most sensitive to unit and proportional change in adult female survival during the breeding and non-breeding seasons, but much less so to changes in fecundity parameters. Interestingly, population growth rate was also highly sensitive to unit and proportional changes in the mean of nesting success, duckling survival, and juvenile survival. Given the small samples of data for key aspects of the Lesser Scaup life cycle, we recommend additional research on vital rates that demonstrate a strong effect on population growth and size (e.g., adult survival probabilities). Our life-cycle models should be tested and regularly updated in the future to simultaneously guide science and management of Lesser Scaup populations in an adaptive context.

Population Change in a Marine Bird Colony is Driven By Changes in Recruitment

The population dynamics of long-lived birds are thought to be very sensitive to changes in adult survival. However, where natal philopatry is low, recruitment from the larger metapopulation may have the strongest effect on population growth rate even in long-lived species. Here, we illustrate such a situation where changes in a seabird colony size appeared to be the consequence of changes in recruitment. We studied the population dynamics of a declining colony of Ancient Murrelets (Synthliboramphus antiquus) at East Limestone Island, British Columbia. During 1990-2010, Ancient Murrelet chicks were trapped at East Limestone Island while departing to sea, using a standard trapping method carried on throughout the departure period. Adult murrelets were trapped while departing from the colony during 1990-2003. Numbers of chicks trapped declined during 1990-1995, probably because of raccoon predation, increased slightly from 1995-2000 and subsequently declined again. Reproductive success was 30% lower during 2000-2003 than in earlier years, mainly because of an increase in desertions. The proportion of nonbreeders among adult birds trapped at night also declined over the study period. Mortality of adult birds, thought to be mainly prebreeders, from predators more than doubled over the same period. Apparent adult survival of breeders remained constant during 1991-2002 once the first year after banding was excluded, but the apparent survival rates in the first year after banding fell and the survival of birds banded as chicks to age three halved over the same period. A matrix model of population dynamics suggested that even during the early part of the study immigration from other breeding areas must have been substantial, supporting earlier observations that natal philopatry in this species is low. The general colony decline after 2000 probably was related to diminished recruitment, as evidenced by the lower proportion of nonbreeders in the trapped sample. Hence the trend is determined by the recruitment decisions of externally reared birds, rather than demographic factors operating on the local breeding population, an unusual situation for a colonial marine bird. Because of the contraction in the colony it may now be subject to a level of predation pressure from which recovery will be impossible without some form of intervention.

Patterns of pollen and seed dispersal in a small, fragmented population of the wind-pollinated tree Araucaria angustifolia in southern Brazil

Paternity analysis based on eight microsatellite loci was used to investigate pollen and seed dispersal patterns of the dioecious wind- pollinated tree, Araucaria angustifolia. The study sites were a 5.4 ha isolated forest fragment and a small tree group situated 1.7 km away, located in Paran alpha State, Brazil. In the forest fragment, 121 males, 99 females, 66 seedlings and 92 juveniles were mapped and genotyped, together with 210 seeds. In the tree group, nine male and two female adults were mapped and genotyped, together with 20 seeds. Paternity analysis within the forest fragment indicated that at least 4% of the seeds, 3% of the seedlings and 7% of the juveniles were fertilized by pollen from trees in the adjacent group, and 6% of the seeds were fertilized by pollen from trees outside these stands. The average pollination distance within the forest fragment was 83 m; when the tree group was included the pollination distance was 2006m. The average number of effective pollen donors was estimated as 12.6. Mother- trees within the fragment could be assigned to all seedlings and juveniles, suggesting an absence of seed immigration. The distance of seedlings and juveniles from their assigned mother- trees ranged from 0.35 to 291m ( with an average of 83m). Significant spatial genetic structure among adult trees, seedlings, and juveniles was detected up to 50m, indicating seed dispersal over a short distance. The effective pollination neighborhood ranged from 0.4 to 3.3 ha. The results suggest that seed dispersal is restricted but that there is longdistance pollen dispersal between the forest fragment and the tree group; thus, the two stands of trees are not isolated.

Uncertainties in annual riverine phosphorus load estimation: Impact of load estimation methodology, sampling frequency, baseflow index and catchment population density

Models developed to identify the rates and origins of nutrient export from land to stream require an accurate assessment of the nutrient load present in the water body in order to calibrate model parameters and structure. These data are rarely available at a representative scale and in an appropriate chemical form except in research catchments. Observational errors associated with nutrient load estimates based on these data lead to a high degree of uncertainty in modelling and nutrient budgeting studies. Here, daily paired instantaneous P and flow data for 17 UK research catchments covering a total of 39 water years (WY) have been used to explore the nature and extent of the observational error associated with nutrient flux estimates based on partial fractions and infrequent sampling. The daily records were artificially decimated to create 7 stratified sampling records, 7 weekly records, and 30 monthly records from each WY and catchment. These were used to evaluate the impact of sampling frequency on load estimate uncertainty. The analysis underlines the high uncertainty of load estimates based on monthly data and individual P fractions rather than total P. Catchments with a high baseflow index and/or low population density were found to return a lower RMSE on load estimates when sampled infrequently than those with a tow baseflow index and high population density. Catchment size was not shown to be important, though a limitation of this study is that daily records may fail to capture the full range of P export behaviour in smaller catchments with flashy hydrographs, leading to an underestimate of uncertainty in Load estimates for such catchments. Further analysis of sub-daily records is needed to investigate this fully. Here, recommendations are given on load estimation methodologies for different catchment types sampled at different frequencies, and the ways in which this analysis can be used to identify observational error and uncertainty for model calibration and nutrient budgeting studies. (c) 2006 Elsevier B.V. All rights reserved.

Determining the effect of asymmetric data on the variogram. I. Underlying asymmetry

Matheron's usual variogram estimator can result in unreliable variograms when data are strongly asymmetric or skewed. Asymmetry in a distribution can arise from a long tail of values in the underlying process or from outliers that belong to another population that contaminate the primary process. This paper examines the effects of underlying asymmetry on the variogram and on the accuracy of prediction, and the second one examines the effects arising from outliers. Standard geostatistical texts suggest ways of dealing with underlying asymmetry; however, this is based on informed intuition rather than detailed investigation. To determine whether the methods generally used to deal with underlying asymmetry are appropriate, the effects of different coefficients of skewness on the shape of the experimental variogram and on the model parameters were investigated. Simulated annealing was used to create normally distributed random fields of different size from variograms with different nugget:sill ratios. These data were then modified to give different degrees of asymmetry and the experimental variogram was computed in each case. The effects of standard data transformations on the form of the variogram were also investigated. Cross-validation was used to assess quantitatively the performance of the different variogram models for kriging. The results showed that the shape of the variogram was affected by the degree of asymmetry, and that the effect increased as the size of data set decreased. Transformations of the data were more effective in reducing the skewness coefficient in the larger sets of data. Cross-validation confirmed that variogram models from transformed data were more suitable for kriging than were those from the raw asymmetric data. The results of this study have implications for the 'standard best practice' in dealing with asymmetry in data for geostatistical analyses. (C) 2007 Elsevier Ltd. All rights reserved.

Determining the effect of asymmetric data on the variogram. II. Outliers

Asymmetry in a distribution can arise from a long tail of values in the underlying process or from outliers that belong to another population that contaminate the primary process. The first paper of this series examined the effects of the former on the variogram and this paper examines the effects of asymmetry arising from outliers. Simulated annealing was used to create normally distributed random fields of different size that are realizations of known processes described by variograms with different nugget:sill ratios. These primary data sets were then contaminated with randomly located and spatially aggregated outliers from a secondary process to produce different degrees of asymmetry. Experimental variograms were computed from these data by Matheron's estimator and by three robust estimators. The effects of standard data transformations on the coefficient of skewness and on the variogram were also investigated. Cross-validation was used to assess the performance of models fitted to experimental variograms computed from a range of data contaminated by outliers for kriging. The results showed that where skewness was caused by outliers the variograms retained their general shape, but showed an increase in the nugget and sill variances and nugget:sill ratios. This effect was only slightly more for the smallest data set than for the two larger data sets and there was little difference between the results for the latter. Overall, the effect of size of data set was small for all analyses. The nugget:sill ratio showed a consistent decrease after transformation to both square roots and logarithms; the decrease was generally larger for the latter, however. Aggregated outliers had different effects on the variogram shape from those that were randomly located, and this also depended on whether they were aggregated near to the edge or the centre of the field. The results of cross-validation showed that the robust estimators and the removal of outliers were the most effective ways of dealing with outliers for variogram estimation and kriging. (C) 2007 Elsevier Ltd. All rights reserved.

Direct versus indirect sexual selection: genetic basis of colour, size and recruitment in a wild bird

Indirect and direct models of sexual selection make different predictions regarding the quantitative genetic relationships between sexual ornaments and fitness. Indirect models predict that ornaments should have a high heritability and that strong positive genetic covariance should exist between fitness and the ornament. Direct models, on the other hand, make no such assumptions about the level of genetic variance in fitness and the ornament, and are therefore likely to be more important when environmental sources of variation are large. Here we test these predictions in a wild population of the blue tit (Parus caeruleus), a species in which plumage coloration has been shown to be under sexual selection. Using 3 years of cross-fostering data from over 250 breeding attempts, we partition the covariance between parental coloration and aspects of nestling fitness into a genetic and environmental component. Contrary to indirect models of sexual selection, but in agreement with direct models, we show that variation in coloration is only weakly heritable (h(2) < 0.11), and that two components of offspring fitness-nestling size and fledgling recruitment-are strongly dependent on parental effects, rather than genetic effects. Furthermore, there was no evidence of significant positive genetic covariation between parental colour and offspring traits. Contrary to direct benefit models, however, we find little evidence that variation in colour reliably indicates the level of parental care provided by either males or females. Taken together, these results indicate that the assumptions of indirect models of sexual selection are not supported by the genetic basis of the traits reported on here.

Managing threatened species – the ecological toolbox, evolutionary theory and the declining-population paradigm

1. The management of threatened species is an important practical way in which conservationists can intervene in the extinction process and reduce the loss of biodiversity. Understanding the causes of population declines (past, present and future) is pivotal to designing effective practical management. This is the declining-population paradigm identified by Caughley. 2. There are three broad classes of ecological tool used by conservationists to guide management decisions for threatened species: statistical models of habitat use, demographic models and behaviour-based models. Each of these is described here, illustrated with a case study and evaluated critically in terms of its practical application. 3. These tools are fundamentally different. Statistical models of habitat use and demographic models both use descriptions of patterns in abundance and demography, in relation to a range of factors, to inform management decisions. In contrast, behaviourbased models describe the evolutionary processes underlying these patterns, and derive such patterns from the strategies employed by individuals when competing for resources under a specific set of environmental conditions. 4. Statistical models of habitat use and demographic models have been used successfully to make management recommendations for declining populations. To do this, assumptions are made about population growth or vital rates that will apply when environmental conditions are restored, based on either past data collected under favourable environmental conditions or estimates of these parameters when the agent of decline is removed. As a result, they can only be used to make reliable quantitative predictions about future environments when a comparable environment has been experienced by the population of interest in the past. 5. Many future changes in the environment driven by management will not have been experienced by a population in the past. Under these circumstances, vital rates and their relationship with population density will change in the future in a way that is not predictable from past patterns. Reliable quantitative predictions about population-level responses then need to be based on an explicit consideration of the evolutionary processes operating at the individual level. 6. Synthesis and applications. It is argued that evolutionary theory underpins Caughley’s declining-population paradigm, and that it needs to become much more widely used within mainstream conservation biology. This will help conservationists examine critically the reliability of the tools they have traditionally used to aid management decision-making. It will also give them access to alternative tools, particularly when predictions are required for changes in the environment that have not been experienced by a population in the past.

Aggregation of parasitism risk in an aphid-parasitoid system: Effects of plant patch size and aphid density

Few studies have linked density dependence of parasitism and the tritrophic environment within which a parasitoid forages. In the non-crop plant-aphid, Centaurea nigra-Uroleucon jaceae system, mixed patterns of density-dependent parasitism by the parasitoids Aphidius funebris and Trioxys centaureae were observed in a survey of a natural population. Breakdown of density-dependent parasitism revealed that density dependence was inverse in smaller colonies but direct in large colonies (>20 aphids), suggesting there is a threshold effect in parasitoid response to aphid density. The CV2 of searching parasitoids was estimated from parasitism data using a hierarchical generalized linear model, and CV2>1 for A. funebris between plant patches, while for T. centaureae CV2>1 within plant patches. In both cases, density independent heterogeneity was more important than density-dependent heterogeneity in parasitism. Parasitism by T. centaureae increased with increasing plant patch size. Manipulation of aphid colony size and plant patch size revealed that parasitism by A. funebris was directly density dependent at the range of colony sizes tested (50-200 initial aphids), and had a strong positive relationship with plant patch size. The effects of plant patch size detected for both species indicate that the tritrophic environment provides a source of host density independent heterogeneity in parasitism, and can modify density-dependent responses. (c) 2007 Gessellschaft fur Okologie. Published by Elsevier GmbH. All rights reserved.

On the question of proportionality of the count of observed Scrapie cases and the size of holding

Background: The present paper investigates the question of a suitable basic model for the number of scrapie cases in a holding and applications of this knowledge to the estimation of scrapie-ffected holding population sizes and adequacy of control measures within holding. Is the number of scrapie cases proportional to the size of the holding in which case it should be incorporated into the parameter of the error distribution for the scrapie counts? Or, is there a different - potentially more complex - relationship between case count and holding size in which case the information about the size of the holding should be better incorporated as a covariate in the modeling? Methods: We show that this question can be appropriately addressed via a simple zero-truncated Poisson model in which the hypothesis of proportionality enters as a special offset-model. Model comparisons can be achieved by means of likelihood ratio testing. The procedure is illustrated by means of surveillance data on classical scrapie in Great Britain. Furthermore, the model with the best fit is used to estimate the size of the scrapie-affected holding population in Great Britain by means of two capture-recapture estimators: the Poisson estimator and the generalized Zelterman estimator. Results: No evidence could be found for the hypothesis of proportionality. In fact, there is some evidence that this relationship follows a curved line which increases for small holdings up to a maximum after which it declines again. Furthermore, it is pointed out how crucial the correct model choice is when applied to capture-recapture estimation on the basis of zero-truncated Poisson models as well as on the basis of the generalized Zelterman estimator. Estimators based on the proportionality model return very different and unreasonable estimates for the population sizes. Conclusion: Our results stress the importance of an adequate modelling approach to the association between holding size and the number of cases of classical scrapie within holding. Reporting artefacts and speculative biological effects are hypothesized as the underlying causes of the observed curved relationship. The lack of adjustment for these artefacts might well render ineffective the current strategies for the control of the disease.

Local adaptation in moss life histories: population-level variation and a reciprocal transplant experiment

We examine the extent of population-level differentiation in life history traits of Pogonatum aloides, Polytrichum commune and Polytrichum juniperinum (Polytrichaceae) between upland and lowland localities within Britain. Reciprocal transplant studies are used to estimate the relative importance of genetic versus environmental effects on observed differences. We demonstrate significant life history differentiation between moss populations, and show that at least some of these are genetically determined, although environment and phenotypic plasticity are also significant components of the observed variation. The transplant experiments indicate divergence among populations in plasticity of male reproductive effort and of investment in vegetative shoots by females. Two tradeoffs are identified; one between the number and the size of spores, and the second between reproduction by spores versus vegetative reproduction. The patterns of life history variation observed between populations of Polytrichum juniperinum are consistent with selection along these implied tradeoff curves, and we propose that they reflect selective pressures arising from the spatial and demographic distribution of mortality at upland versus lowland sites. The results underscore the need for more studies of intra-specific life history variation in mosses.