Epidemiology and strategy for the control of halo-blight of beans

A halo-blight epidemic model based on the equation of Van der Plank (1963) is described. The model has been used to determine tolerance levels for seed infection and to compare the effectiveness of chemical control measures based on foliar sprays and seed treatments.
Reduction of primary inoculum, derived from infected seed, by disease exclusion through seed testing, or by chemical seed treatment will give effective disease control under British conditions (i.e. with an expected apparent infection rate ( r ) of 0.15 per infected plant per day). Under climatic conditions more favourable for the disease where higher r values would occur, control treatments directed against primary inoculum only would be less effective. Under such conditions, it is predicted that chemical sprays, which have no effect on primary inoculum but cause a reduction in the rate of disease increase, would be more effective. The most effective disease control, however, would be a combination of treatments.     

Effects of patch characteristics and isolation on relative abundance of the scarce heath butterfly <Emphasis Type="Italic">Coenonympha hero</Emphasis> (Nymphalidae)

The scarce heath (Coenonympha hero) is an internationally threatened butterfly in Western Europe, where it occurs primarily on hay fields and abandoned arable land in a small-scale agricultural landscape of south-central Scandinavia. Due to afforestation, this habitat is becoming increasingly fragmented in Sweden, and it can be expected that the scarce heath will decline abruptly when threshold conditions for metapopulation persistence are no longer met. We used stepwise polychotomous logistic regression to compare habitat characteristics and isolation measures for patches that harbour large, small or no populations, respectively, in an area of south-western Sweden. We found that patch area, distance to the nearest large population and amount of Galium spp. explained a significant part of the variation in relative abundance among patches. Distance to nearest large population resulted in a better model to predict occupancy than both distance to the nearest inhabited patch and connectivity, which suggests that primarily large populations act as sources for small satellite populations. Today, sites of three of the eight larger populations in the study area have been planted with spruce or pine and will disappear within 20 years. We argue that the disappearance of these patches may very well lead to rapid extinction of the whole metapopulation system.     

Use of restriction fragment length polymorphisms for genetic counseling: Population genetic considerations

Two-locus population genetic models are analyzed to evaluate the utility of restriction fragment length polymorphisms for purposes of genetic counseling. It is shown that the linkage disequilibrium between a neutral marker and a tightly linked overdominant mutant will increase rapidly as the mutant moves to its polymorphic equilibrium. The linkage disequilibrium decays for deleterious recessive mutants. Two measures involving the linkage disequilibrium are investigated to determine how much information the transmission of the neutral marker provides about the transmission of the selected gene. In certain kinds of matings, where the parental two-locus genotypes and linkage phases are known, it is possible to determine whether or not a progeny is homozygous for the selected gene on the basis of the fetal genotype at the marker locus. A quantity of primary interest is the fraction of matings between individuals heterozygous for the selected gene in which exact diagnosis can be made in this way. The expected proportion of such matings, taken over all two-locus matings involving heterozygotes at the selected locus, is calculated as a function of the gene frequencies at the two loci and the linkage disequilibrium between them. This expected value is maximized when the linkage disequilibrium is at its maximum in absolute value. Fewer than half of all matings are informative if the linkage disequilibrium is small in magnitude or if the gene frequencies at the two loci are quite different. Consideration is also given to various conditional measures of association that may be useful when the parental two-locus genotypes are unknown. The results suggest that the utility of tightly linked neutral marker genes in predicting the transmission of a selected gene is generally less when selection acts against a recessive gene than for overdominant selection.     

Indicators of the Ecological Impact of Bottom-Trawl Disturbance on Seabed Communities

The Ecosystem Approach to Fisheries requires that managers take account of the environmental impacts of fishing. We develop linked state and pressure indicators that show the impact of bottom-trawling on benthic communities. The state indicator measures the proportion of an area where benthic invertebrate biomass (B) or production (P) is more than 90% of pristine benthic biomass (B _0.9) or production (P_0.9). The pressure indicator measures the proportion of the area where trawling frequency is sufficiently high to prevent reaching predicted B_0.9 or P_0.9. Time to recovery to B_0.9 and P_0.9 after trawling, depending on the habitat, was estimated using a validated size-based model of the benthic community. Based on trawling intensity in 2003, 53.5% of the southern North Sea was trawled too frequently for biomass to reach B_0.9, and 27.1% was trawled too frequently for production to reach P_0.9. As a result of bottom-trawling in 2003, in 56% of the southern North Sea benthic biomass was below B_0.9, whereas in 27% of the southern North Sea benthic production was below P_0.9. Modeled recovery times were comparable to literature estimates (2.5 to more than 6 years). The advantages of using the area with an ecological impact of trawling as a pressure indicator are that it is conceptually easy to understand, it responds quickly to changes in management action, it can be implemented at a relevant scale for fisheries management, and the necessary effort distribution data are centrally collected. One of this approach’s greatest utilities, therefore, will be to communicate to policy makers and fishing enterprises the expected medium- to long-term ecological benefits that will accrue if the frequency of trawling in particular parts of fishing grounds is reduced.     

Using model selection to choose a size-based condition index that is consistent with operational welfare indicators

Quantitative and qualitative measures of fish health and welfare are essential for management of both wild capture and aquaculture species. These measures include morphometric body condition indices, energetic condition and aquaculture operational welfare indicators (OWIs). Measures vary in ease of measurement (and may require destructive sampling), and it is critical to know how well they correlate with fish health and welfare so appropriate management decisions can be based on them. Lumpfish (Cyclopterus lumpus) is a new farming species that needs nondestructive OWIs to be developed and validated. In this study, we developed a C. lumpus fin damage score. Four different body condition indexes based on individual weight relative to either length–weight relationships or relative to other fish in its local environment were tested (using model selection) as predictors of individual fin damage. Results showed severity of fin damage was predicted by small size relative to the other individuals in the tank or cage. Body condition based on length–weight relationship was not found to predict fin damage, indicating that using established indices from fisheries or from other species would not predict welfare risks from fin damage. Implications are that especially in hatchery conditions grading will improve the condition index, and is expected to mitigate fin damage, but that low weight at length was not of use in predicting fin damage. Model selection to choose between a suite of possible indices proved powerful and should be considered in other applications where an easily measured index is needed to correlate with other health measures.     

Life history patterns and ecology of macaque species

Macaques are found both in broadleaf evergreen forest and in more variable habitats. The former group might be expected to be subject to less variability in their environment and hence to suffer lower rates of density independent mortality. Life history evolution models predict that species in such conditions will have lower rates of development and breeding than those found in more variable habitats where density independent mortality is high. This prediction is tested here by comparing the breeding and development rates of nine species of macaque. Although measures of developmental rate are not found to vary in a predictable way with habitat, measures of breeding rate do correlate with habitat categories used. As predicted, species that are found in more variable habitats tend to have higher birth rates and a higher intrinsic rate of natural increase than do species in more stable, forest habitats. Contrary to prediction selection does not always act to produce an early age at first reproduction in macaques living in seasonal environments. This is discussed with relation to physiological and environmental constraints.     

The inexorable spread of a newly arisen neo-Y chromosome

A newly arisen Y-chromosome can become established in one part of a species range by genetic drift or through the effects of selection on sexually antagonistic alleles. However, it is difficult to explain why it should then spread throughout the species range after this initial episode. As it spreads into new populations, it will actually enter females. It would then be expected to perform poorly since it will have been shaped by the selective regime of the male-only environment from which it came. We address this problem using computer models of hybrid zone dynamics where a neo-XY chromosomal race meets the ancestral karyotype. Our models consider that the neo-Y was established by the fusion of an autosome with the ancestral X-chromosome (thereby creating the Y and the ‘fused X’). Our principal finding is that sexually antagonistic effects of the Y induce indirect selection in favour of the fused X-chromosomes, causing their spread. The Y-chromosome can then spread, protected behind the advancing shield of the fused X distribution. This mode of spread provides a robust explanation of how newly arisen Y-chromosomes can spread. A Y-chromosome would be expected to accumulate mutations that would cause it to be selected against when it is a rare newly arrived migrant. The Y can spread, nevertheless, because of the indirect selection induced by gene flow (which can only be observed in models comprising multiple populations). These results suggest a fundamental re-evaluation of sex-chromosome hybrid zones. The well-understood evolutionary events that initiate the Y-chromosome's degeneration will actually fuel its range expansion.     

Estimating and comparing the rates of gene discovery and expressed sequence tag (EST) frequencies in EST surveys

MOTIVATION: Expressed sequence tag (EST) surveys are an efficient way to characterize large numbers of genes from an organism. The rate of gene discovery in an EST survey depends on the degree of redundancy of the cDNA libraries from which sequences are obtained. However, few statistical methods have been developed to assess and compare redundancies of various libraries from preliminary EST surveys. RESULTS: We consider statistics for the comparison of EST libraries based upon the frequencies with which genes occur in subsamples of reads. These measures are useful in determining which one of several libraries is more likely to yield new genes in future reads and what proportion of additional reads one might want to take from the libraries in order to be likely to obtain new genes. One approach is to compare single sample measures that have been successfully used in species estimation problems, such as coverage of a library, defined as the proportion of the library that is represented in the given sample of reads. Another single library measure is an estimate of the expected number of additional genes that will be found in a new sample of reads. We also propose statistics that jointly use data from all the libraries. Analogous formulas for coverage and the expected numbers of new genes are presented. These measures consider coverage in a single library based upon reads from all libraries and similarly, the expected numbers of new genes that will be discovered by taking reads from all libraries with fixed proportions. Together, the statistics presented provide useful comparative measures for the libraries that can be used to guide sampling from each of the libraries to maximize the rate of gene discovery. Finally, we present tests for whether genes are equally represented or expressed in a set of libraries. Binomial and chi2 tests are presented for gene-by-gene comparisons of expression. Overall tests of the equality of proportional representation are presented and multiple comparisons issues are addressed. These methods can be used to evaluate changes in gene expression reflected in the composition of EST libraries prepared from different tissue types or cells exposed to different environmental conditions. AVAILABILITY: Software will be made available at http://www.mathstat.dal.ca/~tsusko     

How long before a change in soil organic carbon can be detected?

When planning sampling in an experiment where soil organic carbon (SOC) content is expected to change, it is necessary to know how many samples will need to be taken to demonstrate a change in SOC and after how long this change will be detectable. Much has been published on the number of samples required to demonstrate the minimum detectable difference in SOC, but less on how long it takes for this change to be detectable. In this paper, a model of SOC dynamics is used to estimate the minimum time taken for a change in total SOC content to become measurable under different carbon inputs, land uses and soil types. For free air carbon dioxide enrichment (FACE), and other experiments in which SOC is expected to increase, relationships between the percentage change in C inputs and the time taken to measure a change in SOC are presented, for two levels of sampling intensity corresponding to the maximum that is practically possible in most experiments (～100 samples) and that used regularly in field experiments (10–20 samples). In FACE experiments, where C inputs increase by a maximum of about 20–25%, SOC change could be detected with 90% confidence after about 6–10 years if a sampling regime allowing 3% change in background SOC level (probably requiring a very large number of samples) were used, but could not be detected at all if a sampling regime were used that allowed only a 15% change in background SOC to be detected. If increases in C inputs are much below 15%, it might not be possible to detect a change in soil C without an enormous number of samples. Relationships between the change in C inputs and the time taken to measure a change in SOC are robust over a range of soil types and land uses. The results demonstrate how models of SOC dynamics can be used to complement statistical power analyses for planning when, and how intensively, to sample soils during experiments. An advantage of the modelling approach demonstrated here is that estimates of the minimum time taken for a change in soil carbon to become detectable can be made, even before any detailed soil samples are taken, simply from estimates of the likely increase in carbon inputs to the soil (via expected changes in net primary production).     

Dragonfly Assemblages in Arid Tropical Environments: A Case Study from Western Namibia

Dragonflies have been proposed as indicators for the ecosystem health of freshwater wetlands. For their useful functioning as indicators it is, however, necessary to identify species compositions in specific habitats and species-habitat associations, particularly in the tropics, where such knowledge is still weak. We examined the dragonfly species composition of 133 localities in the arid environment of western Namibia. An analysis of nestedness indicated that distinct, and predictable patterns of species associations can be expected. Discriminant analyses revealed that most of the nine habitat types separated by structural and hydrological parameters are well discriminated by their dragonfly assemblages. Spring brooks in particular host a specific assemblage, which is threatened due to the habitat restriction of several species, as well as by recent habitat loss and degradation. Using a hierarchical method of several criteria we demonstrated the selection of a set of potential indicator species from the species set, most of these being useful indicators for spring brook assemblages. The conservation status of certain habitats and species is discussed. We propose that dragonflies will have a high indicator potential for threatened freshwater wetlands in such areas and may also serve as an indication of the sustainable use of water resources including evaluating measures to rehabilitate environments.     

A comparison of linkage disequilibrium patterns and estimated population recombination rates across multiple populations

Large-scale studies of linkage disequilibrium (LD) have shown considerable variation in the extent and distribution of pairwise LD within and between populations. Taken at face value, these results suggest that genomewide LD maps for one population may not be generalizable to other populations. However, at least part of this diversity is due to some undesirable features of pairwise LD measures, which are well documented for the D' and r2 measures. In this report, we compare patterns of LD derived from pairwise measures with statistical estimates of population recombination rates ( rho ) along a 10-Mb stretch of chromosome 20 in four population samples, comprising East Asians, African Americans, and U.K. and U.S. individuals of western European descent. The results reveal the expected variability of D' within and between populations but show better concordance in estimates of r2 for the same markers across the population samples. Estimates of rho correlate well across populations, but there is still evidence of population-specific spikes and troughs in rho values. We conclude that it is unlikely that a single haplotype map will provide a definitive guide for association studies of many populations; rather, multiple maps will need to be constructed to provide the best-possible guides for gene mapping.     

A general multivariate approach to linear modeling in human genetics.

The general linear structural equation model is applied to problems in human genetics where there may be more than one measured phenotype per individual. A modeling convention, termed conditional associations, is developed to extend the general linear model so that it can handle the unique problems in human genetic models that arise from the pairing up of individuals or families under assortment between mates and the assortative placement of adoptees. Formulas are presented to generate expected covariance matrices for assortment or assortative placement on many variables simultaneously. It is demonstrated that all linear models in human genetics can be reduced in form to two fundamental equations. An algorithm is presented that will allow the application of these two equations to linear modeling in human genetics.     

TREATMENT NEEDS IN HIV PREVENTION TRIALS: USING BENEFICENCE TO CLARIFY SPONSOR‐INVESTIGATOR RESPONSIBILITIES

Some participants will get HIV‐infected in HIV prevention trials, despite risk reduction measures. The subsequent treatment responsibilities of sponsor‐investigators have been widely debated, especially where access to antiretroviral therapy (ART) is not available. In this paper, we explore two accounts of beneficence to establish whether they can shed light on sponsor‐investigator responsibilities. We find the notion of general beneficence helpful insofar as it clarifies that some beneficent actions will be obligatory where they can be dispensed without scuppering the trial. We find the notion of specific beneficence helpful insofar as it directs investigators to attend to the needs of trial participants; however the range of interventions that could be provided remains unhelpfully broad. We then examine accounts of the investigator‐participant relationship to narrow the range of interventions that investigators should provide, concluding that health‐care, and HIV infection, are appropriate foci. We conclude that when investigators are able to meet the ART needs of their participants (e.g. referral, assisted referral or direct provision) without sacrificing trial quality, they must do so. However, there is little of this explicit direction to be found in the account of specific beneficence itself, but rather it is found in accounts of the relationship that are compatible with beneficence.     

Implementing the Habitats Directive: How science can support decision making

The overall goal of the Habitats Directive is to maintain or restore natural habitats and species in a favourable conservation status. An important role in the implementation process is assigned to science. For three core elements, defining the favourable conservation status, development of best practice measures, and monitoring of the conservation status, we outline how science can support decision making. To do so, we use experiences from the ongoing process in Flanders (northern Belgium). First, when determining the favourable conservation status, information on reference values are embedded in a specifically developed calibration model where thresholds on range, area, and quality are set for habitats. Subsequently, socio-economical requirements are taken into consideration, without compromising the favourable conservation status. When it comes to conducting measures, science adds to the knowledge on developing and optimizing cost-effective conservation and restoration management measures. Finally, monitoring of the conservation status will be based on the principle of statistically sound methodologies, enabling the identification of reliability in the assessments made. For habitats, information on area will be gathered through a surface-covering mapping, while quality will be assessed via a sample-oriented monitoring scheme. For species, maximal collaboration with non-governmental organisations will be undertaken, with scientific support on data recording and processing. Overall, the obtained insights will help policy makers to define the framework and set priorities, take the appropriate measures, and keep a finger on the pulse through monitoring data.     

The Ethics of Antenatal Screening: Lessons from Canute

Modern medicine has given us the power to identify many diseases before they occur and apply preventative measures so that morbidity and mortality may be avoided. When these screening measures are offered to someone who is capable of making an informed decision to proceed, they may be uncontroversial but may actually cause more harm than good. In antenatal screening, it is difficult to define who the patient is, because there are several possibilities: the pregnant woman, the foetus, or the family. Consequently, it can be difficult to identify whether the treatment offered is in the best interest of all concerned. Our growing knowledge about the human genome will in future give us more power to be able to identify undesirable traits, but there is no strict definition where the line of acceptability lies. The eugenic excesses of the mid-20^th century are often cited as a reason why antenatal screening is bad. The story of King Canute informs us that defining a ‘line in the sand’ cannot prevent the rising tide of medical capability overwhelming any arbitrary level of acceptability. This paper discusses the history of eugenics from Sparta to the modern day and attempts to give some perspective on this crucial policy area. No one paper can provide the answer: it is necessary that society as a whole debates where it wishes to go…     

On the increasing threat of extermination of the unique Caspian sturgeon populations and the urgent measures required to save them.

Sturgeon populations in the Caspian Sea are now in serious danger of extinction. This is primarily a result of reduced natural recruitment following a deterioration in the quality of habitats in both the river and the sea, combined with irrational fishing activities. Within this context, the desire of the newly-arisen Republics bordering the Caspian to re-open the sturgeon fishery in the sea has absolutely no scientific foundation and will prove to be an ecological disaster. There is an urgent need to conclude the International Agreement between Russia, Kazakhstan, Azerbaijan, Turkmenistan and Iran on the conservation, reproduction and rational exploitation of the Caspian sturgeon. The bases for this agreement must be (1) recognition of the fact that sturgeon populations are sustained by an ecosystem that comprises the entire Caspian Sea and the rivers that flow into it (primarily the Volga); (2) an absolute ban on uncontrolled fishing for sturgeon in the sea, and (3) that national fishing quotas must reflect the real contribution of a particular state to overall sturgeon stocks. Without adequate measures to save them, it is to be expected that the unique runs of Caspian sturgeons will be exterminated within 5–1 years.     

从化街良高速公路建设中的水土流失及防治

高速公路不仅推动了我国经济的发展,而且给人类的生活带来了极大的方便。然而,高速公路建设也会引起水土流失以及生态环境的破坏。论文对街良高速公路建设项目施工期的水土流失进行了分析并对公路建设期间新增的水土流失量进行了预测。选择了美国通用土壤流失方程预测了公路施工期工程占地的新增土壤流失量。经预测,施工期新增的水土流失总量为81.2×10³t。然后根据项目建设自身的特点,对项目区的水土流失进行分区防治,并且分别提出相应的防治措施,这些水土保持措施实施后,预计能控制115.8×10³t的土壤的流失。     

An explicit model for the inbreeding load in the evolutionary analysis of selfing

I present analytical predictions for the equilibrium inbreeding load expected in a population under mutation, selection, and a regular mating system for any population size and for any magnitude and recessivity of the deleterious effects. Using this prediction, I deduce the relative fitness of mutant alleles with small effect on selfing to explore the situations where selfing or outcrossing are expected to evolve. The results obtained are in agreement with previous literature, showing that natural selection is expected to lead to stable equilibria where populations show either complete outcrossing or complete selfing, and that selfing is promoted by large deleterious mutation rates. I find that the evolution of selfing is favored by a large recessivity of deleterious effects, while the magnitude of homozygous deleterious effects only becomes relevant in relatively small populations. This result contradicts the standard assumption that purging in large populations will only promote selfing when homozygous deleterious effects are large, and implies that previously published results obtained assuming lethal mutations in large populations can be extrapolated to nonlethal alleles of similar recessivity. This conclusion and the general approach used in this analysis can be useful in the study of the evolution of mating systems.     

The prospect for international regulatory interventions in embryo transfer and reproductive technologies in the next century

Historically, international regulatory interventions in the area of animal reproductive technologies have focused on the need for mitigation against the dissemination of diseases with the movement of genetics and germplasm across international borders. The continued globalization of agriculture under the Sanitary/Phytosanitary (SPS) Agreement of the World Trade Organization (WTO) ensures that disease considerations arising from third and fourth generation reproductive technologies such as in vitro fertilized embryos, transgenics and xenotransplantation will continue to give rise to animal health regulatory measures. Furthermore, in the aftermath of the raising of the public consciousness and the ensuing consumer confidence crisis concerning animal husbandry and livestock production practices following the Bovine Spongiform Encephalopathy outbreak, evolving societal values are expected to expand regulatory considerations to address veterinary public health and ethical concerns. Consequently, it is expected that the role of the International Embryo Transfer Society in fostering meaningful dialogue and profiling of the research necessary to provide for appropriate science based regulation development will increase in importance.