Emerging prion disease drives host selection in a wildlife population

Infectious diseases are increasingly recognized as an important force driving population dynamics, conservation biology, and natural selection in wildlife populations. Infectious agents have been implicated in the decline of small or endangered populations and may act to constrain population size, distribution, growth rates, or migration patterns. Further, diseases may provide selective pressures that shape the genetic diversity of populations or species. Thus, understanding disease dynamics and selective pressures from pathogens is crucial to understanding population processes, managing wildlife diseases, and conserving biological diversity. There is ample evidence that variation in the prion protein gene (PRNP) impacts host susceptibility to prion diseases. Still, little is known about how genetic differences might influence natural selection within wildlife populations. Here we link genetic variation with differential susceptibility of white-tailed deer to chronic wasting disease (CWD), with implications for fitness and disease-driven genetic selection. We developed a single nucleotide polymorphism (SNP) assay to efficiently genotype deer at the locus of interest (in the 96th codon of the PRNP gene). Then, using a Bayesian modeling approach, we found that the more susceptible genotype had over four times greater risk of CWD infection; and, once infected, deer with the resistant genotype survived 49% longer (8.25 more months). We used these epidemiological parameters in a multi-stage population matrix model to evaluate relative fitness based on genotype-specific population growth rates. The differences in disease infection and mortality rates allowed genetically resistant deer to achieve higher population growth and obtain a long-term fitness advantage, which translated into a selection coefficient of over 1% favoring the CWD-resistant genotype. This selective pressure suggests that the resistant allele could become dominant in the population within an evolutionarily short time frame. Our work provides a rare example of a quantifiable disease-driven selection process in a wildlife population, demonstrating the potential for infectious diseases to alter host populations. This will have direct bearing on the epidemiology, dynamics, and future trends in CWD transmission and spread. Understanding genotype-specific epidemiology will improve predictive models and inform management strategies for CWD-affected cervid populations.     

The effects of aggregation on the performance of the inverse method and indicators of network analysis

Food webs are usually aggregated into a manageable size for their interpretation and analysis. The aggregation of food web components in trophic or other guilds is often at the choice of the modeler as there is little guidance in the literature as to what biases might be introduced by aggregation decisions. We examined the impacts of the choice of the a priori model on the subsequent estimation of missing flows using the inverse method and on the indices derived from ecological network analysis of both inverse method-derived flows and on the actual values of flows, using the fully determined Sylt-Rømø Bight food web model. We used the inverse method, with the least squares minimization goal function, to estimate ‘missing’ values in the food web flows on 14 aggregation schemes varying in number of compartments and in methods of aggregation. The resultant flows were compared to known values; the performance of the inverse method improved with increasing number of compartments and with aggregation based on both habitat and feeding habits rather than diet similarity. Comparison of network analysis indices of inverse method-derived flows with that of actual flows and the original value for the unaggregated food web showed that the use of both the inverse method and the aggregation scheme affected indices derived from ecological network analysis. The inverse method tended to underestimate the size and complexity of food webs, while an aggregation scheme explained as much variability in some network indices as the difference between inverse-derived and actual flows. However, topological network indices tended to be most robust to both the method of determining flows and to the inverse method. These results suggest that a goal function other than minimization of flows should be used when applying the inverse method to food web models. Comparison of food web models should be done with extreme care when different methodologies are used to estimate unknown flows and to aggregate system components. However, we propose that indices such as relative ascendency and relative redundancy are most valuable for comparing ecosystem models constructed using different methodologies for determining missing flows or for aggregating system components.     

目前针对水环境化学品风险评估的方法是正确的么？

我们想要保护水生生态环境,通过测试数以千计的化学物质和成百上千的水生物种之间交互作用,得到成千上万的结果,但仍然不可能考虑到所有物质的混合情况。污染物对野生鱼类的内分泌干扰作用的课题推动了人们对如药物之类的微污染物的研究。尽管我们担心鱼类会因污染而繁殖能力下降,但并没有足够的证据表明鱼类种群处于危险之中。事实上,许多鱼类生物学家认为,在过去的30 - 40年里,鲤科的数量已经在逐步恢复中。目前的风险评估的关键在于其核心假设,也就是实验室观测或者模型预测的结果简单地适用于群体水平,显而易见这个假设是值得质疑的。 我们明白了疏于监测野生动物种群的变化成为了我们的环境保护战略的关键弱点。如果我们不知道水生野生动物物种是在减少或增加,那么我们研究的其他生态毒理行为又有多少价值呢？
精选自Andrew C. Johnson, John P. Sumpter. Are we going about chemicals risk assessment for the aquatic environment the wrong way?. Environmental Toxicology and Chemistry: Volume 35, Issue 7, pages 1609–1616, July 2016. DOI: 10.1002/etc.3441
详情请见http://onlinelibrary.wiley.com/doi/10.1002/etc.3441/full
     

Participatory assessment of soil degradation in the uplands of southwestern Tanzania: Implications for sustainable agriculture and rural livelihoods

Rural household food insecurity and poverty are closely linked to soil degradation in Sub-Saharan Africa. However, causes, degradation processes, coping strategies and need for interventions may vary from one place to another. This study was conducted in Mbinga District, SW Tanzania, to investigate causes and biophysical processes of soil degradation; effects on livelihoods, coping strategies and entry points for interventions. Implications for sustainable production and rural livelihoods are discussed. Participatory Rural Appraisal (PRA), household surveys using a short open-ended questionnaire and biophysical exploration were the research tools used. Soil fertility depletion resulting from continuous cropping and erosion losses is the main form of soil degradation. Maize yield was 57% lower in fertility-depleted farms than in productive farms. Soil pH, Ca²⁺, Mg²⁺ and CEC accounted for 79% of variations in maize yield. Organic soil fertility amelioration was a common strategy used by smallholders. Use of beneficial tree and shrub fallows is the most environmentally, economically and socially promising improvement that can be used to build on the existing strengths of farmers' knowledge and strategies. Subsidy for the right type of fertilizers, infrastructure improvement and education of farmers on proper use of fertilizers should significantly contribute to improved and sustainable production and livelihoods.     

Asexual viviparity and population genetics of Actinia tenebrosa

The intertidal anemone Actinia tenebrosa is viviparous. An electrophoretic study of 3 polymorphic enzymes in Western Australian populations has confirmed genetic identity of adults and their brood young, indicating asexual reproduction. The population effects of this clonal reproduction are seen as linkage disequilibrium and departures from Hardy-Weinberg equilibrium within populations, and large differences between populations. The data also suggest occasional sexual reproduction, and the likelihood of a mixture of reproductive modes in this species.     

Concordance of genetic and fin photo identification in the great white shark, Carcharodon carcharias, off Mossel Bay, South Africa

Visual identification of naturally acquired marks has been a popular if subjective method of animal identification and population estimation over the last 40 years. Molecular genetics has also independently developed objective individual marking techniques during the same period. Here, we assess the concordance of individual great white shark (Carcharodon carharias) dorsal fin recognition and identification, using seven microsatellite loci as the independent unbiased arbiter, over a period of 5 years. As a monitoring technique, fin photographs offer a very good individual identification key for white sharks over a relatively short period of time (5 years), matching with genetic data in about 85% of cases, whilst caution and a continuously updated database is required for animal recognition over a longer period.