Generalized site occupancy models allowing for false positive and false negative errors

Site occupancy models have been developed that allow for imperfect species detection or "false negative" observations. Such models have become widely adopted in surveys of many taxa. The most fundamental assumption underlying these models is that "false positive" errors are not possible. That is, one cannot detect a species where it does not occur. However, such errors are possible in many sampling situations for a number of reasons, and even low false positive error rates can induce extreme bias in estimates of site occupancy when they are not accounted for. In this paper, we develop a model for site occupancy that allows for both false negative and false positive error rates. This model can be represented as a two-component finite mixture model and can be easily fitted using freely available software. We provide an analysis of avian survey data using the proposed model and present results of a brief simulation study evaluating the performance of the maximum-likelihood estimator and the naive estimator in the presence of false positive errors.     

Estimating species richness and accumulation by modeling species occurrence and detectability

A statistical model is developed for estimating species richness and accumulation by formulating these community-level attributes as functions of model-based estimators of species occurrence while accounting for imperfect detection of individual species. The model requires a sampling protocol wherein repeated observations are made at a collection of sample locations selected to be representative of the community. This temporal replication provides the data needed to resolve the ambiguity between species absence and nondetection when species are unobserved at sample locations. Estimates of species richness and accumulation are computed for two communities, an avian community and a butterfly community. Our model-based estimates suggest that detection failures in many bird species were attributed to low rates of occurrence, as opposed to simply low rates of detection. We estimate that the avian community contains a substantial number of uncommon species and that species richness greatly exceeds the number of species actually observed in the sample. In fact, predictions of species accumulation suggest that even doubling the number of sample locations would not have revealed all of the species in the community. In contrast, our analysis of the butterfly community suggests that many species are relatively common and that the estimated richness of species in the community is nearly equal to the number of species actually detected in the sample. Our predictions of species accumulation suggest that the number of sample locations actually used in the butterfly survey could have been cut in half and the asymptotic richness of species still would have been attained. Our approach of developing occurrence-based summaries of communities while allowing for imperfect detection of species is broadly applicable and should prove useful in the design and analysis of surveys of biodiversity.     

不同碳源条件下草菇内切型纤维素酶基因（eg1）转录表达的分析

利用Northernblot方法分析了不同碳源条件下草菇切型纤维素酶基因(eg1)的表达.结果发现,在含有纤维素的液体培养基中生长10d,eg1在草菇菌丝中有高效表达;纤维二糖、α-乳糖、β-乳糖,也能诱导eg1的表达,但和纤维素相比,eg1的表达量相对较低,并且它们的诱导效应在加入这类糖12h后迅速减弱;槐糖和龙胆二糖的诱导作用非常弱.在天然稻草为基质的固体栽培料生长时,草菇eg1的表达和草菇菌丝生长与出菇相对应,在菌丝生长期(d8)可见eg1的表达,d12时菌丝已长满,表达减弱,在出菇及菇体的分化及增大期,eg1的表达量逐渐增强,在成熟期达到最高水平;表明在草菇菇体发育中需要更多碳源及能源的补充,eg1在这方面起着非常重要的作用.图4参14     

A hierarchical model for spatial capture-recapture data

Estimating density is a fundamental objective of many animal population studies. Application of methods for estimating population size from ostensibly closed populations is widespread, but ineffective for estimating absolute density because most populations are subject to short-term movements or so-called temporary emigration. This phenomenon invalidates the resulting estimates because the effective sample area is unknown. A number of methods involving the adjustment of estimates based on heuristic considerations are in widespread use. In this paper, a hierarchical model of spatially indexed capture-recapture data is proposed for sampling based on area searches of spatial sample units subject to uniform sampling intensity. The hierarchical model contains explicit models for the distribution of individuals and their movements, in addition to an observation model that is conditional on the location of individuals during sampling. Bayesian analysis of the hierarchical model is achieved by the use of data augmentation, which allows for a straightforward implementation in the freely available software WinBUGS. We present results of a simulation study that was carried out to evaluate the operating characteristics of the Bayesian estimator under variable densities and movement patterns of individuals. An application of the model is presented for survey data on the flat-tailed horned lizard (Phrynosoma mcallii) in Arizona, USA.     

Metal and oxalate contamination in a suburban watershed in the greater Toronto area: the benefits of combining acid leach and selective extraction procedures

Environmentally available concentrations of Fe, Mn, Zn, Cu, Pb, Cr and Ni in soils and sediments from a small suburban catchment, obtained using an acid leach procedure, are compared to the Ontario Ministry of the Environment lowest effect level (LEL) and severe effect levels (SEL) and to Provincial sediment quality guidelines (PSQG's). These data are then compared to the bioavailability, potential bioavailability and non-bioavailability of the same metals, plus oxalate concentration, identified using a selective extraction procedure. This combination of techniques enhanced analytical interpretation with respect to metal mobility and potential metal contamination. Selective extraction highlighted the presence of oxalate as a potential contaminant, especially in poorly drained valley floor deposits (33,633 mg kg(-1) and 26,284 mg kg(-1)) and lakeshore sediments (27,095 mg kg(-1) and 13,729 mg kg(-1)). These levels are considerably in excess of those previously documented in a similar study from Rio de Janeiro, where contamination of urban sediment by sewage is a recognised environmental problem, and could possibly be used both as an indicator of similar contamination and the identification of those areas that warrant further investigation.     

Reserve design to optimize functional connectivity and animal density

Ecological distance-based spatial capture–recapture models (SCR) are a promising approach for simultaneously estimating animal density and connectivity, both of which affect spatial population processes and ultimately species persistence. We explored how SCR models can be integrated into reserve-design frameworks that explicitly acknowledge both the spatial distribution of individuals and their space use resulting from landscape structure. We formulated the design of wildlife reserves as a budget-constrained optimization problem and conducted a simulation to explore 3 different SCR-informed optimization objectives that prioritized different conservation goals by maximizing the number of protected individuals, reserve connectivity, and density-weighted connectivity. We also studied the effect on our 3 objectives of enforcing that the space-use requirements of individuals be met by the reserve for individuals to be considered conserved (referred to as home-range constraints). Maximizing local population density resulted in fragmented reserves that would likely not aid long-term population persistence, and maximizing the connectivity objective yielded reserves that protected the fewest individuals. However, maximizing density-weighted connectivity or preemptively imposing home-range constraints on reserve design yielded reserves of largely spatially compact sets of parcels covering high-density areas in the landscape with high functional connectivity between them. Our results quantify the extent to which reserve design is constrained by individual home-range requirements and highlight that accounting for individual space use in the objective and constraints can help in the design of reserves that balance abundance and connectivity in a biologically relevant manner.     

Changing contaminant mobility in a dredged canal sediment during a three-year phytoremediation trial

Metal mobility and degradation of organic pollutants were investigated in a contaminated canal sediment in NW England. Sediment was dredged and exposed above the water surface, planted with multiple taxa of Salix, Populus and Alnus and monitored over 32 months. Short-term metal fractionation and phytotoxicity during sediment oxidation were also evaluated in separate laboratory studies. Zinc and Pb redistributed into more mobile fractions, which increased toxicity of the sediment to plants in the laboratory. In contrast, at the canal site, mobility of most elements decreased and total concentrations of Zn, Pb, Cu and Cd fell. Petroleum hydrocarbon concentrations decreased, but the tree-planted treatments appeared less effective at reducing PAH concentrations than treatments colonised by invasive plants. Tree survivorship decreased over time, suggesting increasing phytotoxicity of the exposed sediment in the longer term. Trees provided little benefit in terms of sediment remediation. Options for future management of the sediment are evaluated.