Evaluation of Scat Deposition Transects versus Radio Telemetry for Developing a Species Distribution Model for a Rare Desert Carnivore,the Kit Fox

Development and evaluation of noninvasive methods for monitoring species distribution and abundance is a growing area of ecological research. While noninvasive methods have the advantage of reduced risk of negative factors associated with capture, comparisons to methods using more traditional invasive sampling is lacking. Historically kit foxes (Vulpes macrotis) occupied the desert and semi-arid regions of southwestern North America. Once the most abundant carnivore in the Great Basin Desert of Utah, the species is now considered rare. In recent decades, attempts have been made to model the environmental variables influencing kit fox distribution. Using noninvasive scat deposition surveys for determination of kit fox presence, we modeled resource selection functions to predict kit fox distribution using three popular techniques (Maxent, fixed-effects, and mixed-effects generalized linear models) and compared these with similar models developed from invasive sampling (telemetry locations from radio-collared foxes). Resource selection functions were developed using a combination of landscape variables including elevation, slope, aspect, vegetation height, and soil type. All models were tested against subsequent scat collections as a method of model validation. We demonstrate the importance of comparing multiple model types for development of resource selection functions used to predict a species distribution, and evaluating the importance of environmental variables on species distribution. All models we examined showed a large effect of elevation on kit fox presence, followed by slope and vegetation height. However, the invasive sampling method (i.e., radio-telemetry) appeared to be better at determining resource selection, and therefore may be more robust in predicting kit fox distribution. In contrast, the distribution maps created from the noninvasive sampling (i.e., scat transects) were significantly different than the invasive method, thus scat transects may be appropriate when used in an occupancy framework to predict species distribution. We concluded that while scat deposition transects may be useful for monitoring kit fox abundance and possibly occupancy, they do not appear to be appropriate for determining resource selection. On our study area, scat transects were biased to roadways, while data collected using radio-telemetry was dictated by movements of the kit foxes themselves. We recommend that future studies applying noninvasive scat sampling should consider a more robust random sampling design across the landscape (e.g., random transects or more complete road coverage) that would then provide a more accurate and unbiased depiction of resource selection useful to predict kit fox distribution.     

Mark-Recapture and Mark-Resight Methods for Estimating Abundance with Remote Cameras: A Carnivore Case Study

Abundance estimation of carnivore populations is difficult and has prompted the use of non-invasive detection methods, such as remotely-triggered cameras, to collect data. To analyze photo data, studies focusing on carnivores with unique pelage patterns have utilized a mark-recapture framework and studies of carnivores without unique pelage patterns have used a mark-resight framework. We compared mark-resight and mark-recapture estimation methods to estimate bobcat (Lynx rufus) population sizes, which motivated the development of a new "hybrid" mark-resight model as an alternative to traditional methods. We deployed a sampling grid of 30 cameras throughout the urban southern California study area. Additionally, we physically captured and marked a subset of the bobcat population with GPS telemetry collars. Since we could identify individual bobcats with photos of unique pelage patterns and a subset of the population was physically marked, we were able to use traditional mark-recapture and mark-resight methods, as well as the new “hybrid” mark-resight model we developed to estimate bobcat abundance. We recorded 109 bobcat photos during 4,669 camera nights and physically marked 27 bobcats with GPS telemetry collars. Abundance estimates produced by the traditional mark-recapture, traditional mark-resight, and “hybrid” mark-resight methods were similar, however precision differed depending on the models used. Traditional mark-recapture and mark-resight estimates were relatively imprecise with percent confidence interval lengths exceeding 100% of point estimates. Hybrid mark-resight models produced better precision with percent confidence intervals not exceeding 57%. The increased precision of the hybrid mark-resight method stems from utilizing the complete encounter histories of physically marked individuals (including those never detected by a camera trap) and the encounter histories of naturally marked individuals detected at camera traps. This new estimator may be particularly useful for estimating abundance of uniquely identifiable species that are difficult to sample using camera traps alone.     

荒漠地区野生动物调查方法探讨——一种新的调查方法介绍

本文全面总结了我国野生动物调查的主要方法及应用,分析了已有方法在应用中的问题和缺陷,介绍了国际狩猎场的盘羊资源调查方法--地图样带法,并比较了该方法与样线法得出的调查结果差异和两种方法在实际应用中的区别.地图样带法没有长度和宽度概念,也没有规定样带的既定形状,提供了一种确定调查范围和计算样带面积的便捷方法,解决了过去调查中样带面积计算的难题.该方法完全根据实际调查的区域和地形地貌来确定样带的范围,使调查更具灵活性、机动性,并使密度的计算回归到了其本身的意义.该方法没有技术门槛,对广大基层野生动物保护工作者更具可操作性.     

Review of the Methods Frequently Used to Estimate the Abundance of Orthoptera in Grassland Ecosystems

Ecologists have quantified Orthoptera (grasshoppers and crickets) density in a wide variety of conservation studies. Objective determination of Orthoptera population size is possible using mark-release recapture techniques but these are time-consuming and of little use for all but the smallest scale studies. Therefore, a wide range of sampling techniques have been devised to quantify population density and the most commonly used methods include sweep netting and quadrat counts. It is the aim of this paper to critically review studies that have used these techniques and to provide useful suggestions for non-specialists on which method may be most applicable to their study site. This paper reviews a selection of the extensive literature reporting studies estimating the abundance of grasshoppers (Acrididae) in a wide range of grassland ecosystems. Where possible, studies on bush-crickets (Tettigoniidae) and crickets (Gryllidae) are included reflecting their overall contribution to assemblage diversity in grassland ecosystems and to highlight the need for further investigations of sampling efficiency on these two under-researched families.The most rapid and inexpensive sampling methods, such as quadrat and transect counts, involve ‘flushing’ grasshoppers from the sward. These techniques are fairly accurate in short, open swards (<50 cm sward height) where grasshopper densities are low (<2 adults per m²). At higher population densities (>2 adults per m²), methods which require the capture of grasshoppers such as box quadrats and sweep netting may be more appropriate. Sampling grasshopper populations in taller vegetation (>50 cm sward height) is more problematic as the efficiency of many techniques may be reduced by vegetation structure. Methods such as timed counts can be used at low densities (<2 adults per m²) and night trapping might be most applicable where high numbers of grasshoppers are present (>2 adults per m²).There is an urgent need for development of a standardised sampling technique that can produce comparable data from studies with a wide variety of observers in grasslands with differing vegetation structures and grasshopper densities.     

Toward Reliable Estimates of Abundance: Comparing Index Methods to Assess the Abundance of a Mammalian Predator

Due to time and financial constraints indices are often used to obtain landscape-scale estimates of relative species abundance. Using two different field methods and comparing the results can help to detect possible bias or a non monotonic relationship between the index and the true abundance, providing more reliable results. We used data obtained from camera traps and feces counts to independently estimate relative abundance of red foxes in the Black Forest, a forested landscape in southern Germany. Applying negative binomial regression models, we identified landscape parameters that influence red fox abundance, which we then used to predict relative red fox abundance. We compared the estimated regression coefficients of the landscape parameters and the predicted abundance of the two methods. Further, we compared the costs and the precision of the two field methods. The predicted relative abundances were similar between the two methods, suggesting that the two indices were closely related to the true abundance of red foxes. For both methods, landscape diversity and edge density best described differences in the indices and had positive estimated effects on the relative fox abundance. In our study the costs of each method were of similar magnitude, but the sample size obtained from the feces counts (262 transects) was larger than the camera trap sample size (88 camera locations). The precision of the camera traps was lower than the precision of the feces counts. The approach we applied can be used as a framework to compare and combine the results of two or more different field methods to estimate abundance and by this enhance the reliability of the result.     

Evaluation of the Performance of Information Theory-Based Methods and Cross-Correlation to Estimate the Functional Connectivity in Cortical Networks

Functional connectivity of in vitro neuronal networks was estimated by applying different statistical algorithms on data collected by Micro-Electrode Arrays (MEAs). First we tested these “connectivity methods” on neuronal network models at an increasing level of complexity and evaluated the performance in terms of ROC (Receiver Operating Characteristic) and PPC (Positive Precision Curve), a new defined complementary method specifically developed for functional links identification. Then, the algorithms better estimated the actual connectivity of the network models, were used to extract functional connectivity from cultured cortical networks coupled to MEAs. Among the proposed approaches, Transfer Entropy and Joint-Entropy showed the best results suggesting those methods as good candidates to extract functional links in actual neuronal networks from multi-site recordings.     

Selecting Habitat to Survive: The Impact of Road Density on Survival in a Large Carnivore

Habitat selection studies generally assume that animals select habitat and food resources at multiple scales to maximise their fitness. However, animals sometimes prefer habitats of apparently low quality, especially when considering the costs associated with spatially heterogeneous human disturbance. We used spatial variation in human disturbance, and its consequences on lynx survival, a direct fitness component, to test the Hierarchical Habitat Selection hypothesis from a population of Eurasian lynx Lynx lynx in southern Norway. Data from 46 lynx monitored with telemetry indicated that a high proportion of forest strongly reduced the risk of mortality from legal hunting at the home range scale, while increasing road density strongly increased such risk at the finer scale within the home range. We found hierarchical effects of the impact of human disturbance, with a higher road density at a large scale reinforcing its negative impact at a fine scale. Conversely, we demonstrated that lynx shifted their habitat selection to avoid areas with the highest road densities within their home ranges, thus supporting a compensatory mechanism at fine scale enabling lynx to mitigate the impact of large-scale disturbance. Human impact, positively associated with high road accessibility, was thus a stronger driver of lynx space use at a finer scale, with home range characteristics nevertheless constraining habitat selection. Our study demonstrates the truly hierarchical nature of habitat selection, which aims at maximising fitness by selecting against limiting factors at multiple spatial scales, and indicates that scale-specific heterogeneity of the environment is driving individual spatial behaviour, by means of trade-offs across spatial scales.     

Evaluation of Small Intestine Grafts Decellularization Methods for Corneal Tissue Engineering

Advances in the development of cornea substitutes by tissue engineering techniques have focused on the use of decellularized tissue scaffolds. In this work, we evaluated different chemical and physical decellularization methods on small intestine tissues to determine the most appropriate decellularization protocols for corneal applications. Our results revealed that the most efficient decellularization agents were the SDS and triton X-100 detergents, which were able to efficiently remove most cell nuclei and residual DNA. Histological and histochemical analyses revealed that collagen fibers were preserved upon decellularization with triton X-100, NaCl and sonication, whereas reticular fibers were properly preserved by decellularization with UV exposure. Extracellular matrix glycoproteins were preserved after decellularization with SDS, triton X-100 and sonication, whereas proteoglycans were not affected by any of the decellularization protocols. Tissue transparency was significantly higher than control non-decellularized tissues for all protocols, although the best light transmittance results were found in tissues decellularized with SDS and triton X-100. In conclusion, our results suggest that decellularized intestinal grafts could be used as biological scaffolds for cornea tissue engineering. Decellularization with triton X-100 was able to efficiently remove all cells from the tissues while preserving tissue structure and most fibrillar and non-fibrillar extracellular matrix components, suggesting that this specific decellularization agent could be safely used for efficient decellularization of SI tissues for cornea TE applications.     

Disease Risk Perception and Safety Practices: A Survey of Australian Flying Fox Rehabilitators

Interactions with flying foxes pose disease transmission risks to volunteer rehabilitators (carers) who treat injured, ill, and orphaned bats. In particular, Australian bat lyssavirus (ABLV) can be transmitted directly from flying foxes to humans in Australia. Personal protective equipment (PPE) and rabies vaccination can be used to protect against lyssavirus infection. During May and June 2014, active Australian flying fox carers participated in an online survey (SOAR: Survey Of Australian flying fox Rehabilitators) designed to gather demographic data, assess perceptions of disease risk, and explore safety practices. Responses to open-ended questions were analysed thematically. A logistic regression was performed to assess whether rehabilitators’ gender, use of PPE, threat perception, and years of experience predicted variation in their odds of being bitten or scratched. Eligible responses were received from 122 rehabilitators located predominantly on the eastern coast of Australia. Eighty-four percent of respondents were female. Years of experience ranged from <1 to 30 years (median 5 years). Respondents were highly educated. All rehabilitators were vaccinated against rabies and 94% received a rabies titre check at least every two years. Sixty-three percent of carers did not perceive viruses in flying foxes as a potential threat to their health, yet 74% of carers reported using PPE when handling flying foxes. Eighty-three percent of rehabilitators had received a flying fox bite or scratch at some point during their career. Carers provide an important community service by rescuing and rehabilitating flying foxes. While rehabilitators in this study have many excellent safety practices, including a 100% vaccination rate against rabies, there is room for improvement in PPE use. We recommend 1) the establishment of an Australia-wide set of guidelines for safety when caring for bats and 2) that the responsible government agencies in Australia support carers who rescue potentially ABLV-infected bats by offering compensation for PPE.     

Evaluation of Exome Sequencing to Estimate Tumor Burden in Plasma

Accurate estimation of systemic tumor load from the blood of cancer patients has enormous potential. One avenue is to measure the presence of cell-free circulating tumor DNA in plasma. Various approaches have been investigated, predominantly covering hotspot mutations or customized, patient-specific assays. Therefore, we investigated the utility of using exome sequencing to monitor circulating tumor DNA levels through the detection of single nucleotide variants in plasma. Two technologies, claiming to offer efficient library preparation from nanogram levels of DNA, were evaluated. This allowed us to estimate the proportion of starting molecules measurable by sequence capture (<5%). As cell-free DNA is highly fragmented, we designed and provide software for efficient identification of PCR duplicates in single-end libraries with a varying size distribution. On average, this improved sequence coverage by 38% in comparison to standard tools. By exploiting the redundant information in PCR-duplicates the background noise was reduced to ∼1/35000. By applying our optimized analysis pipeline to a simulation analysis, we determined the current sensitivity limit to ∼1/2400, starting with 30 ng of cell-free DNA. Subsequently, circulating tumor DNA levels were assessed in seven breast- and one prostate cancer patient. One patient carried detectable levels of circulating tumor DNA, as verified by break-point specific PCR. These results demonstrate exome sequencing on cell-free DNA to be a powerful tool for disease monitoring of metastatic cancers. To enable a broad implementation in the diagnostic settings, the efficiency limitations of sequence capture and the inherent noise levels of the Illumina sequencing technology must be further improved.     

Use of the Robust Design to Estimate Seasonal Abundance and Demographic Parameters of a Coastal Bottlenose Dolphin (Tursiops aduncus) Population

As delphinid populations become increasingly exposed to human activities we rely on our capacity to produce accurate abundance estimates upon which to base management decisions. This study applied mark–recapture methods following the Robust Design to estimate abundance, demographic parameters, and temporary emigration rates of an Indo-Pacific bottlenose dolphin (Tursiops aduncus) population off Bunbury, Western Australia. Boat-based photo-identification surveys were conducted year-round over three consecutive years along pre-determined transect lines to create a consistent sampling effort throughout the study period and area. The best fitting capture–recapture model showed a population with a seasonal Markovian temporary emigration with time varying survival and capture probabilities. Abundance estimates were seasonally dependent with consistently lower numbers obtained during winter and higher during summer and autumn across the three-year study period. Specifically, abundance estimates for all adults and juveniles (combined) varied from a low of 63 (95% CI 59 to 73) in winter of 2007 to a high of 139 (95% CI 134 to148) in autumn of 2009. Temporary emigration rates (γ'') for animals absent in the previous period ranged from 0.34 to 0.97 (mean  =  0.54; ±SE 0.11) with a peak during spring. Temporary emigration rates for animals present during the previous period (γ'''') were lower, ranging from 0.00 to 0.29, with a mean of 0.16 (± SE 0.04). This model yielded a mean apparent survival estimate for juveniles and adults (combined) of 0.95 (± SE 0.02) and a capture probability from 0.07 to 0.51 with a mean of 0.30 (± SE 0.04). This study demonstrates the importance of incorporating temporary emigration to accurately estimate abundance of coastal delphinids. Temporary emigration rates were high in this study, despite the large area surveyed, indicating the challenges of sampling highly mobile animals which range over large spatial areas.     

An Estimate of Mortality in a Pre-Columbian Urban Population

The excavation of an apartment compound, Tlajinga 33, of the city of Teotihuacan yielded a representative skeletal sample for a first paleodemographic study of a New World pre-Columbian urban population. Life-table analysis revealed a population with high juvenile mortality and a relatively short life span. Comparison with other populations revealed basic similarities in mortality between Teotihuacan and Old World preindustrial cities and differences with other non-urban North American populations.     

Mating Strategies in Relation to Sexually Selected Infanticide in a Non-Social Carnivore: the Brown Bear

Based on the sexually selected infanticide (SSI) hypothesis, infanticide can be an adaptive mating strategy for males, but this is has rarely been documented in non‐social mammals. This phenomenon should not benefit females, so one would expect females to evolve mating counter strategies in order to protect their infants from infanticidal males. Cases of SSI are extremely difficult to document in the field, especially for non‐social species. Using field observations and genetic methods, we describe mating strategies employed by both sexes of brown bears (Ursus arctos) in relation to SSI. We present evidence for the first time suggesting that infanticide is an adaptive male mating strategy in this non‐social carnivore, as all requirements for SSI are fulfilled (1) infanticide shortens the time to the mother's next estrus, (2) the perpetrator is not the father of the killed infants, and (3) putative perpetrators sire the next litter. Moreover, all infanticide cases occurred during the mating season. We expected that primarily immigrant males were infanticidal, as in social species. However, we found that resident adult males commonly committed infanticide. Perhaps they recognize females they have mated with previously. Moreover, we used DNA‐based parentage testing to demonstrate a minimum of 14.5% of multiple paternities (up to 28% for litters with at least three young). Female promiscuity to confuse paternity may be an adaptive counter strategy to avoid infanticide.     

An Equation to Estimate the Concentration of Serum Apolipoprotein B

Background

Several large prospective studies have demonstrated that apolipoprotein B (apoB) has greater value in predicting cardiovascular risk than any other lipid measurements. Currently, however, serum apoB levels are not routinely measured, because of the additional cost. The aim of this study was to develop an equation to estimate apoB from conventional lipid measurements including total cholesterol, HDL cholesterol, and triglycerides.

Methods

Data from a total of 78,127 subjects (47,057 men and 31,070 women), aged 15 to 88 years (mean age 41.8 years) were reviewed to develop an apoB equation. Additional datasets from the same institution and the NHANES obtained in 2007–2008 were used for internal (n = 73,445) and external validation (n = 3,097), respectively.

Results

We developed an apoB equation based on a linear regression model that contains total cholesterol, triglycerides, and HDL cholesterol as terms (model 1). To more precisely estimate the serum apoB level, we adjusted mode1 1 using a cutoff serum triglyceride value of 270 mg/dl (model 2). Model 2 showed more randomly distributed residuals in patients with diabetes, atherogenic dyslipidemia, and those taking lipid-lowering agents than model 1. The residuals in the development, internal validation, and external validation datasets were also randomly distributed around 0 with no clear trends.

Conclusion

The new equation we developed to estimate serum apoB concentrations is accurate and can be used in diverse subgroups of patients including those with diabetes, atherogenic dyslipidemia, and those taking lipid-lowering agents.     

Support Measures to Estimate the Reliability of Evolutionary Events Predicted by Reconciliation Methods

The genome content of extant species is derived from that of ancestral genomes, distorted by evolutionary events such as gene duplications, transfers and losses. Reconciliation methods aim at recovering such events and at localizing them in the species history, by comparing gene family trees to species trees. These methods play an important role in studying genome evolution as well as in inferring orthology relationships. A major issue with reconciliation methods is that the reliability of predicted evolutionary events may be questioned for various reasons: Firstly, there may be multiple equally optimal reconciliations for a given species tree–gene tree pair. Secondly, reconciliation methods can be misled by inaccurate gene or species trees. Thirdly, predicted events may fluctuate with method parameters such as the cost or rate of elementary events. For all of these reasons, confidence values for predicted evolutionary events are sorely needed. It was recently suggested that the frequency of each event in the set of all optimal reconciliations could be used as a support measure. We put this proposition to the test here and also consider a variant where the support measure is obtained by additionally accounting for suboptimal reconciliations. Experiments on simulated data show the relevance of event supports computed by both methods, while resorting to suboptimal sampling was shown to be more effective. Unfortunately, we also show that, unlike the majority-rule consensus tree for phylogenies, there is no guarantee that a single reconciliation can contain all events having above 50% support. In this paper, we detail how to rely on the reconciliation graph to efficiently identify the median reconciliation. Such median reconciliation can be found in polynomial time within the potentially exponential set of most parsimonious reconciliations.     

Self-Contained Gene-Set Analysis of Expression Data: An Evaluation of Existing and Novel Methods

Gene set methods aim to assess the overall evidence of association of a set of genes with a phenotype, such as disease or a quantitative trait. Multiple approaches for gene set analysis of expression data have been proposed. They can be divided into two types: competitive and self-contained. Benefits of self-contained methods include that they can be used for genome-wide, candidate gene, or pathway studies, and have been reported to be more powerful than competitive methods. We therefore investigated ten self-contained methods that can be used for continuous, discrete and time-to-event phenotypes. To assess the power and type I error rate for the various previously proposed and novel approaches, an extensive simulation study was completed in which the scenarios varied according to: number of genes in a gene set, number of genes associated with the phenotype, effect sizes, correlation between expression of genes within a gene set, and the sample size. In addition to the simulated data, the various methods were applied to a pharmacogenomic study of the drug gemcitabine. Simulation results demonstrated that overall Fisher''s method and the global model with random effects have the highest power for a wide range of scenarios, while the analysis based on the first principal component and Kolmogorov-Smirnov test tended to have lowest power. The methods investigated here are likely to play an important role in identifying pathways that contribute to complex traits.     

Looking for Progenitors: A Molecular Approach to Finding the Origins of An Invasive Weed

One of the major problems in determining the origin of invasive species is that often their arrival is unnoticed. Only when population levels increase is their presence noticed but by this time determining the point of arrival is confounded by the extensive spread of the species. Here we use molecular markers (ISSRs) to determine the origin of an invasive weed in the Kalahari region, a species for which several origins could be possible. We show that molecular markers can be useful tools in determining the origin of invasive species     

Occult HCV Infection: An Unexpected Finding in a Population Unselected for Hepatic Disease

Background

Occult Hepatitis C virus (HCV) infection is a new pathological entity characterized by presence of liver disease and absence or very low levels of detectable HCV-RNA in serum. Abnormal values of liver enzymes and presence of replicative HCV-RNA in peripheral blood mononuclear cells are also observed. Aim of the study was to evaluate occult HCV occurrence in a population unselected for hepatic disease.

Methodology/Principal Findings

We chose from previous epidemiological studies three series of subjects (n = 276, age range 40–65 years) unselected for hepatic disease. These subjects were tested for the presence of HCV antibodies and HCV-RNA in plasma and in the peripheral blood mononuclear cells (PBMCs) by using commercial systems. All subjects tested negative for HCV antibodies and plasma HCV-RNA and showed normal levels of liver enzymes; 9/276 patients (3.3%) were positive for HCV-RNA in PBMCs, identifying a subset of subjects with potential occult HCV infection. We could determine the HCV type for 8 of the 9 patients finding type 1a (3 patients), type 1b (2 patients), and type 2a (3 patients).

Conclusions

The results of this study show evidence that occult HCV infection may occur in a population unselected for hepatic disease. A potential risk of HCV infection spread by subjects harbouring occult HCV infection should be considered. Design of prospective studies focusing on the frequency of infection in the general population and on the clinical evolution of occult HCV infection will be needed to verify this unexpected finding.