Linking multidimensional functional diversity to quantitative methods: a graphical hypothesis-evaluation framework

Functional trait analysis is an appealing approach to study differences among biological communities because traits determine species' responses to the environment and their impacts on ecosystem functioning. Despite a rapidly expanding quantitative literature, it remains challenging to conceptualize concurrent changes in multiple trait dimensions (“trait space”) and select quantitative functional diversity methods to test hypotheses prior to analysis. To address this need, we present a widely applicable framework for visualizing ecological phenomena in trait space to guide the selection, application, and interpretation of quantitative functional diversity methods. We describe five hypotheses that represent general patterns of responses to disturbance in functional community ecology and then apply a formal decision process to determine appropriate quantitative methods to test ecological hypotheses. As a part of this process, we devise a new statistical approach to test for functional turnover among communities. Our combination of hypotheses and metrics can be applied broadly to address ecological questions across a range of systems and study designs. We illustrate the framework with a case study of disturbance in freshwater communities. This hypothesis-driven approach will increase the rigor and transparency of applied functional trait studies.Keywords: community assembly, trait-based ecology, disturbance, ordination, functional diversity, multivariate analysis, multidimensional trait spaceThis is the publisher’s final pdf. The article is copyrighted by Ecological Society of America and published by John Wiley & Sons, Inc. It can be found at: http://esajournals.onlinelibrary.wiley.com/hub/journal/10.1002/%28ISSN%291939-9170

The effects of taurolidine alone and in combination with doxorubicin or carboplatin in canine osteosarcoma in vitro

Background: Osteosarcoma (OS) affects over 8000 dogs/year in the United States. The disease usually arises in the appendicular skeleton and metastasizes to the lung. Dogs with localized appendicular disease benefit from limb amputation and chemotherapy but most die within 6–12 months despite these treatments. Taurolidine, a derivative of taurine, has anti-tumor and anti-angiogenic effects against a variety of cancers. The following in vitro studies tested taurolidine as a candidate for adjuvant therapy for canine OS. Tests for p53 protein status and caspase activity were used to elucidate mechanisms of taurolidine-induced cell death. Results: Taurolidine was cytotoxic to osteosarcoma cells and increased the toxicity of doxorubicin and carboplatin in vitro. Apoptosis was greatly induced in cells exposed to 125 μM taurolidine and less so in cells exposed to 250 μM taurolidine. Taurolidine cytotoxicity appeared caspase-dependent in one cell line; with apparent mutant p53 protein. This cell line was the most sensitive to single agent taurolidine treatment and had a taurolidine-dependent reduction in accumulated p53 protein suggesting taurolidine’s effects may depend on the functional status of p53 in canine OS. Conclusion: Taurolidine’s cytotoxic effect appears dependent on cell specific factors which may be explained, in part, by the functional status of p53. Taurolidine initiates apoptosis in canine OS cells and this occurs to a greater extent at lower concentrations. Mechanisms of cell death induced by higher concentrations were not elucidated here. Taurolidine combined with doxorubicin or carboplatin can increase the toxicity of these chemotherapy drugs and warrants further investigation in dogs with osteosarcoma.KEYWORDS: Carboplatin, In vitro, Apoptosis, Osteosarcoma, Taurolidine, DoxorubicinThis is the publisher’s final pdf. The published article is copyrighted by BioMed Central Ltd. and can be found at: http://www.biomedcentral.com

Use of aliphatic n-alkynes to discriminate soil nitrification activities of ammonia-oxidizing thaumarchaea and bacteria

Ammonia (NH₃)-oxidizing bacteria (AOB) and thaumarchaea (AOA) co-occupy most soils, yet no short-term growth-independent method exists to determine their relative contributions to nitrification in situ. Microbial monooxygenases differ in their vulnerability to inactivation by aliphatic n-alkynes, and we found that NH₃ oxidation by the marine thaumarchaeon Nitrosopumilus maritimus was unaffected during a 24-h exposure to ≤20 μM concentrations of 1-alkynes C₈ and C₉. In contrast, NH₃ oxidation by two AOB (Nitrosomonas europaea and Nitrosospira multiformis) was quickly and irreversibly inactivated by 1 μM C₈ (octyne). Evidence that nitrification carried out by soilborne AOA was also insensitive to octyne was obtained. In incubations (21 or 28 days) of two different whole soils, both acetylene and octyne effectively prevented NH₄⁺-stimulated increases in AOB population densities, but octyne did not prevent increases in AOA population densities that were prevented by acetylene. Furthermore, octyne-resistant, NH₄⁺-stimulated net nitrification rates of 2 and 7 μg N/g soil/day persisted throughout the incubation of the two soils. Other evidence that octyne-resistant nitrification was due to AOA included (i) a positive correlation of octyne-resistant nitrification in soil slurries of cropped and noncropped soils with allylthiourea-resistant activity (100 μM) and (ii) the finding that the fraction of octyne-resistant nitrification in soil slurries correlated with the fraction of nitrification that recovered from irreversible acetylene inactivation in the presence of bacterial protein synthesis inhibitors and with the octyne-resistant fraction of NH₄⁺-saturated net nitrification measured in whole soils. Octyne can be useful in short-term assays to discriminate AOA and AOB contributions to soil nitrification.This is an author's peer-reviewed final manuscript, as accepted by the publisher. The published article is copyrighted by the American Society for Microbiology and can be found at: http://aem.asm.org/

The scaled [alpha]-Winsorized estimate of exponential scale for censored data: an analysis based on two influence functions

A new view of the maximum likelihood estimator (MLE) of exponential scale for censored data is presented. This is done by adapting Reid's (Ann. Statist. 9 (1981) 78) approach for obtaining the two influence functions (IF) for the Kaplan-Meier estimate of the survival function; one for uncensored and one for censored data, respectively. The MLEs two IFs are derived. Via this analysis, we propose a new robust estimator, the scaled [alpha]-Winsorized estimator (WE). Under Type II censoring, the WE is the MLE and, hence, is asymptotically efficient in that case. Its two IFs are bounded; hence,WE is B-robust. Its breakdown point is [alpha]. A comparison is made with respect to asymptotic bias and mean square error at contaminated exponential and Weibull survival models.Bivariate functionals B-robust Exponential MLE Random censoring von Mises expansion Winsorized mean

Simultaneous tests for homogeneity of two zero-inflated (beta) populations

<p>Motivated by an example in marine science, we use Fisher’s method to combine independent likelihood ratio tests (LRTs) and asymptotic independent score tests to assess the equivalence of two zero-inflated Beta populations (mixture distributions with three parameters). For each test, test statistics for the three individual parameters are combined into a single statistic to address the overall difference between the two populations. We also develop non parametric and semiparametric permutation-based tests for simultaneously comparing two or three features of unknown populations. Simulations show that the likelihood-based tests perform well for large sample sizes and that the statistics based on combining LRT statistics outperforms the ones based on combining score test statistics. The permutation-based tests have overall better performance in terms of both power and type I error rate. Our methods are easy to implement and computationally efficient, and can be expanded to more than two populations and to other multiple parameter families. The permutation tests are entirely generic and can be useful in various applications dealing with zero (or other) inflation.</p

Carryover aquatic effects on survival of metamorphic frogs during pond emigration. Ecological Applications

Abstract. In organisms with complex life cycles, physiological stressors during early life stages may have fitness-level impacts that are delayed into later stages or habitats. We tested the hypothesis that body size and date of metamorphosis, which are highly responsive to aquatic stressors, influence post-metamorphic survival and movement patterns in the terrestrial phase of an ephemeral pond-breeding frog by examining these traits in two populations of northern red-legged frogs (Rana aurora aurora). To increase variation of body size at metamorphosis, we manipulated food availability for 314 of 1045 uniquely marked tadpoles and estimated the probability that frogs survived and emigrated using concentric rings of drift fencing surrounding ponds and Bayesian capture-recapture modeling. The odds of surviving and emigrating from the ponds to the innermost drift fences, ϳ12 m, increased by factors of 2.20 (95% credibility intervals 1.39-4.23) and 2.54 (0.94-4.91) with each millimeter increase in snout-vent length and decreased by factors of 0.91 (0.85-0.96) and 0.89 (0.80-1.00) with each day&apos;s delay in metamorphosis for the two ponds. The odds of surviving and moving to the next ring of fencing, 12 m to ϳ40 m from the ponds, increased by a factor of 1.20 (0.45-4.06) with each millimeter increase in size. Our results demonstrated that body size and timing of metamorphosis relate strongly to the performance of newly metamorphosed frogs during their initial transition into terrestrial habitat. Carryover effects of aquatic stressors that reduce size and delay metamorphosis may have population-level impacts that are not expressed until terrestrial stages. Since changes in both aquatic and terrestrial systems are implicated in many amphibian declines, quantifying both immediate and delayed effects of stressors on demographic rates is critical to sound management

Quantifying partial migration with sex-ratio balancing

Partial migration, the phenomenon in which animal populations are composed of both migratory and non-migratory individuals, is widespread among migrating animals. The proportion of migrants in these populations has direct influences on population genetics and dynamics, ecosystem dynamics, mating systems, evolution, and responses to environmental change, yet there are very few studies that measure the proportion of migrants. This is because existing methods to estimate the proportion of migrants are time-consuming and expensive. In this paper, we demonstrate a new method for estimating the proportion of migrants in a population, based on sex-ratio measurements. Many partially migratory taxa exhibit sex-biased migration or residency, and in these cases, the sex ratios of migrants and non-migrants are fundamentally related to the proportion of migrants in the population. We define this relationship quantitatively and show how it can be used to infer the proportion of migrants in a population through a process we term â sex-ratio balancing.â We obtain Bayesian estimates of proportion of migrants, and quantify the uncertainty in these estimates with highest posterior density intervals. Lastly, we validate the sex-ratio balancing approach with a Chinook salmon (Oncorhynchus tshawytscha Walbaum, 1792) data set. Sex-ratio balancing holds promise as a tool for quantifying partial migration and filling a key data gap about partially migratory taxa.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

Designing a Monitoring Program to Estimate Estuarine Survival of Anadromous Salmon Smolts: Simulating the Effect of Sample Design on Inference

<div><p>A number of researchers have attempted to estimate salmonid smolt survival during outmigration through an estuary. However, it is currently unclear how the design of such studies influences the accuracy and precision of survival estimates. In this simulation study we consider four patterns of smolt survival probability in the estuary, and test the performance of several different sampling strategies for estimating estuarine survival assuming perfect detection. The four survival probability patterns each incorporate a systematic component (constant, linearly increasing, increasing and then decreasing, and two pulses) and a random component to reflect daily fluctuations in survival probability. Generally, spreading sampling effort (tagging) across the season resulted in more accurate estimates of survival. All sampling designs in this simulation tended to under-estimate the variation in the survival estimates because seasonal and daily variation in survival probability are not incorporated in the estimation procedure. This under-estimation results in poorer performance of estimates from larger samples. Thus, tagging more fish may not result in better estimates of survival if important components of variation are not accounted for. The results of our simulation incorporate survival probabilities and run distribution data from previous studies to help illustrate the tradeoffs among sampling strategies in terms of the number of tags needed and distribution of tagging effort. This information will assist researchers in developing improved monitoring programs and encourage discussion regarding issues that should be addressed prior to implementation of any telemetry-based monitoring plan. We believe implementation of an effective estuary survival monitoring program will strengthen the robustness of life cycle models used in recovery plans by providing missing data on where and how much mortality occurs in the riverine and estuarine portions of smolt migration. These data could result in better informed management decisions and assist in guidance for more effective estuarine restoration projects.</p></div