Testing methods in species distribution modelling using virtual species: what have we learnt and what are we missing?

Species distribution models (SDMs) have become one of the major predictive tools in ecology. However, multiple methodological choices are required during the modelling process, some of which may have a large impact on forecasting results. In this context, virtual species, i.e. the use of simulations involving a fictitious species for which we have perfect knowledge of its occurrence–environment relationships and other relevant characteristics, have become increasingly popular to test SDMs. This approach provides for a simple virtual ecologist framework under which to test model properties, as well as the effects of the different methodological choices, and allows teasing out the effects of targeted factors with great certainty. This simplification is therefore very useful in setting up modelling standards and best practice principles. As a result, numerous virtual species studies have been published over the last decade. The topics covered include differences in performance between statistical models, effects of sample size, choice of threshold values, methods to generate pseudo‐absences for presence‐only data, among many others. These simulations have therefore already made a great contribution to setting best modelling practices in SDMs. Recent software developments have greatly facilitated the simulation of virtual species, with at least three different packages published to that effect. However, the simulation procedure has not been homogeneous, which introduces some subtleties in the interpretation of results, as well as differences across simulation packages. Here we 1) review the main contributions of the virtual species approach in the SDM literature; 2) compare the major virtual species simulation approaches and software packages; and 3) propose a set of recommendations for best simulation practices in future virtual species studies in the context of SDMs.     

Amyloids of multiple species: are they helpful in survival?

Amyloids are primarily known for their roles in neurodegenerative disorders, as well as in systemic diseases like diabetes. Evolutionary forces tend to maintain a healthy set of heritable characteristics, while eliminating toxic or unfavourable elements; but amyloids seem to represent an exception to this fundamental concept. In addition to their presence in mammals, amyloids also persist in the proteome of many lower organisms that may be linked with possible roles in survival, which are still unexplored. Herein, we address some unanswered questions regarding amyloids: are these well‐structured proteinaceous aggregates a by‐product of inefficient folding events, or have they been retained in our protein repertoire for as yet unknown functional roles; and how do protein misfolding and associated disorders originate, despite the presence of protein quality‐control systems inside the cells? This review aims to extend our current understanding about the multifaceted useful properties of amyloids and their functional interactions with other molecular pathways in various species; this may provide new insights to identify novel therapeutic strategies for ageing and neurodegenerative diseases.     

How effective are non-destructive sampling methods to assess aquatic invertebrate diversity in bromeliads?

With the growing interest in small aquatic water bodies, especially as naturally replicated model systems for ecological research, aquatic invertebrate communities in phytotelmata are increasingly receiving attention these days. The recognition of the substantial contribution to the regional species pool of specialised species draws further attention to these small and often temporary habitats. The methods currently used for studying communities in some types of phytotelma, such as bromeliads, tend to be destructive, typically involving complete dissection of the plant. The expected increase in sampling intensity associated with the increasing interest in phytotelmata may result in a negative impact on plant populations in some areas, decreasing numbers in an unsustainable way, especially in locations with ongoing, intensive research. We therefore aimed to investigate whether less-destructive sampling methods can achieve sufficient data quality to allow their use as alternatives to complete plant dissection. We tested the effectiveness of three such methods in measuring the aquatic invertebrate communities in tank bromeliads (Tillandsia guatemalensis) in Cusuco National Park, Honduras. The three methods were pipetting the water out of the bromeliad, turning the bromeliad upside down and dissecting only the outer part of the plant (the oldest, often deteriorating leaves). Overall, we found that these methods were poor predictors of richness and abundance of the organisms in communities. However, we found big differences between taxonomic groups, depending in part on the ecology of the organisms, and we suggest that some less-destructive alternative methods may be appropriate for studying some specific groups (e.g. Culicidae). Based on these results and a rapid survey of the abundance of bromeliads in the national park, we question whether intensive, ongoing research into aquatic invertebrate communities in similar phytotelma populations is sustainable. From the point of view of conservation, alternative model systems need to be found.     

Who are we when we are doing what we are doing?: the case for mindful embodiment in ethics case consultation

This paper explores the theory and practice of embodied epistemology or mindful embodiment in ethics case consultation. I argue that not only is this epistemology an ethical imperative to safeguard the integrity of this emerging profession, but that it has the potential to improve the quality of ethics consultation (EC). It also has implications for how ethics consultants are trained and how consultation services are organized. My viewpoint is informed by ethnographic research and by my experimental application of mindful embodiment to the development of an ethics consultation service. My argument proceeds in four phases. First I explore the notion of 'situatedness' in the bioethics literature, identifying gaps in the field's theories as they apply to EC. I then describe my theoretical approach to embodiment grounded in critical-interpretive medical anthropology and autoethnography. I use embodiment to refer to a moral epistemology grounded in the body, comprised of the interplay of physical, symbolic, intersubjective and political elements. Third, I describe how mindful embodiment can inform the role of the ethics consultant and the development of effective training techniques, vocabularies and processes for EC. I also discuss the benefits of this orientation, and the potential harms of ignoring the embodied dimensions of EC. My goals are to expose the fallacy of the 'theory-practice gap', to demonstrate how my own EC practice is deeply informed by this theoretical orientation, and to argue for a wider definition of what 'counts' as relevant theory for ethics consultation.     

Who wants to live forever? Roe deer survival in a favourable environment

The survival rates and body masses of roe deer (Capreolus capreolus) were studied on the island of Storfosna in central Norway in relation to sex, age, season and year. There were no predators on the island, and hunting was halted during the study period, resulting in a population increase from 10 to 40 individuals per km² during the period 1991–1994. A total of 352 individual roe deer were radio-monitored on a monthly basis. Survival rates were analyzed using the MARK software. An age effect in survival was found separating fawns from yearlings and adults, and for yearlings and adults we furthermore found a year effect. There was evidence for density dependence in body masses of fawns and yearlings, but no density effect in survival rates. We found no sex effect in winter body mass, but a significant sex effect in survival rates. We conclude that (1) increased population density can have an effect on body masses without causing a change in survival rates (2) roe deer can maintain very high survival rates under favourable environmental conditions even at very high population densities (3) male adults can reach equally high survival rates as females under favourable circumstances.     

Rotifer sampling — a complete species list from one visit?

This paper describes a possible method of compiling a rotifer species list for any site from a single visit. Sediment samples collected from Loch Leven on one occasion in winter were exposed to light and a range of temperature conditions in the laboratory. Resting eggs in the sediment were induced to hatch. The resultant species list was very similar to that obtained from regular plankton collections over the previous six year period.     

Who are the Kuchi? Nomad self-identities in Afghanistan

'Kuchi', an Afghan Persian word meaning 'those who go on migrations', is the common generic term, used by both Afghans and foreigners, for the nomads of Afghanistan, as it has been for many decades. Most if not all the nomads, and indeed many long-settled former nomads, now acknowledge this name, yet in the 1960s and 1970s few of those so labelled used the term for themselves. This article examines the usage of both 'Kuchi' and 'nomad', and locates them in the wider contexts of ethnic labelling practices in Afghanistan, anthropological debates about pastoral nomadism, and government-nomad relations in both Afghanistan and neighbouring Iran.  

Résumé

« Kuchi >>, un mot farsi d'Afghanistan désignant « ceux qui migrent >>, est le nom générique donné depuis des dizaines d'années par les Afghans, aussi bien que par les étrangers, aux nomades d'Afghanistan. Alors qu'aujourd'hui, la plupart de ces nomades, sinon tous, ainsi d'ailleurs que beaucoup d'anciens nomades sédentarisés depuis longtemps, se réclament de ce nom, ils étaient peu nombreux à se désigner ainsi dans les années 1960 et 1970. L'auteur examine ici l'usage des mots « Kuchi >> et « nomades >> et les resitue dans le contexte plus large des pratiques de dénomination ethniques en Afghanistan, des débats anthropologiques sur le nomadisme pastoral et des relations entre gouvernement et nomades en Afghanistan et dans l'Iran voisin.     

Ecological integrity assessment as a metric of biodiversity: are we measuring what we say we are?

As the recognition of the importance of biological diversity in biological conservation grows, an ongoing challenge is to develop metrics that can be used for effective conservation and management. The ecological integrity assessment has been proposed as such a metric. It is held by some to measure species composition, diversity, and habitat quality, as well as ecosystem structure, composition, and function. The methodology relies on proxy variables that include data on landscape characteristics such as patch size, abiotic factors such as hydrology, and some features of vegetation structure and composition. We suggest that the measure is flawed on four levels. First, its putative representation of general ecological form and function, and its lack of specific detail about how it actually represents those attributes, leaves the metric without the focus needed to be useful for measuring ecological features on the ground and testing associated hypotheses and predictions. Second, the proxy variables used to represent biological diversity, such as habitat (vegetation) metrics and vascular plant species diversity, are not empirically correlated with diversity of a range of taxa or of other components of the biota. Third, like other ecological indices that integrate many distinct features, the ecological integrity index is subject to the loss of information in its condensation of multi-dimensional variability into a one-dimensional index, and it may be subject to systematic bias from the conversion of raw data into categorical scores. Fourth, the sampling protocols are at risk of sampling bias, observer bias, and measurement error, any of which can confound the estimation of conservation value. In terms of biological diversity, the methodology produces an unreliable estimate of the number of vascular plant species and their relative percentages of occurrence, and an absence of any protocols for taxa other than plants. For these reasons we believe that ecological integrity assessment is currently of limited value as a measure of site-specific biological diversity and its change over time. A considerable amount of investigation is needed in order to have confidence in the results of an ecological integrity assessment, especially if it is to be used for regulatory purposes. We suggest further refinements and discuss alternative measures of biological diversity that provide reliable metrics for assessing change. A thoughtful choice among measures can help to identify the most appropriate assessment for conservation decisions.     

Commentary: do we have a consistent terminology for species diversity? We are on the way

A consistent terminology for species diversity is subject of an ongoing debate. Recently Tuomisto (Oecologia 164:853–860, 2010) stated that a consistent terminology for diversity already exists. The paper comments on recent papers by ourselves (Jurasinski et al. Oecologia 159:15–26, 2009) and by Moreno and Rodriguez (Oecologia 163:279–282, 2010). Both started from Whittaker’s diversity concept to discuss the ambiguities of the terminology and propose a new, more consistent terminology that is based on the different approaches to diversity analysis. In contrast, Tuomisto adheres to a strict school of thinking and derives a diversity framework in the sense of Whittaker (alpha, beta, gamma) from the conceptual definition of diversity itself. A third group of papers discusses appropriate methods for the analysis of the variation in species composition. Here, we support the idea that alpha, beta and gamma diversity should be used in a strict sense that is based only on the conceptual definition of diversity. We accordingly extend and modify our terminological concept for species diversity. All approaches to the analysis and quantification of species composition and diversity can be assigned to three abstraction levels (species composition, variation in species composition,and variation in variation in species composition) and two scale levels (sample scale, aggregation scale). All methods that investigate the variation in species composition across scale levels evaluate beta relation with beta diversity being just one form of beta relation, which is calculated by dividing gamma diversity of order q by the appropriate alpha diversity of the same order. In contrast, differentiation refers to a pairwise calculation of resemblance in species composition. It is restricted to sample scale and is therefore most often only an intermediate step of analysis. Many ecological questions can be addressed either by direct analysis of the variation in species composition using raw data approaches or by further analysis of differentiation datasets on aggregation scale with or without respect to an external gradient.     

Structure-based methods for predicting mutagenicity and carcinogenicity: are we there yet?

There is a great deal of current interest in the use of commercial, automated programs for the prediction of mutagenicity and carcinogenicity based on chemical structure. However, the goal of accurate and reliable toxicity prediction for any chemical, based solely on structural information remains elusive. The toxicity prediction challenge is global in its objective, but limited in its solution, to within local domains of chemicals acting according to similar mechanisms of action in the biological system; to predict, we must be able to generalize based on chemical structure, but the biology fundamentally limits our ability to do so. Available commercial systems for mutagenicity and/or carcinogenicity prediction differ in their specifics, yet most fall in two major categories: (1) automated approaches that rely on the use of statistics for extracting correlations between structure and activity; and (2) knowledge-based expert systems that rely on a set of programmed rules distilled from available knowledge and human expert judgement. These two categories of approaches differ in the ways that they represent, process, and generalize chemical-biological activity information. An application of four commercial systems (TOPKAT, CASE/MULTI-CASE, DEREK, and OncoLogic) to mutagenicity and carcinogenicity prediction for a particular class of chemicals—the haloacetic acids (HAs)—is presented to highlight these differences. Some discussion is devoted to the issue of gauging the relative performance of commercial prediction systems, as well as to the role of prospective prediction exercises in this effort. And finally, an alternative approach that stops short of delivering a prediction to a user, involving structure-searching and data base exploration, is briefly considered.     

Pim kinases in hematological malignancies: where are we now and where are we going?

The proviral insertion in murine (PIM) lymphoma proteins are a serine/threonine kinase family composed of three isoformes: Pim-1, Pim-2 and Pim-3. They play a critical role in the control of cell proliferation, survival, homing and migration. Recently, overexpression of Pim kinases has been reported in human tumors, mainly in hematologic malignancies. In vitro and in vivo studies have confirmed their oncogenic potential. Indeed, PIM kinases have shown to be involved in tumorgenesis, to enhance tumor growth and to induce chemo-resistance, which is why they have become an attractive therapeutic target for cancer therapy. Novel molecules inhibiting Pim kinases have been evaluated in preclinical studies, demonstrating to be effective and with a favorable toxicity profile. Given the promising results, some of these compounds are currently under investigation in clinical trials. Herein, we provide an overview of the biological activity of PIM-kinases, their role in hematologic malignancies and future therapeutic opportunities.