Multi-species occupancy models: review,roadmap, and recommendations

Recent technological and methodological advances have revolutionized wildlife monitoring. Although most biodiversity monitoring initiatives are geared towards focal species of conservation concern, researchers are increasingly studying entire communities, specifically the spatiotemporal drivers of community size and structure and interactions among species. This has resulted in the emergence of multi-species occupancy models (MSOMs) as a promising and efficient approach for the study of community ecology. Given the potential of MSOMs for conservation and management action, it is critical to know whether study design and model assumptions are consistent with inference objectives. This is especially true for studies that are designed for a focal species but can give insights about a community. Here, we review the recent literature on MSOMs, identify areas of improvement in the multi-species study workflow, and provide a reference model for best practices for focal species and community monitoring study design. We reviewed 92 studies published between 2009 and early 2018, spanning 27 countries and a variety of taxa. There is a consistent under-reporting of details that are central to determining the adequacy of designs for generating data that can be used to make inferences about community-level patterns of occupancy, including the spatial and temporal extent, types of detectors used, covariates considered, and choice of field methods and statistical tools. This reporting bias could consequently result in skewed estimates, affecting conservation actions and management plans. On the other hand, comprehensive reporting is likely to help researchers working on MSOMs assess the robustness of inferences, in addition to making strides in terms of reproducibility and reusability of data. We use our literature review to inform a roadmap with best practices for MSOM studies, from simulations to design considerations and reporting, for the collection of new data as well as those involving existing datasets.     

Conceptual Site Models and Multimedia Modeling: Comparing MEPAS,MMSOILS, and RESRAD

The use of multimedia models to assess current and future human and ecological exposure to contamination at hazardous waste sites has become common practice in recent years. The U.S. Environmental Protection Agency has identified development of a conceptual site model as a critical part of the risk assessment process. This paper investigates the relationship between the choice of conceptual site models and application of multimedia models and the variation in risk estimates obtained when using data and default parameter values suggested by the individual model developers.     

Updated Models for the Effects of Temperature,Initial pH,NaCl, and NaNO2 on the Aerobic and Anaerobic Growth of Listeria monocytogenes

Data from several studies were appended to aerobic and anaerobic data sets that had been previously used to develop response surface models describing the growth kinetics of Listeria monocytogenes (Buchanan and Phillips, 1990). The expanded data sets included 709 aerobic and 358 anaerobic growth curves fitted with the Gompertz equation, and representing 189 and 150 unique combinations of four variables (temperature, pH, NaCl, NaNO₂), respectively. Response surface models were developed for (1) the Gompertz B and M terms and (2) lag phase durations (LPD) and generation times (GT). In addition to modeling NaCl as a variable, a second set of response surface models was developed by substituting calculated water activity as a variable. A number of data transformations were evaluated in an attempt to better utilize no-growth data. Full quadratic models of the natural logarithm transformation of the data (no-growth data excluded) predicted values that fit the observed data well. The assignment of GT=50[emsp4 ]h and LPD=600[emsp4 ]h (the approximate maximum duration of experiments) for the variable combinations that did not support growth proved to be the most effective means of making use of the no-growth data. However, this approach did not offer any clear advantage over quadratic models where the no-growth data were excluded. Error matrices were developed for the LPD and GT models to provide 95 % confidence intervals. The agreement between observed and predicted growth kinetics was excellent considering the number and ranges of the variables encompassed in the models. The models provide reasonable predictions of the growth of L. monocytogenes in foods. The full quadratic models of LPD and GT without inclusion of the no-growth data were selected for inclusion in the USDA Pathogen Modeling Program, release 5.1.     

Configural and elemental processing in associative learning: commentary on Melchers, Shanks and Lachnit

The paper by Melchers, Shanks, and Lachnit (2007) reviews the available evidence suggesting that there is flexible processing, such that some associative learning tasks can be solved either configurally or elementally. We find the evidence provocative but limited in its demonstrated generality and silent with respect to the theoretical mechanisms that might regulate the alleged flexibility of processing. Further research is invited to determine the scope of the variation involved and how best to account for it. At present, theories, either elemental or configural, that include mechanisms to shift the weight assigned to component stimuli appear to be potential candidates for embracing the data.     

Murine models of blastomycosis,coccidioidomycosis, and histoplasmosis

Animal models have contributed much to the knowledge of fungal infections and their corresponding therapeutic treatments. This is true for animal models of the primary fungal pathogens, Blastomyces dermatitidis, Coccidioides immitis, and Histoplasma capsulatum. This review gives a brief background of human diseases associated with these organisms and describes the development, details, and utility of murine models of blastomycosis, as well as coccidioidomycosis and histoplasmosis. This revised version was published online in June 2006 with corrections to the Cover Date.     

Modeling competition between Laurencia obtusa (Ceramiales,Rhodophyta) and Hypnea spinella (Gigartinales,Rhodophyta) at Cabo Frio Island,Rio de Janeiro,Brazil

The Lotka-Volterra competition model was used to represent the interaction between Laurencia obtusa and Hypnea spinella. A new model that considers effects of competition on algal carrying capacity is suggested. To test the models, data from field experiments conducted in an intertidal region at Cabo Frio Island, Rio de Janeiro, Brazil, were used. Both models showed that Hypnea was a stronger competitor than Laurencia. The model of interaction through the carrying capacity showed a stable coexistence between the algal populations and better represented the experimental data.     

Likelihood, parsimony, and heterogeneous evolution

Evolutionary rates vary among sites and across the phylogenetic tree (heterotachy). A recent analysis suggested that parsimony can be better than standard likelihood at recovering the true tree given heterotachy. The authors recommended that results from parsimony, which they consider to be nonparametric, be reported alongside likelihood results. They also proposed a mixture model, which was inconsistent but better than either parsimony or standard likelihood under heterotachy. We show that their main conclusion is limited to a special case for the type of model they study. Their mixture model was inconsistent because it was incorrectly implemented. A useful nonparametric model should perform well over a wide range of possible evolutionary models, but parsimony does not have this property. Likelihood-based methods are therefore the best way to deal with heterotachy.     

Mating,births, and transitions: a flexible two-sex matrix model for evolutionary demography

Models of sexually-reproducing populations that consider only a single sex cannot capture the effects of sex-specific demographic differences and mate availability. We present a new framework for two-sex demographic models that implements and extends the birth-matrix mating-rule approach of Pollak. The model is a continuous-time matrix model that explicitly includes the processes of mating (which is nonlinear but homogeneous), offspring production, and demographic transitions and survival. The resulting nonlinear model converges to exponential growth with an equilibrium population composition. The model can incorporate age- or stage-structured life histories and flexible mating functions. As an example, we apply the model to analyze the effects of mating strategies (polygamy or monogamy, and mated unions composed of males and females, of variable duration) on the response to sex-biased harvesting. The combination of demographic complexity with the interaction of the sexes can have major population dynamic effects and can change the outcome of evolution on sex-related characters.     

Mixture models, robustness, and the weighted likelihood methodology

Problems associated with the analysis of data from a mixture of distributions include the presence of outliers in the sample, the fact that a component may not be well represented in the data, and the problem of biases that occur when the model is slightly misspecified. We study the performance of weighted likelihood in this context. The method produces estimates with low bias and mean squared error, and it is useful in that it unearths data substructures in the form of multiple roots. This in turn indicates multiple potential mixture model fits due to the presence of more components than originally specified in the model. To compute the weighted likelihood estimates, we use as starting values the method of moment estimates computed on bootstrap subsamples drawn from the data. We address a number of important practical issues involving bootstrap sample size selection, the role of starting values, and the behavior of the roots. The algorithm used to compute the weighted likelihood estimates is competitive with EM, and it is similar to EM when the components are not well separated. Moreover, we propose a new statistical stopping rule for the termination of the algorithm. An example and a small simulation study illustrate the above points.     

Complex systems, evolution, and animal models

In this paper, we respond to arguments made concerning our position regarding animal models (Shelley, 2010) by briefly examining the fact that animals (human and nonhuman) are complex systems that have different evolutionary trajectories. This historical fact has implications for using animals as predictive models for human response to drugs and disease.     

The muddle of ages,turnover, transit,and residence times in the carbon cycle

Comparisons among ecosystem models or ecosystem dynamics along environmental gradients commonly rely on metrics that integrate different processes into a useful diagnostic. Terms such as age, turnover, residence, and transit times are often used for this purpose; however, these terms are variably defined in the literature and in many cases, calculations ignore assumptions implicit in their formulas. The aim of this opinion piece was i) to make evident these discrepancies and the incorrect use of formulas, ii) highlight recent results that simplify calculations and may help to avoid confusion, and iii) propose the adoption of simple and less ambiguous terms.     

Spatial mismatch in morphological,ecological and phylogenetic diversity,in historical and contemporary European freshwater fish faunas

Biodiversity encompasses multiple facets, among which taxonomic, functional and phylogenetic aspects are the most often considered. Understanding how those diversity facets are distributed and what are their determinants has become a central concern in the current context of biodiversity crisis, but such multi‐faceted measures over large geographical areas are still pending. Here, we measured the congruence between the biogeographical patterns of freshwater fish morphological, ecological and phylogenetic diversity across Europe and identified the natural and anthropogenic drivers shaping those patterns. Based on freshwater fish occurrence records in 290 European river catchments, we computed richness and evenness for morphological, ecological and phylogenetic diversity using standardized effect sizes for each diversity index. We then used linear models including climatic, geo‐morphological, biotic and human‐related factors to determine the key drivers shaping freshwater fish biodiversity patterns across Europe. We found a weak spatial congruence between facets of diversity. Patterns of diversity were mainly driven by elevation range, climatic seasonality and species richness while other factors played a minor role. Finally, we found that non‐native species introductions significantly affected diversity patterns and influenced the effects of some environmental drivers. Morphological, ecological and phylogenetic diversity constitute complementary facets of fish diversity rather than surrogates, testifying that they deserve to be considered altogether to properly assess biodiversity. Although the same environmental and anthropogenic factors overall explained those diversity facets, their relative influence varied. In the current context of global change, non‐native species introductions may also lead to important reshuffling of assemblages resulting in profound changes of diversity patterns.     

DNA-damage repair; the good, the bad, and the ugly

Organisms have developed several DNA-repair pathways as well as DNA-damage checkpoints to cope with the frequent challenge of endogenous and exogenous DNA insults. In the absence or impairment of such repair or checkpoint mechanisms, the genomic integrity of the organism is often compromised. This review will focus on the functional consequences of impaired DNA-repair pathways. Although each pathway is addressed individually, it is essential to note that cross talk exists between repair pathways, and that there are instances in which a DNA-repair protein is involved in more than one pathway. It is also important to integrate DNA-repair process with DNA-damage checkpoints and cell survival, to gain a better understanding of the consequences of compromised DNA repair at both cellular and organismic levels. Functional consequences associated with impaired DNA repair include embryonic lethality, shortened life span, rapid ageing, impaired growth, and a variety of syndromes, including a pronounced manifestation of cancer.     

Cryptic phenology in plants: Case studies,implications, and recommendations

Plant phenology—the timing of cyclic or recurrent biological events in plants—offers insight into the ecology, evolution, and seasonality of plant‐mediated ecosystem processes. Traditionally studied phenologies are readily apparent, such as flowering events, germination timing, and season‐initiating budbreak. However, a broad range of phenologies that are fundamental to the ecology and evolution of plants, and to global biogeochemical cycles and climate change predictions, have been neglected because they are “cryptic”—that is, hidden from view (e.g., root production) or difficult to distinguish and interpret based on common measurements at typical scales of examination (e.g., leaf turnover in evergreen forests). We illustrate how capturing cryptic phenology can advance scientific understanding with two case studies: wood phenology in a deciduous forest of the northeastern USA and leaf phenology in tropical evergreen forests of Amazonia. Drawing on these case studies and other literature, we argue that conceptualizing and characterizing cryptic plant phenology is needed for understanding and accurate prediction at many scales from organisms to ecosystems. We recommend avenues of empirical and modeling research to accelerate discovery of cryptic phenological patterns, to understand their causes and consequences, and to represent these processes in terrestrial biosphere models.     

Thyroid hormones, learning and memory

Thyroid hormones (THs), T3 and T4, have many physiological actions and are essential for normal behavioral, intellectual and neurological development. THs have a broad spectrum of effects on the developing brain and mediate important effects within the CNS throughout life. Insufficient maternal iodine intake during gestation and TH deficiency during human development are associated to pathological alterations such as cretinism and mental retardation. In adulthood, thyroid dysfunction is related to neurological and behavioral abnormalities, including memory impairment. Analysis of different experimental models suggests that most of the effects on cognition as a result of thyroid dysfunction rely on hippocampal modifications. Insufficiency of THs during development thus alters hippocampal synaptic function and impairs behavioral performance of hippocampal-dependent learning and memory tasks that persist in euthyroid adult animals. In the present review, we summarize the current knowledge obtained by clinical observations and experimental models that shows the importance of THs in learning and mnemonic processes.     

Super folds,networks, and barriers

Exhaustive enumeration of sequences and folds is conducted for a simple lattice model of conformations, sequences, and energies. Examination of all foldable sequences and their nearest connected neighbors (sequences that differ by no more than a point mutation) illustrates the following: (i) There exist unusually large number of sequences that fold into a few structures (super‐folds). The same observation was made experimentally and computationally using stochastic sampling and exhaustive enumeration of related models. (ii) There exist only a few large networks of connected sequences that are not restricted to one fold. These networks cover a significant fraction of fold spaces (super‐networks). (iii) There exist barriers in sequence space that prevent foldable sequences of the same structure to “connect” through a series of single point mutations (super‐barrier), even in the presence of the sequence connection between folds. While there is ample experimental evidence for the existence of super‐folds, evidence for a super‐network is just starting to emerge. The prediction of a sequence barrier is an intriguing characteristic of sequence space, suggesting that the overall sequence space may be disconnected. The implications and limitations of these observations for evolution of protein structures are discussed. Proteins 2012. © 2011 Wiley Periodicals, Inc.