The ENMTools software package was introduced in 2008 as a platform for making measurements on environmental niche models (ENMs, frequently referred to as species distribution models or SDMs), and for using those measurements in the context of newly developed Monte Carlo tests to evaluate hypotheses regarding niche evolution. Additional functionality was later added for model selection and simulation from ENMs, and the software package has been quite widely used. ENMTools was initially implemented as a Perl script, which was also compiled into an executable file for various platforms. However, the package had a number of significant limitations; it was only designed to fit models using Maxent, it relied on a specific Perl distribution to function, and its internal structure made it difficult to maintain and expand. Subsequently, the R programming language became the platform of choice for most ENM studies, making ENMTools less usable for many practitioners. Here we introduce a new R version of ENMTools that implements much of the functionality of its predecessor as well as numerous additions that simplify the construction, comparison and evaluation of niche models. These additions include new metrics for model fit, methods of measuring ENM overlap, and methods for testing evolutionary hypotheses. The new version of ENMTools is also designed to work within the expanding universe of R tools for ecological biogeography, and as such includes greatly simplified interfaces for analyses from several other R packages.

Gram-negative pathogens are increasingly resistant to extended-spectrum cephalosporins (ESCs). Using a prospective, case-controlled observational study, we examined the prevalence and the risk factors for development of resistance to ESCs in group I beta-lactamase-producing organisms. Of the 386 isolates of Enterobacter species, Pseudomonas aeruginosa, Citrobacter species, and Serratia marsescens from 340 consecutive patients, 70 (18.1%) were resistant to ESCs; the highest rates of resistance were found among Citrobacter freundii (40.9%), Enterobacter cloacae (31.1%), and Enterobacter aerogenes isolates (18.9%). Patients' prior antibiotic use and the mean number of antibiotics used were significantly greater in association with resistant vs. susceptible isolates. Resistance was associated with prior use of ceftizoxime or cefotaxime (P = .008), ceftazidime (P = .004), and piperacillin (P = .001). Other antibiotics were not associated with resistance. Resistance was less frequent in patients receiving ESCs and an aminoglycoside. We conclude that prior use of ESCs is associated with the isolation of resistant group I beta-lactamase-producing organisms. Concomitant use of an aminoglycoside may decrease this risk.

Aim Species distribution models are used across evolution, ecology, conservation and epidemiology to make critical decisions and study biological phenomena, often in cases where experimental approaches are intractable. Choices regarding optimal models, methods and data are typically made based on discrimination accuracy: a model's ability to predict subsets of species occurrence data that were withheld during model construction. However, empirical applications of these models often involve making biological inferences based on continuous estimates of relative habitat suitability as a function of environmental predictor variables. We term the reliability of these biological inferences ‘functional accuracy.’ We explore the link between discrimination accuracy and functional accuracy. Methods Using a simulation approach we investigate whether models that make good predictions of species distributions correctly infer the underlying relationship between environmental predictors and the suitability of habitat. Results We demonstrate that discrimination accuracy is only informative when models are simple and similar in structure to the true niche, or when data partitioning is geographically structured. However, the utility of discrimination accuracy for selecting models with high functional accuracy was low in all cases. Main conclusions These results suggest that many empirical studies and decisions are based on criteria that are unrelated to models’ usefulness for their intended purpose. We argue that empirical modelling studies need to place significantly more emphasis on biological insight into the plausibility of models, and that the current approach of maximizing discrimination accuracy at the expense of other considerations is detrimental to both the empirical and methodological literature in this active field. Finally, we argue that future development of the field must include an increased emphasis on simulation; methodological studies based on ability to predict withheld occurrence data may be largely uninformative about best practices for applications where interpretation of models relies on estimating ecological processes, and will unduly penalize more biologically informative modelling approaches.

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The ‘expensive‐tissue hypothesis’ states that investment in one metabolically costly tissue necessitates decreased investment in other tissues and has been one of the keystone concepts used in studying the evolution of metabolically expensive tissues. The trade‐offs expected under this hypothesis have been investigated in comparative studies in a number of clades, yet support for the hypothesis is mixed. Nevertheless, the expensive‐tissue hypothesis has been used to explain everything from the evolution of the human brain to patterns of reproductive investment in bats. The ambiguous support for the hypothesis may be due to interspecific differences in selection, which could lead to spurious results both positive and negative. To control for this, we conduct a study of trade‐offs within a single species, Thalassoma bifasciatum, a coral reef fish that exhibits more intraspecific variation in a single tissue (testes) than is seen across many of the clades previously analysed in studies of tissue investment. This constitutes a robust test of the constraints posited under the expensive‐tissue hypothesis that is not affected by many of the factors that may confound interspecific studies. However, we find no evidence of trade‐offs between investment in testes and investment in liver or brain, which are typically considered to be metabolically expensive. Our results demonstrate that the frequent rejection of the expensive‐tissue hypothesis may not be an artefact of interspecific differences in selection and suggests that organisms may be capable of compensating for substantial changes in tissue investment without sacrificing mass in other expensive tissues.

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Sleep is a state of immobility characterized by three key criteria: an increased threshold of arousal, rapid reversal to an alert state, and evidence of homeostatic “rebound sleep” in which there is an increase of time spent in this quiescent state following sleep deprivation. Common European cuttlefish, Sepia officinalis, show states of quiescence during which they meet the last two of these three criteria, yet also show spontaneous bursts of arm and eye movements that accompany rapid changes in chromatophore patterns in the skin. Here we report that this rapid-eye movement sleep-like (REMS-like) state is cyclic in nature. Iterations of the REMS-like state last 2.42±0.22 min (±SE) and alternate with 34.01±1.49 min of the quiescent sleep-like state. These states alternate for durations lasting 176.89±36.71 min. We found clear evidence that this REMS-like state (i) occurs in animals younger than previously reported; (ii) follows an ultradian pattern; (iii) includes intermittent dynamic chromatophore patterning, representing fragments of normal patterning seen in the waking state for a wide range of signaling and camouflage; and (iv) shows variability in the intensity of expression of these skin patterns between and within individuals. These data suggest that cephalopods, which are molluscs with an elaborate brain and complex behavior, possess a sleep-like state that resembles behaviorally the vertebrate REM sleep state, although the exact nature and mechanism of this form of sleep may differ from that of vertebrates.

Predicting the response of endemic species to urbanization has emerged as a fundamental challenge in 21st century conservation biology. The factors that underlie population declines of reptiles are particularly nebulous, as these are often the least understood class of vertebrates in a given community. In this study, we assess correlations between feeding ecology and phenotypic traits of the Lesser Antillean endemic Dutch leaf-toed gecko, Phyllodactylus martini, along an urban gradient in the Caribbean island of Curaçao. There has been a marked decline of this species in developed habitats associated with the invasive tropical house gecko Hemidactylus mabouia. We find a correlation between aspects of locomotor morphology and prey in undeveloped habitats that is absent in developed habitats. Analyses of stomach contents further suggest that Phyllodactylus martini alters primary prey items in developed areas. However, changes in prey promote the overlap in foraging niches between Phyllodactylus martini and Hemidactylus mabouia, suggesting that direct resource competition is contributing to the decline of Phyllodactylus martini. In addition to competitive exclusion, we suggest that the urban extirpation of Phyllodactylus martini could also be attributed to a top-down control on population growth by Hemidactylus mabouia. Colonizations of walls put Phyllodactylus martini in direct contact with Hemidactylus mabouia increasing the chances for predation events, as evidenced by our observation of a predation event on a Phyllodactylus martini juvenile by an adult Hemidactylus mabuoia. In total, our results add to a growing body of literature demonstrating the threat that invasive synanthropic reptiles pose to endemics that might otherwise be able to cope with increased urbanization pressures.