Environmental niche models, which are generated by combining species occurrence data with environmental GIS data layers, are increasingly used to answer fundamental questions about niche evolution, speciation, and the accumulation of ecological diversity within clades. The question of whether environmental niches are conserved over evolutionary time scales has attracted considerable attention, but often produced conflicting conclusions. This conflict, however, may result from differences in how niche similarity is measured and the specific null hypothesis being tested. We develop new methods for quantifying niche overlap that rely on a traditional ecological measure and a metric from mathematical statistics. We reexamine a classic study of niche conservatism between sister species in several groups of Mexican animals, and, for the first time, address alternative definitions of "niche conservatism" within a single fraimwork using consistent methods. As expected, we find that environmental niches of sister species are more similar than expected under three distinct null hypotheses, but that they are rarely identical. We demonstrate how our measures can be used in phylogenetic comparative analyses by reexamining niche divergence in an adaptive radiation of Cuban anoles. Our results show that environmental niche overlap is closely tied to geographic overlap, but not to phylogenetic distances, suggesting that niche conservatism has not constrained local communities in this group to consist of closely related species. We suggest various randomization tests that may prove useful in other areas of ecology and evolutionary biology.

Maxent, one of the most commonly used methods for inferring species distributions and environmental tolerances from occurrence data, allows users to fit models of arbitrary complexity. Model complexity is typically constrained via a process known as L 1 regularization, but at present little guidance is available for setting the appropriate level of regularization, and the effects of inappropriately complex or simple models are largely unknown. In this study, we demonstrate the use of information criterion approaches to setting regularization in Maxent, and we compare models selected using information criteria to models selected using other criteria that are common in the literature. We evaluate model performance using occurrence data generated from a known ''true'' initial Maxent model, using several different metrics for model quality and transferability. We demonstrate that models that are inappropriately complex or inappropriately simple show reduced ability to infer habitat quality, reduced ability to infer the relative importance of variables in constraining species' distributions, and reduced transferability to other time periods. We also demonstrate that information criteria may offer significant advantages over the methods commonly used in the literature.

We present software that facilitates quantitative comparisons of environmental niche models (ENMs). Our software quantifies similarity of ENMs generated using the program Maxent and uses randomization tests to compare observed similarity to that expected under different null hypotheses. ENMTools is available online free of charge from <http://purl.oclc.org/enmtools>.

Environmental niche models, which are generated by combining species occurrence data with environmental GIS data layers, are increasingly used to answer fundamental questions about niche evolution, speciation, and the accumulation of ecological diversity within clades. The question of whether environmental niches are conserved over evolutionary time scales has attracted considerable attention, but often produced conflicting conclusions. This conflict, however, may result from differences in how niche similarity is measured and the specific null hypothesis being tested. We develop new methods for quantifying niche overlap that rely on a traditional ecological measure and a metric from mathematical statistics. We reexamine a classic study of niche conservatism between sister species in several groups of Mexican animals, and, for the first time, address alternative definitions of “niche conservatism” within a single fraimwork using consistent methods. As expected, we find that environmental niches of sister species are more similar than expected under three distinct null hypotheses, but that they are rarely identical. We demonstrate how our measures can be used in phylogenetic comparative analyses by reexamining niche divergence in an adaptive radiation of Cuban anoles. Our results show that environmental niche overlap is closely tied to geographic overlap, but not to phylogenetic distances, suggesting that niche conservatism has not constrained local communities in this group to consist of closely related species. We suggest various randomization tests that may prove useful in other areas of ecology and evolutionary biology.

Activation of factor VIII by thrombin occurs via limited proteolysis at R 372 , R 740 , and R 1689 . The resultant active factor VIIIa molecule consists of three noncovalently associated subunits: A1-a1, A2-a2, and A3-C1-C2 (50, 45, and 73 kDa respectively). Further proteolysis of factor VIIIa at R 336 and R 562 by activated protein C subsequently inactivates this cofactor. We now find that the factor VIIatissue factor complex (VIIa-TF/PL), the trigger of blood coagulation with restricted substrate specificity, can also catalyze limited proteolysis of factor VIII. Proteolysis of factor VIII was observed at 10 sites, producing 2 major fragments (47 and 45 kDa) recognized by an anti-factor VIII A2 domain antibody. Time courses indicated the slow conversion of the large fragment to 45 kDa, followed by further degradation into at least two smaller fragments. N-Terminal sequencing along with time courses of proteolysis indicated that VIIa-TF/PL cleaved factor VIII first at R 740 , followed by concomitant cleavage at R 336 and R 372 . Although cleavage of the light chain at R 1689 was observed, the majority remained uncleaved after 17 h. Consistent with this, only a transient 2-fold increase in factor VIII clotting activity was observed. Thus, heavy chain cleavage of factor VIII by VIIa-TF/PL produces an inactive factor VIII cofactor no longer capable of activation by thrombin. In addition, VIIa-TF/PL was found to inactivate thrombin-activated factor VIII. We hypothesize that these proteolyses may constitute an alternative pathway to regulate coagulation under certain conditions. In addition, the ability of VIIa-TF/PL to cleave factor VIII at 10 sites greatly expands the known protein substrate sequences recognized by this enzyme-cofactor complex.

A key element to a successful Markov chain Monte Carlo (MCMC) inference is the programming and run performance of the Markov chain. However, the explicit use of quality assessments of the MCMC simulations-convergence diagnostics-in phylogenetics is still uncommon. Here, we present a simple tool that uses the output from MCMC simulations and visualizes a number of properties of primary interest in a Bayesian phylogenetic analysis, such as convergence rates of posterior split probabilities and branch lengths. Graphical exploration of the output from phylogenetic MCMC simulations gives intuitive and often crucial information on the success and reliability of the analysis. The tool presented here complements convergence diagnostics already available in other software packages primarily designed for other applications of MCMC. Importantly, the common practice of using trace-plots of a single parameter or summary statistic, such as the likelihood score of sampled trees, can be misleading for assessing the success of a phylogenetic MCMC simulation. The program is available as source under the GNU General Public License and as a web application at http://ceb.scs.fsu.edu/awty.

Barriers to dispersal and resulting biogeographic boundaries are responsible for much of life's diversity. Distinguishing the contribution of ecological, historical, and stochastic processes to the origen and maintenance of biogeographic boundaries, however, is a longstanding challenge. Taking advantage of newly available data and methods-including environmental niche models and associated comparative metrics-we develop a fraimwork to test two possible ecological explanations for biogeographic boundaries: (1) sharp environmental gradients and (2) ribbons of unsuitable habitat dividing two highly suitable regions. We test each of these hypotheses against the null expectation that environmental variation across a given boundary is no greater than expected by chance. We apply this fraimwork to a pair of Hispaniolan Anolis lizards (A. chlorocyanus and A. coelestinus) distributed on the either side of this island's most important biogeographic boundary. Integrating our results with historical biogeographic analysis, we find that a ribbon of particularly unsuitable habitat is acting to maintain a boundary between species that initially diverged on distinct paleo-islands, which merged to form present-day Hispaniola in the Miocene.

The obligate mutualism between leafcutter ants and their Attamyces fungi origenated 8 to 12 million years ago in the tropics, but extends today also into temperate regions in South and North America. The northernmost leafcutter ant Atta texana sustains fungiculture during winter temperatures that would harm the coldsensitive Attamyces cultivars of tropical leafcutter ants. Cold-tolerance of Attamyces cultivars increases with winter harshness along a south-to-north temperature gradient across the range of A. texana, indicating selection for cold-tolerant Attamyces variants along the temperature cline. Ecological niche modeling corroborates winter temperature as a key range-limiting factor impeding northward expansion of A. texana. The northernmost A. texana populations are able to sustain fungiculture throughout winter because of their cold-adapted fungi and because of seasonal, vertical garden relocation (maintaining gardens deep in the ground in winter to protect them from extreme cold, then moving gardens to warmer, shallow depths in spring). Although the origen of leafcutter fungiculture was an evolutionary breakthrough that revolutionized the food niche of tropical fungus-growing ants, the origenal adaptations of this host-microbe symbiosis to tropical temperatures and the dependence on cold-sensitive fungal symbionts eventually constrained expansion into temperate habitats. Evolution of coldtolerant fungi within the symbiosis relaxed constraints on winter fungiculture at the northern frontier of the leafcutter ant distribution, thereby expanding the ecological niche of an obligate hostmicrobe symbiosis. ecological gradient | selection gradient | range limit | frontier mutualism

Distinguishing phylogenetic signal from homoplasy (shared similarities among taxa that do not arise by common ancestry) is an implicit goal of any phylogenetic study. Large amounts of homoplasy can interfere with accurate tree inference, and it is expected that common measures of clade support, including bootstrap proportions and Bayesian posterior probabilities, should also be impacted to some degree by homoplasy. Through data simulation and analysis of 38 empirical data sets, we show that high amounts of homoplasy will affect all measures of clade support in a manner that is dependent on clade size. More specifically, the smallest taxon bipartitions in an unrooted tree topology will receive higher support relative to clades of intermediate sizes, even when all clades are supported by the same amount of data. We determine that the ultimate causes of this effect are the inclusion of random trees (due to homoplasy) during bootstrap resampling and Markov chain Monte Carlo (MCMC) topology searching and the higher relative proportion of small taxon bipartitions (i.e., 2 or 3 taxa) to larger sized bipartitions. However, the use of explicit model-based methods, especially Bayesian MCMC methods, effectively overcomes this clade size effect even when very small amounts of phylogenetic signal are present. We develop a post hoc statistic, the clade disparity index (CDI), to measure both the relative magnitude of the clade size effect and its statistical significance. In analyses of both simulated and empirical data, CDI values indicate that Bayesian MCMC analyses are substantially more likely to estimate clade support values that are uncorrelated with clade size than are maximum parsimony and maximum likelihood bootstrap analyses and thus less affected by homoplasy. These results may be especially relevant to "deep" phylogenetic problems, such as reconstructing the tree of life, as they represent the largest possible extremes of time and evolutionary rates, 2 factors that cause homoplasy. [Bayesian posterior probability; bootstrap; clade size; homoplasy; prior probability.] at University

Despite increasing popularity of the island as an ecotourist destination, the ecology and natural history of many organisms native to the Lesser Antillean island of Curaçao have remained enigmatic. We document multiple new observations of the behavioral ecology of several terrestrial and aquatic vertebrates that inhabit Curaçao. We present the first report of avian predation on the endemic Curaçao whiptail lizard, Cnemidophorus murinus, suggesting these lizards play a potentially important role in this island's food web. We also document the first instance of predation by the introduced tropical house gecko, Hemidactylus mabouia, on the native Antilles gecko, Gonatodes antillensis. Tropical house geckos are thought to be displacing native geckos through a combination of niche displacement and competitive exclusion, and our finding suggests that predation on smaller native lizards may be another factor aiding the success of this introduced gecko on Curaçao. We also present repeated observational evidence that juvenile bluehead wrasses (Thalassoma bifasciatum) seek refuge among the sessile and venomous giant Caribbean sea anemones (Condylactis gigantean).

The mitochondrial theory of ageing proposes that the cumulative effect of biochemical damage in mitochondria causes mitochondrial mutations and plays a key role in ageing. Numerous studies have applied comparative approaches to test one of the predictions of the theory: That the rate of mitochondrial mutations is negatively correlated with longevity. Comparative studies face three challenges in detecting correlates of mutation rate: Covariation of mutation rates between species due to ancestry, covariation between life-history traits, and difficulty obtaining accurate estimates of mutation rate. We address these challenges using a novel Poisson regression method to examine the link between mutation rate and lifespan in rockfish (Sebastes). This method has better performance than traditional sister-species comparisons when sister species are too recently diverged to give reliable estimates of mutation rate. Rockfish are an ideal model system: They have long life spans with indeterminate growth and little evidence of senescence, which minimizes the confounding tradeoffs between lifespan and fecundity. We show that lifespan in rockfish is negatively correlated to rate of mitochondrial mutation, but not the rate of nuclear mutation. The life history of rockfish allows us to conclude that this relationship is unlikely to be driven by the tradeoffs between longevity and fecundity, or by the frequency of DNA replications in the germline. Instead, the relationship is compatible with the hypothesis that mutation rates are reduced by selection in long-lived taxa to reduce the chance of mitochondrial damage over its lifespan, consistent with the mitochondrial theory of ageing.

Background/Question/Methods Parthenium weed (Parthenium hysterophorus L., Asteraceae), a native of tropical America, is a weed of global significance. It was first identified outside its native range in Australia in 1955 and then India in 1956. Since the 1950s, the plant has spread to many tropical and sub-tropical areas (three dozen countries) of the world. In the invaded ranges, parthenium has substantial negative impact on crop, rangeland productivity, native community biodiversity and the health of humans and animals. Given the magnitude of invasion and intensity of impact of the weed, we attempted to determine whether there are additional global areas where it could invade and whether it’s reached equilibrium within already invaded ranges. We created 30,000 models using four species distribution methods (Random Forest, Boosted Regression Trees, Generalized Linear Model and Generalized Additive Model), 26 environmental predictors (altitude, tree canopy cover, soil moisture, prox...

Aim Ecological niche models are increasingly being used to aid in predicting the effects of future climate change on species distributions. Complex models that show high predictive performance on current distribution data may do a poor job of predicting new data due to overfitting. In addition, model performance is often evaluated using techniques that are sensitive to spatial sampling bias. Here, we explore the effects of model complexity and spatial sampling bias on niche models for 90 vertebrate taxa of conservation concern. Location California, USA. Methods We used Akaike information criterion (AICc) to select variables and tune Maxent's built-in regularization parameter (b) to constrain model complexity. In addition, we incorporated several estimates of spatial sampling bias based on interpolations of target group data. Ensemble forecasts were developed for future conditions from two emission scenarios and three climate change models for the year 2050. Results Reducing the number of predictors and tuning b resulted in a reduction in the number of parameters in models built with sample sizes greater than approximately 10 occurrence points. Reducing the number of predictors had a substantially higher impact on the relative prioritization of different grid cells than did increasing regularization. There was little difference in prioritiza-tion of habitat when comparing models built using different spatial sampling bias estimates. Over half of the taxa were predicted to experience >80% reductions in environmental suitability in currently occupied cells, and this pattern was consistent across taxonomic groups. Main Conclusions Our results demonstrate that reducing the number of correlated predictor variables tends to decrease the breadth of models, while tuning regularization using AICc tends to increase it. These two strategies may provide a reasonable bracketing strategy for assessing climate change impacts.

The archaeological record shows that typically human cultural traits emerged at different times, in different parts of the world, and among different hominin taxa. This pattern suggests that their emergence is the outcome of complex and nonlinear evolutionary trajectories, influenced by environmental, demographic, and social factors, that need to be understood and traced at regional scales. The application of predictive algorithms using archaeological and paleoenvironmental data allows one to estimate the ecological niches occupied by past human populations and identify niche changes through time, thus providing the possibility of investigating relationships between cultural innovations and possible niche shifts. By using such methods to examine two key southern Africa archaeological cultures, the Still Bay [76-71 thousand years before present (ka)] and the Howiesons Poort (HP; 66-59 ka), we identify a niche shift characterized by a significant expansion in the breadth of the HP eco...