A discrete-time host–parasitoid model with an Allee effect

We introduce a discrete-time host–parasitoid model with a strong Allee effect on the host. We adapt the Nicholson–Bailey model to have a positive density dependent factor due to the presence of an Allee effect, and a negative density dependence factor due to intraspecific competition. It is shown that there are two scenarios, the first with no interior fixed points and the second with one interior fixed point. In the first scenario, we show that either both host and parasitoid will go to extinction or there are two regions, an extinction region where both species go to extinction and an exclusion region in which the host survives and tends to its carrying capacity. In the second scenario, we show that either both host and parasitoid will go to extinction or there are two regions, an extinction region where both species go to extinction and a coexistence region where both species survive.     

Environmental correlates of the Late Quaternary regional extinctions of large and small Palaearctic mammals

Most studies of mammal extinctions during the Pleistocene–Holocene transition explore the relative effects of climate change vs human impacts on these extinctions, but the relative importance of the different environmental factors involved remains poorly understood. Moreover, these studies are strongly biased towards megafauna, which may have been more influenced by human hunting than species of small body size. We examined the potential environmental causes of Pleistocene–Holocene mammal extinctions by linking regional environmental characteristics with the regional extinction rates of large and small mammals in 14 Palaearctic regions. We found that regional extinction rates were larger for megafauna, but extinction patterns across regions were similar for both size groups, emphasizing the importance of environmental change as an extinction factor as opposed to hunting. Still, the bias towards megafauna extinctions was larger in southern Europe and smaller in central Eurasia. The loss of suitable habitats, low macroclimatic heterogeneity within regions and an increase in precipitation were identified as the strongest predictors of regional extinction rates. Suitable habitats for many species of the Last Glacial fauna were grassland and desert, but not tundra or forest. The low‐extinction regions identified in central Eurasia are characterized by the continuous presence of grasslands and deserts until the present. In contrast, forest expansion associated with an increase in precipitation and temperature was likely the main factor causing habitat loss in the high‐extinction regions. The shift of grassland into tundra also contributed to the loss of suitable habitats in northern Eurasia. Habitat loss was more strongly related to the extinctions of megafauna than of small mammals. Ungulate species with low tolerance to deep snow were more likely to go regionally extinct. Thus, the increase in precipitation at the Pleistocene–Holocene transition may have also directly contributed to the extinctions by creating deep snow cover which decreases forage availability in winter.     

Latitudinal gradients in North American avian species richness,turnover rates and extinction probabilities

A decline in species richness moving from equatorial regions to polar regions is a common, but not universal, macroecological pattern. Many studies have focused on this pattern, but few have focused on how the vital rates responsible for species richness patterns, local rates of species extinction and turnover, vary with latitude. We examine patterns of richness, turnover and extinction in North American avian communities inhabiting three ecoregions, using methods that account for failure to detect all species present. We use breeding bird point count data from > 1000 routes in the Breeding Bird Survey collected from 1982 to 2001 to estimate richness, extinction probability and turnover rates. Our analyses differ from others in 1) the use of annual estimates derived at specific locations rather than index data accumulated over numbers of years, 2) the use of estimators that incorporated detection probabilities and 3) a focus on dynamical processes (colonization, extinction) in addition to static patterns (species richness). We find average species richness estimates (48 to 135 species) increasing with latitude for all three regions, contradicting predictions based on the latitudinal diversity gradient. The estimated rates of extinction and turnover declined with latitude across the three ecoregions. We speculate that higher richness might be linked to periods of superabundant food supply in northern areas that support greater numbers of resident and migrant species. Our primary ecological conclusions are that the latitudinal gradient in species richness is reversed for North American birds in the studied ecoregions, and that both local extinction and turnover decrease from southern to northern latitudes. Thus, the vital rates that determine richness show evidence of greater stability and reduced dynamics in northern areas of higher richness. We recommend additional studies examining patterns of colonization, extinction and turnover in communities, that use clearly defined estimators that deal with detection probability.     

Evolution and the latitudinal diversity gradient: speciation, extinction and biogeography

A latitudinal gradient in biodiversity has existed since before the time of the dinosaurs, yet how and why this gradient arose remains unresolved. Here we review two major hypotheses for the origin of the latitudinal diversity gradient. The time and area hypothesis holds that tropical climates are older and historically larger, allowing more opportunity for diversification. This hypothesis is supported by observations that temperate taxa are often younger than, and nested within, tropical taxa, and that diversity is positively correlated with the age and area of geographical regions. The diversification rate hypothesis holds that tropical regions diversify faster due to higher rates of speciation (caused by increased opportunities for the evolution of reproductive isolation, or faster molecular evolution, or the increased importance of biotic interactions), or due to lower extinction rates. There is phylogenetic evidence for higher rates of diversification in tropical clades, and palaeontological data demonstrate higher rates of origination for tropical taxa, but mixed evidence for latitudinal differences in extinction rates. Studies of latitudinal variation in incipient speciation also suggest faster speciation in the tropics. Distinguishing the roles of history, speciation and extinction in the origin of the latitudinal gradient represents a major challenge to future research.     

Large-scale phylogenetic analyses reveal the causes of high tropical amphibian diversity

Many groups show higher species richness in tropical regions but the underlying causes remain unclear. Despite many competing hypotheses to explain latitudinal diversity gradients, only three processes can directly change species richness across regions: speciation, extinction and dispersal. These processes can be addressed most powerfully using large-scale phylogenetic approaches, but most previous studies have focused on small groups and recent time scales, or did not separate speciation and extinction rates. We investigate the origins of high tropical diversity in amphibians, applying new phylogenetic comparative methods to a tree of 2871 species. Our results show that high tropical diversity is explained by higher speciation in the tropics, higher extinction in temperate regions and limited dispersal out of the tropics compared with colonization of the tropics from temperate regions. These patterns are strongly associated with climate-related variables such as temperature, precipitation and ecosystem energy. Results from models of diversity dependence in speciation rate suggest that temperate clades may have lower carrying capacities and may be more saturated (closer to carrying capacity) than tropical clades. Furthermore, we estimate strikingly low tropical extinction rates over geological time scales, in stark contrast to the dramatic losses of diversity occurring in tropical regions presently.     

Extinction and quasi-stationarity in the Verhulst logistic model.

We formulate and analyse a stochastic version of the Verhulst deterministic model for density-dependent growth of a single population. Three parameter regions with qualitatively different behaviours are identified. Explicit approximations of the quasi-stationary distribution and of the expected time to extinction are presented in each of these regions. The quasi-stationary distribution is approximately normal, and the time to extinction is long, in one of these regions. Another region has a short time to extinction and a quasi-stationary distribution that is approximately truncated geometric. A third region is a transition region between these two. Here the time to extinction is moderately long and the quasi-stationary distribution has a more complicated behaviour. Numerical illustrations are given.     

Persistent histone modifications at the BDNF and Cdk‐5 promoters following extinction of nicotine‐seeking in rats

Drugs of addiction lead to a wide range of epigenetic changes at the promoter regions of genes directly implicated in learning and memory processes. We have previously shown that the histone deactylase inhibitor, sodium butyrate (NaB), accelerates the extinction of nicotine‐seeking and provides resistance to relapse. Here, we explore the potential molecular mechanisms underlying this effect. Rats received intravenous nicotine or saline self‐administration, followed by 6 days of extinction training, with each extinction session followed immediately by treatment with NaB or vehicle. On the last day of extinction, rats were killed and the medial ventral prefrontal cortex retained for chromatin immunoprecipitation and quantitative polymerase chain reaction (qPCR). A history of nicotine exposure significantly decreased H3K14 acetylation at the brain‐derived neurotrophic factor (BDNF) exon IV promoter, and this effect was abolished with NaB treatment. In contrast, nicotine self‐administration alone, resulted in a significant decrease in histone methylation at the H3K27me3 and H3K9me2 marks in the promoter regions of BDNF exon IV and cyclin‐dependent kinase 5 (Cdk‐5). Quantitative PCR‐identified changes in several genes associated with NaB treatment that were independent of nicotine exposure; however, an interaction of nicotine history and NaB treatment was detected only in the expression of BDNF IV and BDNF IX. Together these results suggest that nicotine self‐administration leads to a number of epigenetic changes at both the BDNF and Cdk‐5 promoters, and that these changes may contribute to the enhanced extinction of nicotine‐seeking by NaB.     

Global distribution and drivers of language extinction risk

Many of the world''s languages face serious risk of extinction. Efforts to prevent this cultural loss are severely constrained by a poor understanding of the geographical patterns and drivers of extinction risk. We quantify the global distribution of language extinction risk—represented by small range and speaker population sizes and rapid declines in the number of speakers—and identify the underlying environmental and socioeconomic drivers. We show that both small range and speaker population sizes are associated with rapid declines in speaker numbers, causing 25% of existing languages to be threatened based on criteria used for species. Language range and population sizes are small in tropical and arctic regions, particularly in areas with high rainfall, high topographic heterogeneity and/or rapidly growing human populations. By contrast, recent speaker declines have mainly occurred at high latitudes and are strongly linked to high economic growth. Threatened languages are numerous in the tropics, the Himalayas and northwestern North America. These results indicate that small-population languages remaining in economically developed regions are seriously threatened by continued speaker declines. However, risks of future language losses are especially high in the tropics and in the Himalayas, as these regions harbour many small-population languages and are undergoing rapid economic growth.     

Evolutionary and biogeographical shifts in response to the Late Ordovician mass extinction

The Late Ordovician mass extinction was an interval of high extinction with inferred low ecological selectivity, resulting in little change in community structure after the event. In contrast, the mass extinction may have fundamentally changed evolutionary dynamics in the surviving groups. We investigated the phylogenetic relationships among strophomenoid brachiopods, a diverse brachiopod superfamily that was a primary component of Ordovician ecosystems. Four Ordovician families/subfamilies sampled in the analysis (Rafinesquinidae, Strophomeninae, Glyptomenidae and Furcitellinae) were reconstructed as monophyletic groups, and the base of the strophomenoid clade that dominated the Silurian recovery was reconstructed as diversifying alongside these families during the Middle Ordovician. We time‐calibrated the phylogeny and used geographical occurrences to investigate biogeographical changes in the strophomenoids through time with the R package BiogeoBEARS . Our results indicate that extinction was higher in taxa whose ranges were constrained to tropical or subtropical regions. Furthermore, our results suggest important shifts in the diversification patterns of these brachiopods after the mass extinction. While most of the strophomenoid families survived the Late Ordovician event, ecologically abundant taxonomic groups during the Ordovician were either driven to extinction, reduced in diversity, or slowly died off during the Silurian. The new abundant strophomenoid taxa derived from one clade (consisting of Silurian–Devonian groups such as Douvillinidae, Strophodontidae and Amphistrophiidae) that diversified during the post‐extinction radiation. Our results suggest the selective diversification during the Silurian radiation, rather than selective extinction in the Late Ordovician, had a greater impact on the evolutionary history of strophomenoid brachiopods.     

Camera-based visibility estimation: Incorporating multiple regions and unlabeled observations

This paper investigates image processing and pattern recognition techniques to estimate atmospheric visibility based on the visual content of images from off-the-shelf cameras. We propose a prediction model that first relates image contrast measured through standard image processing techniques to atmospheric transmission. This is then related to the most common measure of atmospheric visibility, the coefficient of light extinction. The regression model is learned using a training set of images and corresponding light extinction values as measured using a transmissometer.The major contributions of this paper are twofold. First, we propose two predictive models that incorporate multiple scene regions into the estimation: regression trees and multivariate linear regression. Incorporating multiple regions is important since regions at different distances are effective for estimating light extinction under different visibility regimes. The second major contribution is a semi-supervised learning framework, which incorporates unlabeled training samples to improve the learned models. Leveraging unlabeled data for learning is important since in many applications, it is easier to obtain observations than to label them. We evaluate our models using a dataset of images and ground truth light extinction values from a visibility camera system in Phoenix, Arizona.     

How diversification rates and diversity limits combine to create large-scale species-area relationships

Species-area relationships (SARs) have mostly been treated from an ecological perspective, focusing on immigration, local extinction and resource-based limits to species coexistence. However, a full understanding across large regions is impossible without also considering speciation and global extinction. Rates of both speciation and extinction are known to be strongly affected by area and thus should contribute to spatial patterns of diversity. Here, we explore how variation in diversification rates and ecologically mediated diversity limits among regions of different sizes can result in the formation of SARs. We explain how this area-related variation in diversification can be caused by either the direct effects of area or the effects of factors that are highly correlated with area, such as habitat diversity and population size. We also review environmental, clade-specific and historical factors that affect diversification and diversity limits but are not highly correlated with region area, and thus are likely to cause scatter in observed SARs. We present new analyses using data on the distributions, ages and traits of mammalian species to illustrate these mechanisms; in doing so we provide an integrated perspective on the evolutionary processes shaping SARs.     

Faster Speciation and Reduced Extinction in the Tropics Contribute to the Mammalian Latitudinal Diversity Gradient

The increase in species richness from the poles to the tropics, referred to as the latitudinal diversity gradient, is one of the most ubiquitous biodiversity patterns in the natural world. Although understanding how rates of speciation and extinction vary with latitude is central to explaining this pattern, such analyses have been impeded by the difficulty of estimating diversification rates associated with specific geographic locations. Here, we use a powerful phylogenetic approach and a nearly complete phylogeny of mammals to estimate speciation, extinction, and dispersal rates associated with the tropical and temperate biomes. Overall, speciation rates are higher, and extinction rates lower, in the tropics than in temperate regions. The diversity of the eight most species-rich mammalian orders (covering 92% of all mammals) peaks in the tropics, except that of the Lagomorpha (hares, rabbits, and pikas) reaching a maxima in northern-temperate regions. Latitudinal patterns in diversification rates are strikingly consistent with these diversity patterns, with peaks in species richness associated with low extinction rates (Primates and Lagomorpha), high speciation rates (Diprotodontia, Artiodactyla, and Soricomorpha), or both (Chiroptera and Rodentia). Rates of range expansion were typically higher from the tropics to the temperate regions than in the other direction, supporting the “out of the tropics” hypothesis whereby species originate in the tropics and disperse into higher latitudes. Overall, these results suggest that differences in diversification rates have played a major role in shaping the modern latitudinal diversity gradient in mammals, and illustrate the usefulness of recently developed phylogenetic approaches for understanding this famous yet mysterious pattern.     

The ghosts of mammals past: biological and geographical patterns of global mammalian extinction across the Holocene

Although the recent historical period is usually treated as a temporal base-line for understanding patterns of mammal extinction, mammalian biodiversity loss has also taken place throughout the Late Quaternary. We explore the spatial, taxonomic and phylogenetic patterns of 241 mammal species extinctions known to have occurred during the Holocene up to the present day. To assess whether our understanding of mammalian threat processes has been affected by excluding these taxa, we incorporate extinct species data into analyses of the impact of body mass on extinction risk. We find that Holocene extinctions have been phylogenetically and spatially concentrated in specific taxa and geographical regions, which are often not congruent with those disproportionately at risk today. Large-bodied mammals have also been more extinction-prone in most geographical regions across the Holocene. Our data support the extinction filter hypothesis, whereby regional faunas from which susceptible species have already become extinct now appear less threatened; they may also suggest that different processes are responsible for driving past and present extinctions. We also find overall incompleteness and inter-regional biases in extinction data from the recent fossil record. Although direct use of fossil data in future projections of extinction risk is therefore not straightforward, insights into extinction processes from the Holocene record are still useful in understanding mammalian threat.     

Extinction learning in humans: role of the amygdala and vmPFC

Understanding how fears are acquired is an important step in translating basic research to the treatment of fear-related disorders. However, understanding how learned fears are diminished may be even more valuable. We explored the neural mechanisms of fear extinction in humans. Studies of extinction in nonhuman animals have focused on two interconnected brain regions: the amygdala and the ventral medial prefrontal cortex (vmPFC). Consistent with animal models suggesting that the amygdala is important for both the acquisition and extinction of conditioned fear, amygdala activation was correlated across subjects with the conditioned response in both acquisition and early extinction. Activation in the vmPFC (subgenual anterior cingulate) was primarily linked to the expression of fear learning during a delayed test of extinction, as might have been expected from studies demonstrating this region is critical for the retention of extinction. These results provide evidence that the mechanisms of extinction learning may be preserved across species.     

Rarity and persistence

Rarity is a population characteristic that is usually associated with a high risk of extinction. We argue here, however, that chronically rare species (those with low population densities over many generations across their entire ranges) may have individual‐level traits that make populations more resistant to extinction. The major obstacle to persistence at low density is successful fertilisation (union between egg and sperm), and chronically rare species are more likely to survive when (1) fertilisation occurs inside or close to an adult, (2) mate choice involves long‐distance signals, (3) adults or their surrogate gamete dispersers are highly mobile, or (4) the two sexes are combined in a single individual. In contrast, external fertilisation and wind‐ or water‐driven passive dispersal of gametes, or sluggish or sedentary adult life habits in the absence of gamete vectors, appear to be incompatible with sustained rarity. We suggest that the documented increase in frequency of these traits among marine genera over geological time could explain observed secular decreases in rates of background extinction. Unanswered questions remain about how common chronic rarity actually is, which traits are consistently associated with chronic rarity, and how chronically rare species are distributed among taxa, and among the world's ecosystems and regions.     

Comparative dynamics of avian communities across edges and interiors of North American ecoregions

Aim Based on a priori hypotheses, we developed predictions about how avian communities might differ at the edges vs. interiors of ecoregions. Specifically, we predicted lower species richness and greater local turnover and extinction probabilities for regional edges. We tested these predictions using North American Breeding Bird Survey (BBS) data across nine ecoregions over a 20‐year time period. Location Data from 2238 BBS routes within nine ecoregions of the United States were used. Methods The estimation methods used accounted for species detection probabilities < 1. Parameter estimates for species richness, local turnover and extinction probabilities were obtained using the program COMDYN. We examined the difference in community‐level parameters estimated from within exterior edges (the habitat interface between ecoregions), interior edges (the habitat interface between two bird conservation regions within the same ecoregion) and interior (habitat excluding interfaces). General linear models were constructed to examine sources of variation in community parameters for five ecoregions (containing all three habitat types) and all nine ecoregions (containing two habitat types). Results Analyses provided evidence that interior habitats and interior edges had on average higher bird species richness than exterior edges, providing some evidence of reduced species richness near habitat edges. Lower average extinction probabilities and turnover rates in interior habitats (five‐region analysis) provided some support for our predictions about these quantities. However, analyses directed at all three response variables, i.e. species richness, local turnover, and local extinction probability, provided evidence of an interaction between habitat and region, indicating that the relationships did not hold in all regions. Main conclusions The overall predictions of lower species richness, higher local turnover and extinction probabilities in regional edge habitats, as opposed to interior habitats, were generally supported. However, these predicted tendencies did not hold in all regions.     

Biases,gaps, and opportunities in mammalian extinction risk research

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Neural circuitry underlying the regulation of conditioned fear and its relation to extinction

Recent efforts to translate basic research to the treatment of clinical disorders have led to a growing interest in exploring mechanisms for diminishing fear. This research has emphasized two approaches: extinction of conditioned fear, examined across species; and cognitive emotion regulation, unique to humans. Here, we sought to examine the similarities and differences in the neural mechanisms underlying these two paradigms for diminishing fear. Using an emotion regulation strategy, we examine the neural mechanisms of regulating conditioned fear using fMRI and compare the resulting activation pattern with that observed during classic extinction. Our results suggest that the lateral PFC regions engaged by cognitive emotion regulation strategies may influence the amygdala, diminishing fear through similar vmPFC connections that are thought to inhibit the amygdala during extinction. These findings further suggest that humans may have developed complex cognition that can aid in regulating emotional responses while utilizing phylogenetically shared mechanisms of extinction.     

Functional Richness and Relative Resilience of Bird Communities in Regions with Different Land Use Intensities

Abstract Empirical estimates of the function and resilience of communities under different management regimes can provide valuable information for sustainable natural resource management, but such estimates are scarce to date. We quantified the functional richness and relative resilience of bird communities inhabiting five regions in southeastern Australia that represented different management regimes. First, we show that functional richness and relative resilience were reduced at species-poor sites in all regions. Second, we show that bird communities in agricultural regions had fewer body mass groups and fewer functional groups than expected by chance. This suggests that both the function and the resilience of bird communities in agricultural regions were reduced. The likely mechanisms for the observed loss of function and relative resilience are: (1) the simplification of landscape texture resulting in selective extinction of certain body mass groups; and (2) the selective extinction of certain functional groups that are particularly sensitive to intensive land use. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

The conservation status of African vertebrates is unrelated to environmental and spatial patterns in their geographic ranges

Statistical predictions of the impact of climate change on biodiversity assume that the environmental and spatial characteristics of contemporary species’ distributions reflect the conditions needed for their continued and prolonged existence. Here we explore this assumption by testing whether a species’ threatened status is associated with the amount of variation in its distribution range attributable to environmental and spatial patterns. Using a variation partitioning approach, we decomposed variation in the distribution ranges of 4423 vertebrate species in sub-Saharan Africa into components attributable exclusively to environmental variables (E|S), exclusively to spatial variables (S|E) or to the collinearity between environmental and spatial variables (E∩S). We found that species’ threatened status was unrelated to E|S, S|E or E∩S variation components, but that unexplained variation was higher for species threatened with extinction. This suggests that spatio-environmental patterns in species’ ranges likely underestimate the overall extinction threat caused by climate change. We also found clear geographic patterns in the strength of E|S, S|E or E∩S that differed amongst biogeographical regions, but no component was over- or underrepresented in the present-day protected area network. While there may be benefits to tailoring protected area expansion to differences between biogeographical regions, this should aim to incorporate species-specific information wherever possible.