Integrating detection probabilities in species distribution models of amphibians breeding in Mediterranean temporary ponds

Aim The imperfect detection of species may lead to erroneous conclusions about species–environment relationships. Accuracy in species detection usually requires temporal replication at sampling sites, a time‐consuming and costly monitoring scheme. Here, we applied a lower‐cost alternative based on a double‐sampling approach to incorporate the reliability of species detection into regression‐based species distribution modelling. Location Doñana National Park (south‐western Spain). Methods Using species‐specific monthly detection probabilities, we estimated the detection reliability as the probability of having detected the species given the species‐specific survey time. Such reliability estimates were used to account explicitly for data uncertainty by weighting each absence. We illustrated how this novel framework can be used to evaluate four competing hypotheses as to what constitutes primary environmental control of amphibian distribution: breeding habitat, aestivating habitat, spatial distribution of surrounding habitats and/or major ecosystems zonation. The study was conducted on six pond‐breeding amphibian species during a 4‐year period. Results Non‐detections should not be considered equivalent to real absences, as their reliability varied considerably. The occurrence of Hyla meridionalis and Triturus pygmaeus was related to a particular major ecosystem of the study area, where suitable habitat for these species seemed to be widely available. Characteristics of the breeding habitat (area and hydroperiod) were of high importance for the occurrence of Pelobates cultripes and Pleurodeles waltl. Terrestrial characteristics were the most important predictors of the occurrence of Discoglossus galganoi and Lissotriton boscai, along with spatial distribution of breeding habitats for the last species. Main conclusions We did not find a single best supported hypothesis valid for all species, which stresses the importance of multiscale and multifactor approaches. More importantly, this study shows that estimating the reliability of non‐detection records, an exercise that had been previously seen as a naïve goal in species distribution modelling, is feasible and could be promoted in future studies, at least in comparable systems.     

Climate warming and the decline of amphibians and reptiles in Europe

Aim We explore the relationship between current European distributions of amphibian and reptile species and observed climate, and project species potential distributions into the future. Potential impacts of climate warming are assessed by quantifying the magnitude and direction of modelled distributional shifts for every species. In particular we ask, first, what proportion of amphibian and reptile species are projected to lose and gain suitable climate space in the future? Secondly, do species projections vary according to taxonomic, spatial or environmental properties? And thirdly, what climate factors might be driving projections of loss or gain in suitable environments for species? Location Europe. Methods Distributions of species are modelled with four species–climate envelope techniques (artificial neural networks, generalized linear models, generalized additive models, and classification tree analyses) and distributions are projected into the future using five climate‐change scenarios for 2050. Future projections are made considering two extreme assumptions: species have unlimited dispersal ability and species have no dispersal ability. A novel hybrid approach for combining ensembles of forecasts is then used to group linearly covarying projections into clusters with reduced inter‐model variability. Results We show that a great proportion of amphibian and reptile species are projected to expand distributions if dispersal is unlimited. This is because warming in the cooler northern ranges of species creates new opportunities for colonization. If species are unable to disperse, then most species are projected to lose range. Loss of suitable climate space for species is projected to occur mainly in the south‐west of Europe, including the Iberian Peninsula, whilst species in the south‐east are projected to gain suitable climate. This is because dry conditions in the south‐west are projected to increase, approaching the levels found in North Africa, where few amphibian species are able to persist. Main conclusions The impact of increasing temperatures on amphibian and reptile species may be less deleterious than previously postulated; indeed, climate cooling would be more deleterious for the persistence of amphibian and reptile species than warming. The ability of species to cope with climate warming may, however, be offset by projected decreases in the availability of water. This should be particularly true for amphibians. Limited dispersal ability may further increase the vulnerability of amphibians and reptiles to changes in climate.     

Integrating variability in detection probabilities when designing wildlife surveys: a case study of amphibians from south-eastern Australia

Occupancy-based monitoring programs rely on survey data to infer presence or absence of the target species. However, species may occupy a site and go undetected, leading to erroneous inference of absence (‘false absence’). If detectability is influenced by the time of year or weather conditions, survey protocols can be adjusted to minimize the chance of false absences. In this study, detection probabilities for three amphibian species from south-eastern Australia were modelled using a Bayesian approach. For aural surveys, we compared basic models, which only included effects of survey date, duration and time of day on detection, to models including additional effects of weather. Model selection using deviance information criterion (DIC) suggested that the basic model was the most parsimonious for Crinia signifera, while models including relative humidity and water temperature were most supported for Limnodynastes dumerilii and L. tasmaniensis respectively. When predictive performance was assessed by cross validation, DIC results were largely matched for C. signifera and L. dumerilii, while models of detection for L. tasmaniensis were indistinguishable, AUC scores suggesting inadequate performance. We show how results such as these can be used to design surveys, developing protocols for individual surveys and estimating the number of surveys required under those protocols to achieve a threshold cumulative probability of detection. Conservation managers can use these models to maximize the efficiency of surveys. This will improve the accuracy of occupancy data, and reduce the risk of misdirected conservation actions resulting from false absences.     

Intracellular demography and the dynamics of Salmonella enterica infections

An understanding of within-host dynamics of pathogen interactions with eukaryotic cells can shape the development of effective preventive measures and drug regimes. Such investigations have been hampered by the difficulty of identifying and observing directly, within live tissues, the multiple key variables that underlay infection processes. Fluorescence microscopy data on intracellular distributions of Salmonella enterica serovar Typhimurium (S. Typhimurium) show that, while the number of infected cells increases with time, the distribution of bacteria between cells is stationary (though highly skewed). Here, we report a simple model framework for the intensity of intracellular infection that links the quasi-stationary distribution of bacteria to bacterial and cellular demography. This enables us to reject the hypothesis that the skewed distribution is generated by intrinsic cellular heterogeneities, and to derive specific predictions on the within-cell dynamics of Salmonella division and host-cell lysis. For within-cell pathogens in general, we show that within-cell dynamics have implications across pathogen dynamics, evolution, and control, and we develop novel generic guidelines for the design of antibacterial combination therapies and the management of antibiotic resistance.     

Nonidentifiability of population size from capture-recapture data with heterogeneous detection probabilities

Heterogeneity in detection probabilities has long been recognized as problematic in mark-recapture studies, and numerous models developed to accommodate its effects. Individual heterogeneity is especially problematic, in that reasonable alternative models may predict essentially identical observations from populations of substantially different sizes. Thus even with very large samples, the analyst will not be able to distinguish among reasonable models of heterogeneity, even though these yield quite distinct inferences about population size. The problem is illustrated with models for closed and open populations.     

Entropy and convergence in dynamics and demography

Demographic dynamics is formally equivalent to the dynamics of a Markov chain, as is true of some nonlinear dynamical systems. Convergence to demographic equilibrium can be studied in terms of convergence in the Markov chain. Tuljapurkar (1982) showed that population entropy (Kolmogorov-Sinai entropy) provides information on the rate of this convergence. This paper begins by considering finite state Markov chains, providing elementary proofs of the relationship between convergence rate and entropy, and discusses in detail the uses and limitations of entropy as a convergence measure; these results also apply to Markovian dynamical systems. Next, new qualitative and quantitative arguments are used to discuss the demographic meaning of entropy. An exact relationship is established giving population entropy in terms of the eigenvalues of the Leslie matrix characteristic equation. Finally, the significance of imprimitive and periodic limits is discussed in relation to population entropy.     

Forest dynamics,differential mortality and variable recruitment probabilities

Abstract. Both spatial and temporal variability in recruitment probabilities can lead to coexistence in gap-phase regenerating forests which would otherwise tend to be dominated by fewer species. Using modified Markov models, the potential roles were examined of temporal variability and differential mortality rates among species in the dynamics of a forest for which spatial variability has been rejected as a strong factor leading to coexistence. Differential longevity modifies results obtained from a simple Markov model: it exerts a strong influence on the equilibrium species composition, on the rate of community change and on the time a community requires to reach equilibrium. Simulations with varying transition probabilities mimicked a changing climate, producing four main results: 1. Unless the duration of climate states is very long or very short, forest composition is in a continual state of disequilibrium. 2. Species vary in their response times to changing climate. 3. The mean abundance of each species under a varying climate scenario is different from that expected from the mean climate state. 4. The rare, long-lived species was favored by climatic fluctuations at the expense of more common shorter lived species. Differential mortality rates provide an equilibrium-based mechanism for coexistence, and temporally fluctuating recruitment probabilities a non-equilibrium mechanism. Composition could be maintained by differential longevity among species and climatic fluctuations allowing periodic recruitment of the less common species.     

A general assessment of the conservation status and decline trends of Mexican amphibians

We present a review on the conservation status and population trends of the 372 amphibian species currently recognized for Mexico. We based our analyses on the information gathered by the International Union for the Conservation of Nature-the Global Amphibian Assessment (IUCN-GAA) as well as on available literature about imminent or potential threats to these organisms in Mexico. This country has the fifth largest amphibian fauna in the world and almost 58% of the species that inhabit this country are considered as threatened. We highlight the proportion of species per order, family, and genus that are currently under severe risk in Mexico. In addition, we prepared a detailed list of the main factors that are threatening amphibians in this country. Evidence is provided that the six main mechanisms that are globally leading amphibians to extinction (alien species, over-exploitation, land use change, global changes, pollution, and infectious diseases) are indeed currently operating in Mexico. We discuss the relative importance of each of these causes. We also highlight the paucity of quantitative studies that support the current conservation status of Mexican amphibian species.     

Diversity and distribution of amphibians in Romania

Nineteen species of amphibians inhabit Romania, 9 of which reach their range limit on this territory. Based on published occurrence reports, museum collections and our own data we compiled a national database of amphibian occurrences. We georeferenced 26779 amphibian species occurrences, and performed an analysis of their spatial patterns, checking for hotspots and patterns of species richness. The results of spatial statistic analyses supported the idea of a biased sampling for Romania, with clear hotspots of increased sampling efforts. The sampling effort is biased towards species with high detectability, protected areas, and large cities. Future sampling efforts should be focused mostly on species with a high rarity score in order to accurately map their range. Our results are an important step in achieving the long-term goals of increasing the efficiency of conservation efforts and evaluating the species range shifts under climate change scenarios.     

Global stressors and the global decline of amphibians: tipping the stress immunocompetency axis

There is a widespread consensus that the earth is experiencing a mass extinction event and at the forefront are amphibians, the most threatened of all vertebrate taxa. A recent assessment found that nearly one-third (32%, 1,856 species) of the world’s amphibian species are threatened. Amphibians have existed on the earth for over 300 million years, yet in just the last two decades there have been an alarming number of extinctions, nearly 168 species are believed to have gone extinct and at least 2,469 (43%) more have populations that are declining. Infectious diseases have been recognized as one major cause of worldwide amphibian population declines. This could be the result of the appearance of novel pathogens, or it could be that exposure to environmental stressors is increasing the susceptibility of amphibians to opportunistic pathogens. Here I review the potential effects of stressors on disease susceptibility in amphibians and relate this to disease emergence in human and other wildlife populations. I will present a series of case studies that illustrate the role of stress in disease outbreaks that have resulted in amphibian declines. First, I will examine how elevated sea-surface temperatures in the tropical Pacific since the mid-1970s have affected climate over much of the world and could be setting the stage for pathogen-mediated amphibian declines in many regions. Finally, I will discuss how the apparently rapid increase in the prevalence of amphibian limb deformities is linked to the synergistic effects of trematode infection and exposure to chemical contaminants.     

Complex population dynamics and complex causation: devils, details and demography

Population dynamics result from the interplay of density-independent and density-dependent processes. Understanding this interplay is important, especially for being able to predict near-term population trajectories for management. In recent years, the study of model systems-experimental, observational and theoretical-has shed considerable light on the way that the both density-dependent and -independent aspects of the environment affect population dynamics via impacting on the organism's life history and therefore demography. These model-based approaches suggest that (i) individuals in different states differ in their demographic performance, (ii) these differences generate structure that can fluctuate independently of current total population size and so can influence the dynamics in important ways, (iii) individuals are strongly affected by both current and past environments, even when the past environments may be in previous generations and (iv) dynamics are typically complex and transient due to environmental noise perturbing complex population structures. For understanding population dynamics of any given system, we suggest that 'the devil is in the detail'. Experimental dissection of empirical systems is providing important insights into the details of the drivers of demographic responses and therefore dynamics and should also stimulate theory that incorporates relevant biological mechanism.     

Integrating demography,dispersal and interspecific interactions into bird distribution models

Species’ ranges are primarily limited by the physiological (abiotic) tolerance of the species, described by their fundamental niche. Additionally, demographic processes, dispersal, and interspecific interactions with other species are shaping species distributions, resulting in the realised niche. Understanding the complex interplay between these drivers is vital for making robust biodiversity predictions to novel environments. Correlative species distribution models have been widely used to predict biodiversity response but also remain criticised, as they are not able to properly disentangle the abiotic and biotic drivers shaping species’ niches. Recent developments have thus focussed on 1) integrating demography and dispersal into species distribution models, and on 2) integrating interspecific interactions. Here, I review recent demographic and multi‐species modelling approaches and discuss critical aspects of these models that remain underexplored in general and in respect to birds, for example, the complex life histories of birds and other animals as well as the scale dependence of interspecific interactions. I conclude by formulating modelling guidelines for integrating the abiotic and biotic processes that limit species’ ranges, which will help to disentangle the complex roles of demography, dispersal and interspecific interactions in shaping species niches. Throughout, I pinpoint complexities of avian life cycles that are critical for consideration in the models and identify data requirements for operationalizing the different modelling steps.     

Population structure,demography, and dynamics of mountain baboons: An interim report

Counts of 61 baboon troops (Papio cynocephalus ursinus) at four localities in the Drakensberg mountains confirmed earlier reports of a small mean troop size. This troop size of 22.49 animals changed neither with latitude nor elevation. Data from two of the sites suggested that population density increases from south to north, while a working assumption of 2.5 animals/ km² allowed us to set the population size at 7,540 animals, living in 335 troops. Both the adult sex ratio of 2.07 females/male and the immature/ adult female ratio of 1.17 were unaffected by troop size. Repeated counts from nine known troops revealed that the population is at equilibrium. © 1995 Wiley-Liss, Inc.     

湖南省两栖、爬行动物物种多样性及其地理分布

物种多样性及其地理分布是制定野生动物保护对策的重要依据。两栖、爬行动物在生物演化的历史上占据着重要地位, 又是脊椎动物分类体系变动较大的类群。为了掌握湖南省两栖、爬行动物物种多样性现状, 促进湖南省生物多样性保护和野生动物管理工作, 我们参考分类学及分子生物系统学的最新研究成果, 系统地收集了近10多年来有关湖南省两栖、爬行动物分类的文献资料, 结合团队长期以来的野外调查数据, 对湖南省两栖、爬行动物名录进行了整理与更新(截止到2021年10月31日)。结果表明: 湖南省已记录两栖动物2目10科30属86种(含亚种), 爬行动物2目22科55属105种(含亚种), 其中中国特有种分别有62种和30种, 湖南省特有种分别有10种和4种。列入《国家重点保护野生动物名录》(2021)的两栖动物有11种, 爬行动物有10种; 列为《中国生物多样性红色名录》(2021)受威胁等级的两栖动物有20种, 爬行动物有30种。此外, 湖南省两栖、爬行动物区系特征明显, 以东洋界种类为主(81.2%), 广布种较少(18.8%), 无古北界种。在地理分布上, 湘南山地丘陵区、湘西北山地区是湖南省两栖、爬行动物物种丰富度较高的地区。     

Modeling Daphnia population dynamics and demography under natural conditions

Various approaches to modeling the population dynamics and demography of Daphnia have been published. These methods range from the simple egg-ratio method, to mathematically complex models based on partial differential equations and numerically complex individual-based Daphnia population models. The usefulness of these models in unraveling the population dynamics and demography of Daphnia under natural conditions is discussed. Next to this, an extended version of an existing individual-based Daphnia model is documented (Cladosim) and its application to a typical field data set collected in 1995 in Lake Volkerak is shown. To answer the question which factor was limiting Daphnia numbers during the course of the season food level and temperature in the model were varied and results were compared with those obtained for the observed food level and temperature. These analysis showed that in April temperature was limiting while during May–July and September–October food was limiting. In August neither temperature nor food was limiting. Analysis with a set of size-selective mortality scenarios showed that on average the Daphnia population in Lake Volkerak experienced a mild positive size-selective mortality during the year that was analyzed. Birth rates derived with the detailed individual-based model were compared with those derived with the much simpler egg-ratio method. For the conditions as observed in Lake Volkerak in 1995, both methods gave very comparable results, despite sampling intervals of up to four weeks. The same holds under the environmental scenarios. Using the size-selective mortality scenarios it could be shown, however, that under strong mortality of the smaller daphnids, the egg-ratio method severely underestimates the birth rate. The vices and virtues of the new model and potential extensions are discussed.     

Stochastic demography and population dynamics in the red kangaroo Macropus rufus

1.  Many organisms inhabit strongly fluctuating environments but their demography and population dynamics are often analysed using deterministic models and elasticity analysis, where elasticity is defined as the proportional change in population growth rate caused by a proportional change in a vital rate. Deterministic analyses may not necessarily be informative because large variation in a vital rate with a small deterministic elasticity may affect the population growth rate more than a small change in a less variable vital rate having high deterministic elasticity.
2.  We analyse a stochastic environment model of the red kangaroo ( Macropus rufus ), a species inhabiting an environment characterized by unpredictable and highly variable rainfall, and calculate the elasticity of the stochastic growth rate with respect to the mean and variability in vital rates.
3.  Juvenile survival is the most variable vital rate but a proportional change in the mean adult survival rate has a much stronger effect on the stochastic growth rate.
4.  Even if changes in average rainfall have a larger impact on population growth rate, increased variability in rainfall may still be important also in long-lived species. The elasticity with respect to the standard deviation of rainfall is comparable to the mean elasticities of all vital rates but the survival in age class 3 because increased variation in rainfall affects both the mean and variability of vital rates.
5.  Red kangaroos are harvested and, under the current rainfall pattern, an annual harvest fraction of c . 20% would yield a stochastic growth rate about unity. However, if average rainfall drops by more than c . 10%, any level of harvesting may be unsustainable, emphasizing the need for integrating climate change predictions in population management and increase our understanding of how environmental stochasticity translates into population growth rate.     

Forest decline: Endogenous dynamics,tree defenses,and the elimination of spurious correlation

Two important unresolved problems in pollution impact research are early detection of changes in tree and forest growth and determination of the causes of observed growth declines. Consideration of tree defensive systems can shed light on dieback phenomena. Trees possess both chemical and structural defenses, with both types having both active and passive dimensions. When stress or pollution causes a reduction in vigor, defenses may become ineffective, resulting in insect pest and pathogen attack. This leads to a positive feedback cycle of declining vigor. Level of defenses differs by species, site, and life-stage. Consideration of these factors leads to better statistical methods for correlating pollution dose with tree growth response. It is shown that several recent studies are potentially flawed by inadequate consideration of species type, tree age, or stand density. It is shown that forest growth models can be used to correct for endogenous changes in tree growth rates as long as the trees used to derive parameters for the model were not themselves affected by pollution.     

The electrolyte content of the body of insects, ascidians, fishes, amphibians and mammals and its dynamics in ontogeny

In animals in which sodium is a predominant cation of the blood serum or haemolymph (rat, newt Triturus vulgaris, sturgeon Acipenser güldenst?dti, herring Clupea pallasi, ascidian Goniocarpa rustica), its content in the body amounts up to a half of the total bulk of electrolytes; in insects with potassium type of the haemolymph, the share of sodium is equal to 6.4%. In animals of the same species, total electrolyte content (sodium, potassium, calcium, magnesium) and the relationship between separate ions were found to be remarkably constant. During ontogenetic development of the sturgeon and herring, as well as in rat embryos beginning from the 15th day of gestation, the ratio between separate cations exhibits significant conservatism.     

Metacommunity dynamics of amphibians in years with differing rainfall

Many studies investigated the habitat preference and behaviour ecology of individual amphibian species while we know less about how their community assembly reflects changes in environmental factors, including the role of climatic extremes. Community-level studies also allow us to apply trait-based analyses that are crucial for a better understanding of the functioning of amphibian communities and metacommunities. In two years with contrasting rainfall (2012 and 2013), we found amphibian species in 85 different waterbodies of a heterogeneous landscape in Central Europe (Hungary). Within the metacommunity framework, the contributions of local, landscape and spatial variables to community assembly were assessed. We also measured the local extinction–colonisation rates in the ponds for all species between the two years. To investigate the role of dispersal traits in explaining the spatial distribution of species, we studied the relationship between body size and the pure spatial fraction of variation. According to our results, the main drivers were the same in both the dry and wet year, but their relative contribution changed. Local variables played a predominant role in the assembly of the amphibian metacommunity. Spatial signals were more evident in the dry year. This implies not only the adverse effect of decreased connectivity due to the drying out of several habitats but also a loss of breeding sites for the studied amphibians. Local colonisation rates were higher in primarily terrestrial species (Hyla arborea, Pelobates fuscus, Bufo bufo) which only visit ponds during breeding. We found a negative relationship between the pure spatial effect and body size, suggesting an increased level of dispersal limitation in small-bodied species. Our results showed that while the strength and relative role of local and spatial processes changed between years, the role of dispersal traits in explaining the spatial distribution of species was similar. Specialisation to different habitats seems to be a major process in determining vertebrate metacommunities in landscapes. Dispersal traits of different species should be taken more into consideration in the practical conservation of amphibian habitats.