The contribution of patch topology and demographic parameters to PVA predictions: the case of the European tree frog

Population viability analyses (PVA) are increasingly used in metapopulation conservation plans. Two major types of models are commonly used to assess vulnerability and to rank management options: population-based stochastic simulation models (PSM such as RAMAS or VORTEX) and stochastic patch occupancy models (SPOM). While the first set of models relies on explicit intrapatch dynamics and interpatch dispersal to predict population levels in space and time, the latter is based on spatially explicit metapopulation theory where the probability of patch occupation is predicted given the patch area and isolation (patch topology). We applied both approaches to a European tree frog (Hyla arborea) metapopulation in western Switzerland in order to evaluate the concordances of both models and their applications to conservation. Although some quantitative discrepancies appeared in terms of network occupancy and equilibrium population size, the two approaches were largely concordant regarding the ranking of patch values and sensitivities to parameters, which is encouraging given the differences in the underlying paradigms and input data.

On metapopulation resistance to drift and extinction.

The spatial configuration of metapopulations (numbers, sizes, and localization of patches) affects their ability to resist demographic extinction and genetic drift, but sometimes with opposite effects. Small and isolated patches, for instance, contribute marginally to demography but may play a large role in genetics by maintaining a sizeable amount of genetic variance among demes. In source-sink systems, similarly, connectivity may be beneficial in terms of effective size, but detrimental in terms of survival, by lowering the reproductive value of source populations. How to reconcile these opposite effects? Here we propose an analytical framework that integrates fixation time (ability to resist genetic drift) and extinction time (ability to resist demographic extinction) into a single index of resistance, measuring the ability of a metapopulation to maintain its demo-genetic integrity. We then illustrate with numerical examples how conflicting demands may be resolved.

Sex differences in the neurobiology of fear conditioning and extinction: a preliminary fMRI study of shared sex differences with stress-arousal circuitry.

BACKGROUND: The amygdala, hippocampus, medial prefrontal cortex (mPFC) and brain-stem subregions are implicated in fear conditioning and extinction, and are brain regions known to be sexually dimorphic. We used functional magnetic resonance imaging (fMRI) to investigate sex differences in brain activity in these regions during fear conditioning and extinction. METHODS: Subjects were 12 healthy men comparable to 12 healthy women who underwent a 2-day experiment in a 3 T MR scanner. Fear conditioning and extinction learning occurred on day 1 and extinction recall occurred on day 2. The conditioned stimuli were visual cues and the unconditioned stimulus was a mild electric shock. Skin conductance responses (SCR) were recorded throughout the experiment as an index of the conditioned response. fMRI data (blood-oxygen-level-dependent [BOLD] signal changes) were analyzed using SPM8. RESULTS: Findings showed no significant sex differences in SCR during any experimental phases. However, during fear conditioning, there were significantly greater BOLD-signal changes in the right amygdala, right rostral anterior cingulate (rACC) and dorsal anterior cingulate cortex (dACC) in women compared with men. In contrast, men showed significantly greater signal changes in bilateral rACC during extinction recall. CONCLUSIONS: These results indicate sex differences in brain activation within the fear circuitry of healthy subjects despite similar peripheral autonomic responses. Furthermore, we found that regions where sex differences were previously reported in response to stress, also exhibited sex differences during fear conditioning and extinction.

Shrews in suburbia: an application of Goodman's extinction model

An equation is applied for calculating the expected persistence time of an unstructured population of the white-toothed shrew Crocidura russula from Preverenges, a suburban area in western Switzerland. Population abundance data from March and November between 1977 and 1988 were fit to the logistic density dependence model to estimate mean population growth rate as a function of population density. The variance in mean growth rate was approximated with two different models. The largest estimated persistence time was less than a few decades, the smallest less than 10 years. The results are sensitive to the magnitude of variance in population growth rate. Deviations from the logistic density dependence model in November are quite well explained by weather variables but those in March are uncorrelated with weather variables. Variability in population growth rates measured in winter months may be better explained by behavioural mechanisms. Environmental variability, dispersal of juveniles and refugia within the range of the population may contribute to its long-term survival.

PyRate: a new program to estimate speciation and extinction rates from incomplete fossil data

Despite the advancement of phylogenetic methods to estimate speciation and extinction rates, their power can be limited under variable rates, in particular for clades with high extinction rates and small number of extant species. Fossil data can provide a powerful alternative source of information to investigate diversification processes. Here, we present PyRate, a computer program to estimate speciation and extinction rates and their temporal dynamics from fossil occurrence data. The rates are inferred in a Bayesian framework and are comparable to those estimated from phylogenetic trees. We describe how PyRate can be used to explore different models of diversification. In addition to the diversification rates, it provides estimates of the parameters of the preservation process (fossilization and sampling) and the times of speciation and extinction of each species in the data set. Moreover, we develop a new birth-death model to correlate the variation of speciation/extinction rates with changes of a continuous trait. Finally, we demonstrate the use of Bayes factors for model selection and show how the posterior estimates of a PyRate analysis can be used to generate calibration densities for Bayesian molecular clock analysis. PyRate is an open-source command-line Python program available at http://sourceforge.net/projects/pyrate/.

The influence of environmental conditions on immune responses, morphology and recapture probability of nestling house martins (Delichon urbica)

Nestling birds produced later in the season are hypothesized to be of poor quality with a low probability of survival and recruitment. In a Spanish population of house martins (Delichon urbica), we first compared reproductive success, immune responses and morphological traits between the first and the second broods. Second, we investigated the effects of an ectoparasite treatment and breeding date on the recapture rate the following year. Due probably to a reverse situation in weather conditions during the experiment, with more rain during rearing of the first brood, nestlings reared during the second brood were in better condition and had stronger immune responses compared with nestlings from the first brood. Contrary to other findings on house martins, we found a similar recapture rate for chicks reared during the first and the second brood. Furthermore, ectoparasitic house martin bugs had no significant effect on the recapture rate. Recaptured birds had similar morphology but higher immunoglobulin levels when nestlings compared with non-recaptured birds. This result implies that a measure of immune function is a better predictor of survival than body condition per se.

The fixation of locally beneficial alleles in a metapopulation.

Extinction, recolonization, and local adaptation are common in natural spatially structured populations. Understanding their effect upon genetic variation is important for systems such as genetically modified organism management or avoidance of drug resistance. Theoretical studies on the effect of extinction and recolonization upon genetic variance started appearing in the 1970s, but the role of local adaptation still has no good theoretical basis. Here we develop a model of a haploid species in a metapopulation in which a locally adapted beneficial allele is introduced. We study the effect of different spatial patterns of local adaptation, and different metapopulation dynamics, upon the fixation probability of the beneficial allele. Controlling for the average selection pressure, we find that a small area of positive selection can significantly increase the global probability of fixation. However, local adaptation becomes less important as extinction rate increases. Deme extinction and recolonization have a spatial smoothing effect that effectively reduces spatial variation in fitness.

The role of climatic tolerances and seed traits in reduced extinction rates of temperate polygonaceae.

The latitudinal diversity gradient (LDG) is one of the most striking and consistent biodiversity patterns across taxonomic groups. We investigate the species richness gradient in the buckwheat family, Polygonaceae, which exhibits a reverse LDG and is, thus, decoupled from dominant gradients of energy and environmental stability that increase toward the tropics and confound mechanistic interpretations. We test competing age and evolutionary diversification hypotheses, which may explain the diversification of this plant family over the past 70 million years. Our analyses show that the age hypothesis, which posits that clade richness is positively correlated with the ecological and evolutionary time since clade origin, fails to explain the richness gradient observed in Polygonaceae. However, an evolutionary diversification hypothesis is highly supported, with diversification rates being 3.5 times higher in temperate clades compared to tropical clades. We demonstrate that differences in rates of speciation, migration, and molecular evolution insufficiently explain the observed patterns of differential diversification rates. We suggest that reduced extinction rates in temperate clades may be associated with adaptive responses to selection, through which seed morphology and climatic tolerances potentially act to minimize risk in temporally variable environments. Further study is needed to understand causal pathways among these traits and factors correlated with latitude.

The prelude of the end-Permian mass extinction predates a postulated bolide impact

The mass extinction at the Permian-Triassic Boundary (PTB) is said to have been abrupt and probably caused by an extraterrestrial impact. However, evidence from the Global Stratotype Section and Point (GSSP) of the base of the Induan at Meishan, China, shows that the biotic crisis began prior to the level, in beds 25 and 26 at which the postulated impact event occurred. Evidence of such an earlier biotic crisis occurs in other sections in South China, and in central and western Tethyan regions. This event is characterized by the extinction of a range of faunas, including corals, deep-water radiolarians, most fusulinids and pseudotirolitidammonoids, and many Permian brachiopods. In all sections, this extinction level is usually a few decimeters to meters below that of the main mass extinction in the event beds (25 and 26) at Meishan, and their correlatives elsewhere. This earlier extinction event happened before the postulated bolide impact at the level of beds 25 and 26, and constrains interpretation of the mechanisms that brought about this greatest mass extinction.

Climatic and biotic upheavals following the end-Permian mass extinction

Recovery from the end-Permian mass extinction is frequently described as delayed(1-3), with complex ecological communities typically not found in the fossil record until the Middle Triassic epoch. However, the taxonomic diversity of a number of marine groups, ranging from ammonoids to benthic foraminifera, peaked rapidly in the Early Triassic(4-10). These variations in biodiversity occur amidst pronounced excursions in the carbon isotope record, which are compatible with episodes of massive CO2 outgassing from the Siberian Large Igneous Province(4,11-13). Here we present a high-resolution Early Triassic temperature record based on the oxygen isotope composition of pristine apatite from fossil conodonts. Our reconstruction shows that the beginning of the Smithian substage of the Early Triassic was marked by a cooler climate, followed by an interval of warmth lasting until the Spathian substage boundary. Cooler conditions resumed in the Spathian. We find the greatest increases in taxonomic diversity during the cooler phases of the early Smithian and early Spathian. In contrast, a period of extreme warmth in the middle and late Smithian was associated with floral ecological change and high faunal taxonomic turnover in the ocean. We suggest that climate upheaval and carbon-cycle perturbations due to volcanic outgassing were important drivers of Early Triassic biotic recovery.

Using graphical probability analysis (Bayes Nets) to evaluate a conditional DNA inclusion

This paper discusses the analysis of cases in which the inclusion or exclusion of a particular suspect, as a possible contributor to a DNA mixture, depends on the value of a variable (the number of contributors) that cannot be determined with certainty. It offers alternative ways to deal with such cases, including sensitivity analysis and object-oriented Bayesian networks, that separate uncertainty about the inclusion of the suspect from uncertainty about other variables. The paper presents a case study in which the value of DNA evidence varies radically depending on the number of contributors to a DNA mixture: if there are two contributors, the suspect is excluded; if there are three or more, the suspect is included; but the number of contributors cannot be determined with certainty. It shows how an object-oriented Bayesian network can accommodate and integrate varying perspectives on the unknown variable and how it can reduce the potential for bias by directing attention to relevant considerations and distinguishing different sources of uncertainty. It also discusses the challenge of presenting such evidence to lay audiences.

Decreased Probability of Initial Pain Cessation in Classic Trigeminal Neuralgia Treated With Gamma Knife Surgery in Case of Previous Microvascular Decompression: A Prospective Series of 45 Patients With >1 Year of Follow-up.

BACKGROUND: Microvascular decompression (MVD) is the reference technique for pharmacoresistant trigeminal neuralgia (TN). OBJECTIVE: To establish whether the safety and efficacy of Gamma Knife surgery for recurrent TN are influenced by prior MVD. METHODS: Between July 1992 and November 2010, 54 of 737 patients (45 of 497 with >1 year of follow-up) had a history of MVD (approximately half also with previous ablative procedure) and were operated on with Gamma Knife surgery for TN in the Timone University Hospital. A single 4-mm isocenter was positioned in the cisternal portion of the trigeminal nerve at a median distance of 7.6 mm (range, 3.9-11.9 mm) anterior to the emergence of the nerve. A median maximum dose of 85 Gy (range, 70-90 Gy) was delivered. RESULTS: The median follow-up time was 39.5 months (range, 14.1-144.6 months). Thirty-five patients (77.8%) were initially pain free in a median time of 14 days (range, 0-180 days), much lower compared with our global population of classic TN (P = .01). Their actuarial probabilities of remaining pain-free without medication at 3, 5, 7, and 10 years were 66.5%, 59.1%, 59.1%, and 44.3%. The hypoesthesia actuarial rate at 1 year was 9.1% and remained stable until 12 years (median, 8 months). CONCLUSION: Patients with previous MVD showed a significantly lower probability of initial pain cessation compared with our global population with classic TN (P = .01). The toxicity was low (only 9.1% hypoesthesia); furthermore, no patient reported bothersome hypoesthesia. However, the probability of maintaining pain relief without medication was 44.3% at 10 years, similar to our global series of classic TN (P = .85). ABBREVIATIONS: BNI, Barrow Neurological InstituteCI, confidence intervalCTN, classic trigeminal neuralgiaGKS, Gamma Knife surgeryHR, hazard ratioMVD, microvascular decompressionTN, trigeminal neuralgia.