Modeling species dispersal with occupancy urn models

Models for species dispersal make various simplifications to facilitate analysis, such as ignoring spatial correlations or assuming equal probability of colonization among all sites within a dispersal neighborhood. Here we introduce a variation of the basic contact process (BCP) which allows us to separate the number of offspring produced from the neighborhood size, which are confounded in the original BCP. We then use classical results arising from probability models involving placing balls in urns to study our modified BCP, obtaining bounds for the critical value of the survival probability needed for the population to persist. We also use the probability urn calculations with a local-dispersal mean-field approximation to estimate equilibrium population density. These methods are able to include features such as unequal dispersal probabilities to different sites in the neighborhood, e.g., as would arise when dispersers have a fixed rate of mortality per distance traveled from the parent site. We also show how urn models allow one to generalize these results to two species competing for space.     

Site occupancy models with heterogeneous detection probabilities

Models for estimating the probability of occurrence of a species in the presence of imperfect detection are important in many ecological disciplines. In these "site occupancy" models, the possibility of heterogeneity in detection probabilities among sites must be considered because variation in abundance (and other factors) among sampled sites induces variation in detection probability (p). In this article, I develop occurrence probability models that allow for heterogeneous detection probabilities by considering several common classes of mixture distributions for p. For any mixing distribution, the likelihood has the general form of a zero-inflated binomial mixture for which inference based upon integrated likelihood is straightforward. A recent paper by Link demonstrates that in closed population models used for estimating population size, different classes of mixture distributions are indistinguishable from data, yet can produce very different inferences about population size. I demonstrate that this problem can also arise in models for estimating site occupancy in the presence of heterogeneous detection probabilities. The implications of this are discussed in the context of an application to avian survey data and the development of animal monitoring programs.     

Measuring drug-related receptor occupancy with positron emission tomography

Several techniques can be used to measure indirectly the effect of drugs (e.g., EEG, fMRI) in healthy volunteers and in patients. Although each technique has its merits, a direct link between drug efficacy and site of action in vivo usually cannot be established. In addition, when the specific mode of action of a drug has been determined from preclinical studies, it is often not known whether the administered dose is optimal for humans. Both industry and academia are becoming more and more interested in determining the dose-related occupancy of specific targets caused by administration of drugs under test. Positron emission tomography (PET) and single-photon emission computed tomography (SPECT) are noninvasive imaging techniques that can give insight into the relationship between target occupancy and drug efficacy, provided a suitable radioligand is available. Although SPECT has certain advantages (e.g., a long half-life of the radionuclides), the spatial and temporal resolution as well as the labeling possibilities of this technique are limited. This review focuses on PET methodology for conducting drug occupancy studies in humans.     

Abundance–occupancy relationships

1.  The abundance and distribution of species tend to be linked, such that species declining in abundance often tend also to show declines in the number of sites they occupy, while species increasing in abundance tend also to be increasing in occupancy. Therefore, intraspecific abundance–occupancy relationships are commonly positive.
2.  The intraspecific pattern is mirrored by more general positive interspecific abundance–occupancy relationships: widespread species tend to be abundant, and narrowly distributed species rare.
3.  Here, we review recent research on these patterns based on the flora and fauna of the British Isles. We assess their generality, describe what is currently known about their structure, and summarize the results of tests of the several hypotheses proposed to explain their existence.
4.  The positive form generally exhibited by abundance–occupancy relationships, intraspecific or interspecific, has consequences for several areas of applied ecology, including conservation, harvesting, biological invasions and biodiversity inventorying. These implications are discussed briefly.     

Development of two common dragonfly species with diverging occupancy trends

Journal of Insect Conservation - The two sibling and syntopic odonate species Sympetrum striolatum and Sympetrum vulgatum are common and widespread in Central Europe. While S. striolatum has strong...     

Efficient Bayesian analysis of occupancy models with logit link functions

Occupancy models (Ecology, 2002; 83: 2248) were developed to infer the probability that a species under investigation occupies a site. Bayesian analysis of these models can be undertaken using statistical packages such as WinBUGS, OpenBUGS, JAGS, and more recently Stan, however, since these packages were not developed specifically to fit occupancy models, one often experiences long run times when undertaking an analysis. Bayesian spatial single‐season occupancy models can also be fit using the R package stocc. The approach assumes that the detection and occupancy regression effects are modeled using probit link functions. The use of the logistic link function, however, is algebraically more tractable and allows one to easily interpret the coefficient effects of an estimated model by using odds ratios, which is not easily done for a probit link function for models that do not include spatial random effects. We develop a Gibbs sampler to obtain posterior samples from the posterior distribution of the parameters of various occupancy models (nonspatial and spatial) when logit link functions are used to model the regression effects of the detection and occupancy processes. We apply our methods to data extracted from the 2nd Southern African Bird Atlas Project to produce a species distribution map of the Cape weaver (Ploceus capensis) and helmeted guineafowl (Numida meleagris) for South Africa. We found that the Gibbs sampling algorithm developed produces posterior samples that are identical to those obtained when using JAGS and Stan and that in certain cases the posterior chains mix much faster than those obtained when using JAGS, stocc, and Stan. Our algorithms are implemented in the R package, Rcppocc. The software is freely available and stored on GitHub ( https://github.com/AllanClark/Rcppocc ).     

Platelet receptor occupancy with factor IXa promotes factor X activation

To investigate the activated platelet surface as a locus for factor X activation, the functional consequences of factor IXa binding to platelets were studied. The concentration of factor IXa required for half-maximal rates of factor X activation in the presence of factor VIIIa and thrombin-activated platelets was 0.53 nM, which is close to the Kd (0.56 nM) for factor IXa binding to platelets under identical conditions, determined from equilibrium binding studies. In direct comparative experiments, there was a close correspondence between equilibrium binding of factor IXa to thrombin-activated platelets in the presence of factor VIIIa and kinetic determinations of factor X activation rates. Analysis by polyacrylamide gel electrophoresis revealed that 125I-labeled factor IXa bound to platelets was structurally intact and did not form covalent complexes with platelet proteins. Factor IXa active site-inhibited by 5-dimethylaminonaphthalene-1-sulfonyl glutamyl-glycylarginyl chloromethyl ketone was shown to be a competitive inhibitor of factor IXa binding in the absence (Ki = 2.3 nM) and presence (Ki = 0.43 nM) of factor VIIIa and factor X and of factor X activation (Ki = 0.4 nM) by factor IXa in the presence of factor VIIIa, indicating that the generation of factor Xa is not required for factor IXa binding and that factor IXa bound to activated platelets in the presence of factor VIIIa is closely coupled with rates of factor X activation. We conclude that factor IXa bound tightly to a platelet receptor in the presence of factor VIIIa is the enzyme active in factor X activation.     

Preincubation of Mesorhizobium ciceri with flavonoids improves its nodule occupancy

Strains ofM. ciceri, symbionts of chickpea (Cicer arietinum) were incubated with the flavonoids naringenin, daidzein and quercetin which have earlier been reported as inducers and inhibitors ofnodABC-lacZ fusion ofM. ciceri. Preincubation ofM. ciceri with naringenin and daidzein (100 nmol/L) for 1 d improved the competitive ability of the inoculated strain while preincubation with quercetin decreased the nodule occupancy of inoculated strain under sterile conditions. Under nonsterile conditions induced strains of Rcd 301 and HT-6 formed by 23 and 18% more nodules, respectively, than untreated control. Quercetin-treated strains showed by 13–20% fewer nodules than untreated controls. Therefore, it is possible to regulate the competitive ability of inoculated strains by flavonoid treatment.     

Controlling N-linked glycan site occupancy

N-linked glycosylation, a common co-translational modification in eukaryotic cells, involves the transfer of a lipid-linked oligosaccharide onto asparagine residues in a tripeptide sequon on a nascent protein in the lumen of the endoplasmic reticulum. The attachment of an oligosaccharide unit to the polypeptide at the site of occupancy can enhance solubility, improve folding, facilitate secretion, modulate antigenicity, and increase in vivo half-life of the glycoprotein. A number of proteins exhibit variable site occupancy. The efficiency of protein N-glycosylation is dependent on the kinetics of the individual steps in the biosynthesis of the dolichol-linked oligosaccharide and the transfer of the oligosaccharide from the lipid donor substrate to the nascent polypeptide. In this review, we will discuss the role of N-linked glycan site occupancy and give an overview of the possible limitations associated with variable site occupancy. The characterization of the dolichol pyrophosphate biosynthetic pathway and the recent identification of potential rate limiting enzymes in yeast and mammalian cells has made it possible to investigate their role in site occupancy. Genetic and biochemical characterization of oligosaccharide transferase (OST) complex in yeast and mammalian cells have demonstrated the importance of specific OST subunits in protein N-glycosylation. In addition, insights into the location and residues in and around the acceptor tripeptide sequon suggest an influence on N-glycan site occupancy. Insights from these characterizations are being used to elucidate methodologies to control N-glycosylation site heterogeneity.     

Global nucleosome occupancy in yeast

Background  

Although eukaryotic genomes are generally thought to be entirely chromatin-associated, the activated PHO5 promoter in yeast is largely devoid of nucleosomes. We systematically evaluated nucleosome occupancy in yeast promoters by immunoprecipitating nucleosomal DNA and quantifying enrichment by microarrays.     

Inferring wildlife poaching in southeast Asia with multispecies dynamic occupancy models

Determining the ‘space race’ between co-occurring species is crucial to understand the effects of interspecific interactions on the extinction risk of species threatened by poachers and predators. Dynamic two-species occupancy models provide a flexible framework to decompose complex species interaction patterns, while accounting for imperfect detection. These models can describe poachers–wildlife interactions, as they allow estimating occupancy, extinction and colonisation probabilities of wildlife conditional on the occurrence of poachers and vice versa. We applied our model to a case study on wildlife poaching in the eastern plains of Cambodia. We used co-occurrence data extracted from the database of the SMART partnership to study the distribution dynamics between poachers and six ungulate species pooled together into the tiger prey guild. We used four years of survey data reporting the locations of snares and of presence signs of the ungulates recorded by rangers during their monthly multi-patrolling sessions. Our results showed that a substantial proportion of the sites occupied by ungulate species went extinct over the years of the study while the proportion of sites colonised by poachers increased. We also showed, for the first time, that spatio-temporal heterogeneity in the patrolling effort explains a great deal of the variation in the detection of poachers and ungulates. Our approach provides practitioners with a flexible and robust tool to assess conservation status of species and extinction risk of wildlife populations. It can assist managers in better evaluating, learning and adapting the patrolling strategies of rangers.     

Group Sequential Monitoring with Arbitrary Inspection Times

The classical group sequential test procedures that were proposed by Pocock (1977) and O'Brien and Fleming (1979) rest on the assumption of equal sample sizes between the interim analyses. Regarding this it is well known that for most situations there is not a great amount of additional Type I error if monitoring is performed for unequal sample sizes between the stages. In some cases, however, problems can arise resulting in an unacceptable liberal behavior of the test procedure. In this article worst case scenarios in sample size imbalancements between the inspection times are considered. Exact critical values for the Pocock and the O'Brien and Fleming group sequential designs are derived for arbitrary and for varying but bounded sample sizes. The approach represents a reasonable alternative to the flexible method that is based on the Type I error rate spending function. The SAS syntax for performing the calculations is provided. Using these procedures, the inspection times or the sample sizes in the consecutive stages need to be chosen independently of the data observed so far.     

A definite measure of occupancy exposures,seeking with non-radiolabeled in vivo 5-HT2A receptor occupancy and in vitro free fractions

Abstract

Unbound drug concentration in the brain would be the true exposure responsible for specific target occupancy. Drug exposures from preclinical are total concentrations of those over/underestimate the clinical dose projection. With the application of mass spectrometry, the current work proposes a definite measure of test drug exposures at serotonin-2A occupancy. The 5-HT_2A occupancy of antagonist in the rat brain has determined with non-radiolabeled tracer MDL-100,907 at an optimized dose (3?µg/kg) and treatment time (30?min). Equilibrium dialysis method determines the in vitro free fraction of the test antagonist in untreated rat brain homogenates and plasma. Drug-free fractions derived the unbound concentration (EC₅₀) in plasma and brain at test doses. The corresponding binding affinities (Ki) correlated with the unbound concentrations. Except for quetiapine, the ED₅₀ values in the dose-occupancy curves of antagonists are close and ranged from 1 to 3?mg/kg. The test drug quetiapine, eplivanserin, and clozapine showed high free fractions in plasma, but for ketanserin and olanzapine, the brain free fraction was higher. The correlation between the unbound EC₅₀ of the antagonists and corresponding Ki values was good (r²=0.828). The improved EC₅₀ accuracy with unbound concentrations was 10–250 folds in plasma and 10–170 folds in the brain. Further, the free fractions (f_{u, plasma}/f_{u, brain}) of test drugs had shown a correlation of ～83% with brain permeability (C_{total brain}/C_{total plasma}), a limiting factor. Thus, correlating the occupancy with unbound exposure and pharmacology would result in an accurate measurement of drug potency and optimizes in selecting the clinical dose.     

Salamander occupancy in headwater stream networks

1. Stream ecosystems exhibit a highly consistent dendritic geometry in which linear habitat units intersect to create a hierarchical network of connected branches.
2. Ecological and life history traits of species living in streams, such as the potential for overland movement, may interact with this architecture to shape patterns of occupancy and response to disturbance. Specifically, large-scale habitat alteration that fragments stream networks and reduces connectivity may reduce the probability a stream is occupied by sensitive species, such as stream salamanders.
3. We collected habitat occupancy data on four species of stream salamanders in first-order (i.e. headwater) streams in undeveloped and urbanised regions of the eastern U.S.A. We then used an information–theoretic approach to test alternative models of salamander occupancy based on a priori predictions of the effects of network configuration, region and salamander life history.
4. Across all four species, we found that streams connected to other first-order streams had higher occupancy than those flowing directly into larger streams and rivers. For three of the four species, occupancy was lower in the urbanised region than in the undeveloped region.
5. These results demonstrate that the spatial configuration of stream networks within protected areas affects the occurrences of stream salamander species. We strongly encourage preservation of network connections between first-order streams in conservation planning and management decisions that may affect stream species.     

Decision-Making in Research Tasks with Sequential Testing

Background

In a recent controversial essay, published by JPA Ioannidis in PLoS Medicine, it has been argued that in some research fields, most of the published findings are false. Based on theoretical reasoning it can be shown that small effect sizes, error-prone tests, low priors of the tested hypotheses and biases in the evaluation and publication of research findings increase the fraction of false positives. These findings raise concerns about the reliability of research. However, they are based on a very simple scenario of scientific research, where single tests are used to evaluate independent hypotheses.

Methodology/Principal Findings

In this study, we present computer simulations and experimental approaches for analyzing more realistic scenarios. In these scenarios, research tasks are solved sequentially, i.e. subsequent tests can be chosen depending on previous results. We investigate simple sequential testing and scenarios where only a selected subset of results can be published and used for future rounds of test choice. Results from computer simulations indicate that for the tasks analyzed in this study, the fraction of false among the positive findings declines over several rounds of testing if the most informative tests are performed. Our experiments show that human subjects frequently perform the most informative tests, leading to a decline of false positives as expected from the simulations.

Conclusions/Significance

For the research tasks studied here, findings tend to become more reliable over time. We also find that the performance in those experimental settings where not all performed tests could be published turned out to be surprisingly inefficient. Our results may help optimize existing procedures used in the practice of scientific research and provide guidance for the development of novel forms of scholarly communication.     

Optimal design of butterfly occupancy surveys and testing if occupancy converts to abundance for sparse populations

Occupancy has several important advantages over abundance methods and may be the best choice for monitoring sparse populations. Here we use simulations to evaluate competing designs (number of sites vs. number of surveys) for occupancy monitoring, with emphasis on sparse populations of the endangered Karner blue butterfly (Lycaeides melissa samuelis Nabokov). Because conservation planning is usually abundance-based, we also ask whether detection/non-detection data may reliably convert to abundance, hypothesizing that occupancy provides a more dependable shortcut when populations are sparse. Count-index and distance sampling were conducted across 50 habitat patches containing variably sparse Karner blue populations. We used occupancy-detection model estimates as simulation inputs to evaluate primary replication tradeoffs, and used peak counts and population densities to evaluate the occupancy-abundance relationship. Detection probability and therefore optimal design of occupancy monitoring was strongly temperature dependent. Assuming a quality threshold of 0.075 root-mean square error for the occupancy estimator, the minimum allowable effort was 360 (40 sites?×?9 surveys) for spring generation and 200 (20 sites?×?10 surveys) for summer generation. A mixture model abundance estimator for repeated detection/non-detection data was biased low for high-density and low-density populations, suggesting that occupancy may not provide a reliable shortcut in abundance-based conservation planning for sparse butterfly populations.     

Banding patterns in Drosophila melanogaster polytene chromosomes correlate with DNA-binding protein occupancy

The most enigmatic feature of polytene chromosomes is their banding pattern, the genetic organization of which has been a very attractive puzzle for many years. Recent genome-wide protein mapping efforts have produced a wealth of data for the chromosome proteins of Drosophila cells. Based on their specific protein composition, the chromosomes comprise two types of bands, as well as interbands. These differ in terms of time of replication and specific types of proteins. The interbands are characterized by their association with "active" chromatin proteins, nucleosome remodeling, and origin recognition complexes, and so they have three functions: acting as binding sites for RNA pol II, initiation of replication and nucleosome remodeling of short fragments of DNA. The borders and organization of the same band and interband regions are largely identical, irrespective of the cell type studied. This demonstrates that the banding pattern is a universal principle of the organization of interphase polytene and non-polytene chromosomes.     

Insulator function and topological domain border strength scale with architectural protein occupancy

Background

Chromosome conformation capture studies suggest that eukaryotic genomes are organized into structures called topologically associating domains. The borders of these domains are highly enriched for architectural proteins with characterized roles in insulator function. However, a majority of architectural protein binding sites localize within topological domains, suggesting sites associated with domain borders represent a functionally different subclass of these regulatory elements. How topologically associating domains are established and what differentiates border-associated from non-border architectural protein binding sites remain unanswered questions.

Results

By mapping the genome-wide target sites for several Drosophila architectural proteins, including previously uncharacterized profiles for TFIIIC and SMC-containing condensin complexes, we uncover an extensive pattern of colocalization in which architectural proteins establish dense clusters at the borders of topological domains. Reporter-based enhancer-blocking insulator activity as well as endogenous domain border strength scale with the occupancy level of architectural protein binding sites, suggesting co-binding by architectural proteins underlies the functional potential of these loci. Analyses in mouse and human stem cells suggest that clustering of architectural proteins is a general feature of genome organization, and conserved architectural protein binding sites may underlie the tissue-invariant nature of topologically associating domains observed in mammals.

Conclusions

We identify a spectrum of architectural protein occupancy that scales with the topological structure of chromosomes and the regulatory potential of these elements. Whereas high occupancy architectural protein binding sites associate with robust partitioning of topologically associating domains and robust insulator function, low occupancy sites appear reserved for gene-specific regulation within topological domains.