Non-equilibrium allele frequency spectra via spectral methods

A major challenge in the analysis of population genomics data consists of isolating signatures of natural selection from background noise caused by random drift and gene flow. Analyses of massive amounts of data from many related populations require high-performance algorithms to determine the likelihood of different demographic scenarios that could have shaped the observed neutral single nucleotide polymorphism (SNP) allele frequency spectrum. In many areas of applied mathematics, Fourier Transforms and Spectral Methods are firmly established tools to analyze spectra of signals and model their dynamics as solutions of certain Partial Differential Equations (PDEs). When spectral methods are applicable, they have excellent error properties and are the fastest possible in high dimension; see Press et al. (2007). In this paper we present an explicit numerical solution, using spectral methods, to the forward Kolmogorov equations for a Wright–Fisher process with migration of K populations, influx of mutations, and multiple population splitting events.     

General population growth models with Allee effects in a random environment

Allee effects on population growth are quite common in nature, usually studied through deterministic models with a specific growth rate function.In order to seek the qualitative behaviour of populations induced by such effects, one should avoid model-specific behaviours. So, we use as a basis a general deterministic model, i.e. a model with a general growth rate function, to which we add the effect on the growth rate of the random fluctuations in environmental conditions. The resulting model is the general stochastic differential equation (SDE) model that we propose here.We consider two possible cases, weak Allee effects and strong Allee effects, which lead to different qualitative behaviours of the model.We will study the model properties for both cases in terms of existence and uniqueness of the solution, extinction and stationary behaviour of the population. The two cases will be compared with each other and with the general density-dependent SDE model without Allee effects.We then consider as an example the particular case of the classic logistic model and an Allee effect version of it.     

Viability of the Endangered Little Bustard <Emphasis Type="Italic">Tetrax tetrax</Emphasis> Population of Western France

Stochastic computer simulations are used to evaluate the sensitivity of Little bustard population parameters, estimating the survival probabilities of the seven endangered Little bustard populations of central-western France for which conservation actions are currentlybeing or have been implemented. Different scenarios of parameter compensation for those nuclei to establish parameter levels assuring population viability are discussed. Adult survival, productivity per female, initial population size and carrying capacity were the most sensitive parameters in a hypothetical, isolated population. Juvenile survival also affected population survival, although its sensitivity was lower. Sex ratio did not have a linear effect on population survival, but probability of extinction increased for extreme values. Productivity per female and initial population size, varied strongly among the populations studied, determining their average time of extinction and growth rate. When a metapopulation scenario was simulated, the survival probabilities of each population and the metapopulations stayed close to 1.0 if no mortality was associated to migration. When mortality during migration was included in the simulations, the metapopulation's probability of survival significantly decreased under 90%. This approach may help managers to correctly address conservation measures and design effective strategies, which should be directed mainly to improve productivity, enhance female survival, and minimise mortality during migration (e.g. promoting insect-rich nesting substrates, avoiding female killing and nest destruction at harvesting, reducing the risk of collision with powerlines, or controlling poaching).     

Investigating damselfly populations at springs in Banff National Park, Canada, with special focus on Argia vivida, Amphiagrion abbreviatum, and Ischnura cervula (Odonata: Coenagrionidae)

The objective of this study was to estimate Argia vivida (Odonata: Coenagrionidae) populations, identify breeding habitat, and investigate movement of adults within Banff National Park, Alberta, Canada, during the summer of 2003. Mark-recapture techniques and standardized dip-net surveys were used to monitor Argia vivida at various life stages. A reproductive index identified which sites Argia vivida recognized as suitable breeding habitat, and exuvia surveys confirmed breeding sites. The basic structure of emergent and surrounding vegetation was measured to investigate the importance of available ovipositing or roosting sites and the condition of the matrix habitat. Data was recorded for Amphiagrion abbreviatum and Ischnura cervula (both Odonata: Coenagrionidae) to determine if these spring-associated damselflies were successfully breeding within Banff National Park. Comparisons were made between the highly protected Middle Springs and the heavily altered Cave & Basin Springs. Additional surveys at the Vermilion Lake cool spring and Middle Springs Bog investigated their use as breeding habitat for Amphiagrion abbreviatum and Argia vivida, respectively. Results suggest the ecological value of thermal springs extends beyond their origin to outflows and downstream pools. Conservation of Argia vivida must recognize the value of unobstructed thermal outflows, and consider the condition of the forested habitat surrounding springs with regard to its potential use as nocturnal roosts and dispersal corridors. Amphiagrion abbreviatum was confirmed breeding within Banff National Park, while no sign of breeding activity was recorded for Ischnura cervula.     

Mathematical simulation of the interactions among cyanobacteria, purple sulfur bacteria and chemotrophic sulfur bacteria in microbial mat communities

Abstract: A deterministic one-dimensional reaction diffusion model was constructed to simulate benthic stratification patterns and population dynamics of cyanobacteria, purple and colorless sulfur bacteria as found in marine microbial mats. The model involves the major biogeochemical processes of the sulfur cycle and includes growth metabolism and their kinetic parameters as described from laboratory experimentation. Hence, the metabolic production and consumption processes are coupled to population growth. The model is used to calculate benthic oxygen, sulfide and light profiles and to infer spatial relationships and interactions among the different populations. Furthermore, the model is used to explore the effect of different abiotic and biotic environmental parameters on the community structure. A strikingly clear pattern emerged of the interaction between purple and colorless sulfur bacteria: either colorless sulfur bacteria dominate or a coexistence is found of colorless and purple sulfur bacteria. The model predicts that purple sulfur bacteria only proliferate when the studied environmental parameters surpass well-defined threshold levels. However, once the appropriate conditions do occur, the purple sulfur bacteria are extremely successful as their biomass outweighs that of colorless sulfur bacteria by a factor of up to 17. The typical stratification pattern predicted closely resembles the often described bilayer communities which comprise a layer of purple sulfur bacteria below a cyanobacterial top-layer; colorless sulfur bacteria are predicted to sandwich in between both layers. The profiles of oxygen and sulfide shift on a diel basis similarly as observed in real systems.     

Advances in soil microbial ecology and the biodiversity

Recent studies on the colony formation of soil bacteria opened the way to categorize soil bacteria into colony forming curve (CFC) groups of different growth rates. A bacterial culture collection comprising organisms from every CFC group is called an ecocollection. Outlines of ECs of paddy soil 1992 and grassland soil 1987 and 1992 were described. Phylogenetic studies by 16S rDNA sequencing showed a great diversity of culture strains of the ecocollections (EC). A set of alternative concepts was proposed; the active and the quiescent forms of bacterial cells in soil. The former is able to be cultivated and thus counted by the plate method, while the latter is not unless it transforms into the former. Based on the results several points required for extensive cataloguing of soil bacteria were noted.     

The utility of inflammation and platelet biomarkers in patients with acute coronary syndromes

Introduction

Thrombotic and inflammatory mechanisms are involved in the pathophysiology of acute coronary syndrome (ACS). The aim of the study was the evaluation of inflammation (white blood cells count/WBC, C-reactive protein/CRP, interleukin-6/IL-6) and platelet (platelet count/PLT, mean platelet volume/MPV, large platelet/LPLT, beta-thromboglobulin/β-TG) biomarkers in the groups of ACS patients depending on the severity of signs and symptoms and compared to controls without coronary artery disease.

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.     

Estimating prehistoric American Indian population size for united states area: Implications of the nineteenth century population decline and nadir

Implications of a revised United States American Indian nadir population and the pattern of decline leading to it are examined. Substituting the new nadir for that used by Dobyns (1966) lowers by several million his estimates of Indian population for the United States (and Canada) area. These estimates then become more compatible with ones currently being suggested by other scholars. The nineteenth century decline leading to this nadir is found to be remarkably linear. Assuming linearity in decline from initial European contact through the eighteenth century, an aboriginal population estimate of 1,845,183 for the United States area may be extrapolated, along with estimates for intervening years. The nineteenth century decline is then graphed with the data extrapolated to 1492. The resulting pattern of population decline is quite different from the ones suggested by Mooney (1928) and Dobyns (1966).     

达乌尔黄鼠种群空间分布型研究及其应用

本文根据1987年在内蒙古东北部低山丘陵区和平原区草原的调查资料,应用频数分布比较法研究了达乌尔黄鼠的空间分布型。结果表明：在抽样单位(样方)大小为1公项(1OO米×100米)时,4个样地内达乌尔黄鼠交尾期和幼鼠分居期的空间分布型均属poisson分布(随机分布)。环境与密度制约因素的影响不明显。并经回归分析得到：种群密度(m)与零样方频率(Po)和有鼠样方频率(Px )的曲线关系分别为m=4.5451-0.96721nPo和m=4.5451-0.96721n(1-Px)。经X²检验与poisson分布理论曲线基本一致(x²《x^{2 _0.05},P>0.05)。为达乌尔黄鼠种群密度估计提供了理论依据.