scholarly journals A New Statistic for Detecting Genetic Differentiation

Genetics ◽  
2000 ◽  
Vol 155 (4) ◽  
pp. 2011-2014 ◽  
Author(s):  
Richard R Hudson
Keyword(s):  
Genetic Differentiation ◽  
Dna Sequences ◽  
Genetic Data ◽  
Island Model ◽  
Wide Range ◽  
Infinite Sites Model ◽  
Parameter Values

Abstract A new statistic for detecting genetic differentiation of subpopulations is described. The statistic can be calculated when genetic data are collected on individuals sampled from two or more localities. It is assumed that haplotypic data are obtained, either in the form of DNA sequences or data on many tightly linked markers. Using a symmetric island model, and assuming an infinite-sites model of mutation, it is found that the new statistic is as powerful or more powerful than previously proposed statistics for a wide range of parameter values.

scholarly journals Estimating gene flow in island populations

1996 ◽  
Vol 67 (2) ◽  
pp. 147-158 ◽  
Author(s):  
Bruce Rannala ◽  
J. A. Hartigan
Keyword(s):  
Gene Flow ◽  
Island Model ◽  
Least Mean Square ◽  
Island Populations ◽  
Wide Range ◽  
Continuous Generation ◽  
Subdivided Populations ◽  
The Individual ◽  
Pseudo Maximum Likelihood ◽  
Parameter Values

SummaryA new method is presented for estimating the rate of gene flow into island populations using the distribution of alleles in samples from a number of islands. The pseudo maximum likelihood estimator (PMLE) that we derive may be applied to species with either discrete or continuous generation times. For Wright's discrete-generation island model, the method provides an estimate of θ = 2Nm where N is the (haploid) population size on each island and m is the fraction of individuals replaced by immigrants in each generation. For a continuous-generation island model, the corresponding parameter φ is the ratio of the immigration rate φ to the individual birth rate λ. Monte Carlo simulations are used to compare the statistical properties of the PMLE with those of two alternative estimatorsof θ derived from Wright's F-statistics. The PMLE is shown to have greatest efficiency (least mean square error) in most cases for a wide range of sample sizes and parameter values. The PMLE is applied to estimate θ using mtDNA haplotypes and allozymes for subdivided populations of African elephants and Channel Island foxes.

scholarly journals Genetic Differentiation Within and Between Two Habitats

Genetics ◽  
1999 ◽  
Vol 151 (1) ◽  
pp. 397-407 ◽  
Author(s):  
François Rousset
Keyword(s):  
Population Structure ◽  
Genetic Differentiation ◽  
Population Differentiation ◽  
Gene Diversity ◽  
Isolation By Distance ◽  
Host Races ◽  
Wide Range ◽  
Parameter Values ◽  
Ecological Types ◽  
F Statistics

Abstract We investigate the usefulness of analyses of population differentiation between different ecological types, such as host races of parasites or sources and sink habitats. To that aim, we formulate a model of population structure involving two classes of subpopulations found in sympatry. Extensions of previous results for Wright's F-statistics in island and isolation-by-distance models of dispersal are given. It is then shown that source and sinks cannot in general be distinguished by F-statistics nor by their gene diversities. The excess differentiation between two partially isolated classes with respect to differentiation within classes is shown to decrease with distance, and for a wide range of parameter values it should be difficult to detect. In the same circumstances little differentiation will be observed in “hierarchical analyses between pools of samples from each habitat, and differences between levels of differentiation within each habitat will only reflect differences between levels of gene diversity within each habitat. Exceptions will indicate strong isolation between the different classes or habitat-related divergent selection.

scholarly journals Genetic diversity and population differentiation of the freshwater copepod Sinocalanus tenellus (Calanoida, Centropagidae) in China

2018 ◽  
Vol 77 (2) ◽  
Author(s):  
Xiaoyu Wang ◽  
Xiaolin Ma ◽  
Wei Hu ◽  
Mingbo Yin
Keyword(s):  
Genetic Diversity ◽  
Dna Sequences ◽  
Population Differentiation ◽  
Inner Mongolia ◽  
Genetic Data ◽  
Freshwater Ecosystems ◽  
Coi Gene ◽  
Freshwater Ecosystem ◽  
High Genetic Diversity ◽  
Wide Range

Copepods, present in a wide range of water bodies, are an important component of freshwater ecosystems and their biodiversity has been much studied in marine and freshwater ecosystems. However, no previous genetic data are available that allow an assessment of population-genetic diversity and differentiation of the copepod Sinocalanus tenellus from Chinese freshwaters. We analyzed DNA sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene from eleven S. tenellus populations (individual lakes) from China, ten of which exhibited a high genetic diversity. Low to high population differentiation was detected among the populations. Interestingly, substantial genetic divergence was detected between WLS (Wuliangsu, in Inner Mongolia) and other locations, indicating the presence of two lineages of S. tenellus in East Asia. Moreover, we found that two distinct clades of S. tenellus were separated by the reference “S. sinensis” clade, suggesting they were parts of a complex of cryptic species of S. tenellus. This study will contribute to an understanding of the diversity and biogeography of copepods in freshwater ecosystem in China.

scholarly journals The evolution of latent genes in subdivided populations.

Genetics ◽  
1990 ◽  
Vol 124 (1) ◽  
pp. 187-197
Author(s):  
M E Moody ◽  
C J Basten
Keyword(s):  
Dna Sequences ◽  
Global Dynamics ◽  
Migration Rates ◽  
Wide Range ◽  
The Face ◽  
Subdivided Populations ◽  
Genetic Mechanisms ◽  
And Migration ◽  
Parameter Values ◽  
Insight Into

Abstract We define latent genes as phenotypically silent DNA sequences which may be reactivated by various genetic mechanisms. Of interest is how they and their functional counterparts can be maintained at high frequency in the face of mutation and selection pressure. We propose a two-deme, three-allele model incorporating viability selection, mutation and migration in haploid populations. It is shown that polymorphism for the three alleles can be easily maintained for a wide range of biologically meaningful parameter values. Computer simulations were employed to gain qualitative insight into the global dynamics of the system. It was found that the dynamics of the latent allele is closely correlated with that of the functional allele. In addition, bias in the migration rates can strengthen or weaken selective conditions for preservation of the functional and latent alleles.

scholarly journals β-Lactoglobulin Adsorption Layers at the Water/Air Surface: 5. Adsorption Isotherm and Equation of State Revisited, Impact of pH

2021 ◽  
Vol 5 (1) ◽  
pp. 14
Author(s):  
Georgi G. Gochev ◽  
Volodymyr I. Kovalchuk ◽  
Eugene V. Aksenenko ◽  
Valentin B. Fainerman ◽  
Reinhard Miller
Keyword(s):  
Theoretical Description ◽  
Fluid Interfaces ◽  
Interfacial Behavior ◽  
Current State ◽  
Air Interface ◽  
Direct Measurements ◽  
Wide Range ◽  
Dilational Viscoelasticity ◽  
Parameter Values ◽  
Β Lactoglobulin

The theoretical description of the adsorption of proteins at liquid/fluid interfaces suffers from the inapplicability of classical formalisms, which soundly calls for the development of more complicated adsorption models. A Frumkin-type thermodynamic 2-d solution model that accounts for nonidealities of interface enthalpy and entropy was proposed about two decades ago and has been continuously developed in the course of comparisons with experimental data. In a previous paper we investigated the adsorption of the globular protein β-lactoglobulin at the water/air interface and used such a model to analyze the experimental isotherms of the surface pressure, Π(c), and the frequency-, f-, dependent surface dilational viscoelasticity modulus, E(c)f, in a wide range of protein concentrations, c, and at pH 7. However, the best fit between theory and experiment proposed in that paper appeared incompatible with new data on the surface excess, Γ, obtained from direct measurements with neutron reflectometry. Therefore, in this work, the same model is simultaneously applied to a larger set of experimental dependences, e.g., Π(c), Γ(c), E(Π)f, etc., with E-values measured strictly in the linear viscoelasticity regime. Despite this ambitious complication, a best global fit was elaborated using a single set of parameter values, which well describes all experimental dependencies, thus corroborating the validity of the chosen thermodynamic model. Furthermore, we applied the model in the same manner to experimental results obtained at pH 3 and pH 5 in order to explain the well-pronounced effect of pH on the interfacial behavior of β-lactoglobulin. The results revealed that the propensity of β-lactoglobulin globules to unfold upon adsorption and stretch at the interface decreases in the order pH 3 > pH 7 > pH 5, i.e., with decreasing protein net charge. Finally, we discuss advantages and limitations in the current state of the model.

scholarly journals Inter- and Intra-Continental Genetic Variation in the Generalist Conifer Wood Saprobic Fungus Phlebiopsis gigantea

Forests ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 751
Author(s):  
Francesco Dovana ◽  
Paolo Gonthier ◽  
Matteo Garbelotto
Keyword(s):  
North America ◽  
Genetic Differentiation ◽  
Dna Sequences ◽  
North American ◽  
Fungal Species ◽  
Coniferous Forests ◽  
Native Forest ◽  
Western North America ◽  
Phlebiopsis Gigantea ◽  
Conifer Wood

Phlebiopsis gigantea (Fr.) Jülich is a well-known generalist conifer wood saprobe and a biocontrol fungus used in several world countries to prevent stump infection by tree pathogenic Heterobasidion fungal species. Previous studies have reported the presence of regional and continental genetic differentiation in host-specific fungi, but the presence of such differentiation for generalist wood saprobes such as P. gigantea has not been often studied or demonstrated. Additionally, little information exists on the distribution of this fungus in western North America. The main purposes of this study were: (I) to assess the presence of P. gigantea in California, (II) to explore the genetic variability of P. gigantea at the intra and inter-continental levels and (III) to analyze the phylogeographic relationships between American and European populations. Seven loci (nrITS, ML5–ML6, ATP6, RPB1, RPB2, GPD and TEF1-α) from 26 isolates of P. gigantea from coniferous forests in diverse geographic distribution and from different hosts were analyzed in this study together with 45 GenBank sequences. One hundred seventy-four new sequences were generated using either universal or specific primers designed in this study. The mitochondrial ML5–ML6 DNA and ATP6 regions were highly conserved and did not show differences between any of the isolates. Conversely, DNA sequences from the ITS, RPB1, RPB2, GPD and TEF1-α loci were variable among samples. Maximum likelihood analysis of GPD and TEF1-α strongly supported the presences of two different subgroups within the species but without congruence or geographic partition, suggesting the presence of retained ancestral polymorphisms. RPB1 and RPB2 sequences separated European isolates from American ones, while the GPD locus separated western North American samples from eastern North American ones. This study reports the presence of P. gigantea in California for the first time using DNA-based confirmation and identifies two older genetically distinct subspecific groups, as well as three genetically differentiated lineages within the species: one from Europe, one from eastern North America and one from California, with the latter presumably including individuals from the rest of western North America. The genetic differentiation identified here among P. gigantea individuals from coniferous forests from different world regions indicates that European isolates of this fungus should not be used in North America (or vice versa), and, likewise, commercially available eastern North American P. gigantea isolates should not be used in western North America forests. The reported lack of host specificity of P. gigantea was documented by the field survey and further reinforces the need to only use local isolates of this biocontrol fungus, given that genetically distinct exotic genotypes of a broad generalist microbe may easily spread and permanently alter the microbial biodiversity of native forest ecosystems.

Parasites in Antarctic krill guts inferred from DNA sequences

2019 ◽  
Vol 31 (1) ◽  
pp. 16-22 ◽  
Author(s):  
Alison C. Cleary ◽  
Maria C. Casas ◽  
Edward G. Durbin ◽  
Jaime Gómez-Gutiérrez
Keyword(s):  
Dna Sequences ◽  
High Frequency ◽  
Dna Analysis ◽  
Antarctic Krill ◽  
Euphausia Superba ◽  
Gut Contents ◽  
The West ◽  
West Antarctic ◽  
Wide Range

AbstractThe keystone role of Antarctic krill,Euphausia superbaDana, in Southern Ocean ecosystems, means it is essential to understand the factors controlling their abundance and secondary production. One such factor that remains poorly known is the role of parasites. A recent study of krill diet using DNA analysis of gut contents provided a snapshot of the parasites present within 170E. superbaguts in a small area along the West Antarctic Peninsula. These parasites includedMetschnikowiaspp. fungi,Haptoglossasp. peronosporomycetes,LankesteriaandParalecudinaspp. apicomplexa,Stegophorussp. nematodes, andPseudocolliniaspp. ciliates. Of these parasites,Metschnikowiaspp. fungi andPseudocolliniaspp. ciliates had previously been observed inE. superba, as had other genera of apicomplexans, though notLankesteriaandParalecudina.In contrast, nematodes had previously only been observed in eggs ofE. superba, and there are no literature reports of peronosporomycetes in euphausiids.Pseudocolliniaspp., parasitoids which obligately kill their host, were the most frequently observed infection, with a prevalence of 12%. The wide range of observed parasites and the relatively high frequency of infections suggest parasites may play a more important role than previously acknowledged inE. superbaecology and population dynamics.

Species-specific duplex PCR for the detection of Pratylenchus penetrans

Nematology ◽  
2009 ◽  
Vol 11 (6) ◽  
pp. 847-857 ◽  
Author(s):  
Lieven Waeyenberge ◽  
Nicole Viaene ◽  
Maurice Moens
Keyword(s):  
Internal Control ◽  
Dna Sequences ◽  
Rrna Gene ◽  
Duplex Pcr ◽  
Specific Primers ◽  
5.8S Rrna Gene ◽  
5.8S Rrna ◽  
Wide Range ◽  
Pcr Products ◽  
Species Specific

Abstract ITS1, the 5.8S rRNA gene and ITS2 of the rDNA region were sequenced from 20 different Pratylenchus species. Additionally, the same region was sequenced from seven populations of P. penetrans. After purifying, cloning and sequencing the PCR products, all sequences were aligned in order to find unique sites suitable for the design of species-specific primers for P. penetrans. Since ITS regions showed variability between and even within populations of P. penetrans, only three small DNA sequences were suitable for the construction of three potentially useful species-specific primers. New species-specific primers were paired with existing universal ITS primers and tested in all possible primer combinations. The best performing primer set, supplemented with a universal 28S rDNA primer set that served as an internal control, was tested in duplex PCR. The ideal annealing temperature, Mg2+ concentration and primer ratios were then determined for the most promising primer set. The optimised duplex PCR was subsequently tested on a wide range of different Pratylenchus spp. and 25 P. penetrans populations originating from all over the world. To test the sensitivity, the duplex PCR was conducted on DNA extracted from a single P. penetrans nematode mixed with varying amounts of nematodes belonging to another Pratylenchus species. Results showed that a reliable and sensitive P. penetrans species-specific duplex PCR was constructed.

Motion of slender bodies in unsteady Stokes flow

2011 ◽  
Vol 688 ◽  
pp. 66-87 ◽  
Author(s):  
Efrath Barta
Keyword(s):  
Stokes Flow ◽  
Slenderness Ratio ◽  
Creeping Flow ◽  
Slender Body Theory ◽  
Wide Range ◽  
Unsteady Stokes Flow ◽  
Slender Bodies ◽  
Set Up ◽  
Micro Organisms ◽  
Parameter Values

AbstractThe flow regime in the vicinity of oscillatory slender bodies, either an isolated one or a row of many bodies, immersed in viscous fluid (i.e. under creeping flow conditions) is studied. Applying the slender-body theory by distributing proper singularities on the bodies’ major axes yields reasonably accurate and easily computed solutions. The effect of the oscillations is revealed by comparisons with known Stokes flow solutions and is found to be most significant for motion along the normal direction. Streamline patterns associated with motion of a single body are characterized by formation and evolution of eddies. The motion of adjacent bodies results, with a reduction or an increase of the drag force exerted by each body depending on the direction of motion and the specific geometrical set-up. This dependence is demonstrated by parametric results for frequency of oscillations, number of bodies, their slenderness ratio and the spacing between them. Our method, being valid for a wide range of parameter values and for densely packed arrays of rods, enables simulation of realistic flapping of bristled wings of some tiny insects and of locomotion of flagella and ciliated micro-organisms, and might serve as an efficient tool in the design of minuscule vehicles. Its potency is demonstrated by a solution for the flapping of thrips.

Convective and turbulent motions in non-precipitating Cu. Part 1: Method of separation of convective and turbulent motions

2021 ◽  
Author(s):  
Mark Pinsky ◽  
Eshkol Eytan ◽  
Ilan Koren ◽  
Orit Altaratz ◽  
Alexander Khain
Keyword(s):  
Velocity Field ◽  
Vertical Velocity ◽  
Isotropic Turbulence ◽  
Convective Velocity ◽  
Cloud Dynamics ◽  
Wide Range ◽  
Homogeneous And Isotropic Turbulence ◽  
Microphysical Processes ◽  
Bin Microphysics ◽  
Parameter Values

AbstractAtmospheric motions in clouds and cloud surrounding have a wide range of scales, from several kilometers to centimeters. These motions have different impacts on cloud dynamics and microphysics. Larger-scale motions (hereafter referred to as convective motions) are responsible for mass transport over distances comparable with cloud scale, while motions of smaller scales (hereafter referred to as turbulent motions) are stochastic and responsible for mixing and cloud dilution. This distinction substantially simplifies the analysis of dynamic and microphysical processes in clouds. The present research is Part 1 of the study aimed at describing the method for separating the motion scale into a convective component and a turbulent component. An idealized flow is constructed, which is a sum of an initially prescribed field of the convective velocity with updrafts in the cloud core and downdrafts outside the core, and a stochastic turbulent velocity field obeying the turbulent properties, including the -5/3 law and the 2/3 structure function law. A wavelet method is developed allowing separation of the velocity field into the convective and turbulent components, with parameter values being in a good agreement with those prescribed initially. The efficiency of the method is demonstrated by an example of a vertical velocity field of a cumulus cloud simulated using SAM with bin-microphysics and resolution of 10 m. It is shown that vertical velocity in clouds indeed can be represented as a sum of convective velocity (forming zone of cloud updrafts and subsiding shell) and a stochastic velocity obeying laws of homogeneous and isotropic turbulence.

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