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Sample records for effective population sizes

  1. Effective population size of korean populations.

    PubMed

    Park, Leeyoung

    2014-12-01

    Recently, new methods have been developed for estimating the current and recent changes in effective population sizes. Based on the methods, the effective population sizes of Korean populations were estimated using data from the Korean Association Resource (KARE) project. The overall changes in the population sizes of the total populations were similar to CHB (Han Chinese in Beijing, China) and JPT (Japanese in Tokyo, Japan) of the HapMap project. There were no differences in past changes in population sizes with a comparison between an urban area and a rural area. Age-dependent current and recent effective population sizes represent the modern history of Korean populations, including the effects of World War II, the Korean War, and urbanization. The oldest age group showed that the population growth of Koreans had already been substantial at least since the end of the 19th century.

  2. Effective sizes for subdivided populations

    SciTech Connect

    Chesser, R.K. Univ. of Georgia, Athens, GA ); Rhodes, O.E. Jr.; Sugg, D.W.; Schnabel, A. )

    1993-12-01

    Many derivations of effective population sizes have been suggested in the literature; however, few account for the breeding structure and none can readily be expanded to subdivided populations. Breeding structures influence gene correlations through their effects on the number of breeding individuals of each sex, the mean number of progeny per female, and the variance in the number of progeny produced by males and females. Additionally, hierarchical structuring in a population is determined by the number of breeding groups and the migration rates of males and females among such groups. This study derives analytical solutions for effective sizes that can be applied to subdivided populations. Parameters that encapsulate breeding structure and subdivision are utilized to derive the traditional inbreeding and variance effective sizes. Also, it is shown that effective sizes can be determined for any hierarchical level of population structure for which gene correlations can accrue. Derivations of effective sizes for the accumulation of gene correlations within breeding groups (coancestral effective size) and among breeding groups (intergroup effective size) are given. The results converge to traditional single population measures when similar assumptions are applied. In particular, inbreeding and intergroup effective sizes are shown to be special cases of the coancestral effective size, and intergroup and variance effective sizes will be equal if the population census remains constant. Instantaneous solutions for effective size, at any time after gene correlation begins to accrue, are given in terms of traditional F statistics or transition equations. All effective sizes are shown to converge upon a common asymptotic value when breeding tactics and migration rates are constant. The asymptotic effective size can be expressed in terms of the fixation indices and the number of breeding groups; however, the rate of approach to the asymptote is dependent upon dispersal rates.

  3. Effective Sizes for Subdivided Populations

    PubMed Central

    Chesser, R. K.; Rhodes-Jr., O. E.; Sugg, D. W.; Schnabel, A.

    1993-01-01

    Many derivations of effective population sizes have been suggested in the literature; however, few account for the breeding structure and none can readily be expanded to subdivided populations. Breeding structures influence gene correlations through their effects on the number of breeding individuals of each sex, the mean number of progeny per female, and the variance in the number of progeny produced by males and females. Additionally, hierarchical structuring in a population is determined by the number of breeding groups and the migration rates of males and females among such groups. This study derives analytical solutions for effective sizes that can be applied to subdivided populations. Parameters that encapsulate breeding structure and subdivision are utilized to derive the traditional inbreeding and variance effective sizes. Also, it is shown that effective sizes can be determined for any hierarchical level of population structure for which gene correlations can accrue. Derivations of effective sizes for the accumulation of gene correlations within breeding groups (coancestral effective size) and among breeding groups (intergroup effective size) are given. The results converge to traditional, single population measures when similar assumptions are applied. In particular, inbreeding and intergroup effective sizes are shown to be special cases of the coancestral effective size, and intergroup and variance effective sizes will be equal if the population census remains constant. Instantaneous solutions for effective sizes, at any time after gene correlation begins to accrue, are given in terms of traditional F statistics or transition equations. All effective sizes are shown to converge upon a common asymptotic value when breeding tactics and migration rates are constant. The asymptotic effective size can be expressed in terms of the fixation indices and the number of breeding groups; however, the rate of approach to the asymptote is dependent upon dispersal

  4. Effective Population Sizes with Multiple Paternity

    PubMed Central

    Sugg, D. W.; Chesser, R. K.

    1994-01-01

    While the concept of effective population size is of obvious applicability to many questions in population genetics and conservation biology, its utility has suffered due to a lack of agreement among its various formulations. Often, mathematical formulations for effective sizes apply restrictive assumptions that limit their applicability. Herein, expressions for effective sizes of populations that account for mating tactics, biases in sex ratios, and differential dispersal rates (among other parameters) are developed. Of primary interest is the influence of multiple paternity on the maintenance of genetic variation in a population. In addition to the standard inbreeding and variance effective sizes, intragroup (coancestral) and intergroup effective sizes also are developed. Expressions for effective sizes are developed for the beginning of nonrandom gene exchanges (initial effective sizes), the transition of gene correlations (instantaneous effective sizes), and the steady-state (asymptotic effective size). Results indicate that systems of mating that incorporate more than one male mate per female increase all effective sizes above those expected from polygyny and monogamy. Instantaneous and asymptotic sizes can be expressed relative to the fixation indices. The parameters presented herein can be utilized in models of effective sizes for the study of evolutionary biology and conservation genetics. PMID:7982568

  5. Detecting past changes of effective population size

    PubMed Central

    Nikolic, Natacha; Chevalet, Claude

    2014-01-01

    Understanding and predicting population abundance is a major challenge confronting scientists. Several genetic models have been developed using microsatellite markers to estimate the present and ancestral effective population sizes. However, to get an overview on the evolution of population requires that past fluctuation of population size be traceable. To address the question, we developed a new model estimating the past changes of effective population size from microsatellite by resolving coalescence theory and using approximate likelihoods in a Monte Carlo Markov Chain approach. The efficiency of the model and its sensitivity to gene flow and to assumptions on the mutational process were checked using simulated data and analysis. The model was found especially useful to provide evidence of transient changes of population size in the past. The times at which some past demographic events cannot be detected because they are too ancient and the risk that gene flow may suggest the false detection of a bottleneck are discussed considering the distribution of coalescence times. The method was applied on real data sets from several Atlantic salmon populations. The method called VarEff (Variation of Effective size) was implemented in the R package VarEff and is made available at https://qgsp.jouy.inra.fr and at http://cran.r-project.org/web/packages/VarEff. PMID:25067949

  6. Detecting past changes of effective population size.

    PubMed

    Nikolic, Natacha; Chevalet, Claude

    2014-06-01

    Understanding and predicting population abundance is a major challenge confronting scientists. Several genetic models have been developed using microsatellite markers to estimate the present and ancestral effective population sizes. However, to get an overview on the evolution of population requires that past fluctuation of population size be traceable. To address the question, we developed a new model estimating the past changes of effective population size from microsatellite by resolving coalescence theory and using approximate likelihoods in a Monte Carlo Markov Chain approach. The efficiency of the model and its sensitivity to gene flow and to assumptions on the mutational process were checked using simulated data and analysis. The model was found especially useful to provide evidence of transient changes of population size in the past. The times at which some past demographic events cannot be detected because they are too ancient and the risk that gene flow may suggest the false detection of a bottleneck are discussed considering the distribution of coalescence times. The method was applied on real data sets from several Atlantic salmon populations. The method called VarEff (Variation of Effective size) was implemented in the R package VarEff and is made available at https://qgsp.jouy.inra.fr and at http://cran.r-project.org/web/packages/VarEff.

  7. The Effective Size of a Subdivided Population

    PubMed Central

    Whitlock, M. C.; Barton, N. H.

    1997-01-01

    This paper derives the long-term effective size, N(e), for a general model of population subdivision, allowing for differential deme fitness, variable emigration and immigration rates, extinction, colonization, and correlations across generations in these processes. We show that various long-term measures of N(e) are equivalent. The effective size of a metapopulation can be expressed in a variety of ways. At a demographic equilibrium, N(e) can be derived from the demography by combining information about the ultimate contribution of each deme to the future genetic make-up of the population and Wright's F(ST)'s. The effective size is given by N(e) = 1/(1 + var ( &))<(1 - f(STi))/N(i)n>, where n is the number of demes, &(i) is the eventual contribution of individuals in deme i to the whole population (scaled such that σ(i) &(i) = n), and < > denotes an average weighted by &(i)(2). This formula is applied to a catastrophic extinction model (where sites are either empty or at carrying capacity) and to a metapopulation model with explicit dynamics, where extinction is caused by demographic stochasticity and by chaos. Contrary to the expectation from the standard island model, the usual effect of population subdivision is to decrease the effective size relative to a panmictic population living on the same resource. PMID:9136031

  8. Effective Size of Populations under Selection

    PubMed Central

    Santiago, E.; Caballero, A.

    1995-01-01

    Equations to approximate the effective size (N(e)) of populations under continued selection are obtained that include the possibility of partial full-sib mating and other systems such as assortative mating. The general equation for the case of equal number of sexes and constant number of breeding individuals (N) is N(e) = 4N/[2(1 - α(I)) + (S(k)(2) + 4Q(2)C(2)) (1 + α(I) + 2α(O))], where S(k)(2) is the variance of family size due to sampling without selection, C(2) is the variance of selective advantages among families (the squared coefficient of variation of the expected number of offspring per family), α(I) is the deviation from Hardy-Weinberg proportions, α(O) is the correlation between genes of male and female parents, and Q(2) is the term accounting for the cumulative effect of selection on an inherited trait. This is obtained as Q = 2/[2 - G(1 + r)], where G is the remaining proportion of genetic variance in selected individuals and r is the correlation of the expected selective values of male and female parents. The method is also extended to the general case of different numbers of male and female parents. The predictive value of the formulae is tested under a model of truncation selection with the infinitesimal model of gene effects, where C(2) and G are a function of the selection intensity, the heritability and the intraclass correlation of sibs. Under random mating r = α(I) = -1/(N - 1) and α(O) = 0. Under partial full-sib mating with an average proportion β of full-sib matings per generation, r & β and α(O) & α(I) & β/ (4 - 3β). The prediction equation is compared to other approximations based on the long-term contributions of ancestors to descendants. Finally, based on the approach followed, a system of mating (compensatory mating) is proposed to reduce rates of inbreeding without loss of response in selection programs in which selected individuals from the largest families are mated to those from the smallest families. PMID:7713405

  9. Genetic diversity, population structure, effective population size and demographic history of the Finnish wolf population.

    PubMed

    Aspi, J; Roininen, E; Ruokonen, M; Kojola, I; Vilà, C

    2006-05-01

    The Finnish wolf population (Canis lupus) was sampled during three different periods (1996-1998, 1999-2001 and 2002-2004), and 118 individuals were genotyped with 10 microsatellite markers. Large genetic variation was found in the population despite a recent demographic bottleneck. No spatial population subdivision was found even though a significant negative relationship between genetic relatedness and geographic distance suggested isolation by distance. Very few individuals did not belong to the local wolf population as determined by assignment analyses, suggesting a low level of immigration in the population. We used the temporal approach and several statistical methods to estimate the variance effective size of the population. All methods gave similar estimates of effective population size, approximately 40 wolves. These estimates were slightly larger than the estimated census size of breeding individuals. A Bayesian model based on Markov chain Monte Carlo simulations indicated strong evidence for a long-term population decline. These results suggest that the contemporary wolf population size is roughly 8% of its historical size, and that the population decline dates back to late 19th century or early 20th century. Despite an increase of over 50% in the census size of the population during the whole study period, there was only weak evidence that the effective population size during the last period was higher than during the first. This may be caused by increased inbreeding, diminished dispersal within the population, and decreased immigration to the population during the last study period.

  10. Two measures of effective population size for graphs.

    PubMed

    Broom, Mark; Voelkl, Bernhard

    2012-05-01

    Effective population size is a key parameter in population ecology because it allows prediction of the dynamics of genetic variation and the rate of genetic drift and inbreeding. It is important for the definition of "nearly neutral" mutations and, hence, has consequences for the fixation or extinction probabilities of advantageous and deleterious mutations. As graph-based population models become increasingly popular for studying evolution in spatially or socially structured populations, a neutral theory for evolution on graphs is called for. Here, we derive formulae for two alternative measures of effective population size, the variance effective and inbreeding effective size of general unweighted and undirected graphs. We show how these two quantities relate to each other and we derive effective sizes for the complete graph the cycle and bipartite graphs. For one-dimensional lattices and small-world graphs, we estimate the inbreeding effective size using simulations. The presented method is suitable for any structured population of haploid individuals with overlapping generations.

  11. Effective population size and genetic conservation criteria for bull trout

    Treesearch

    Bruce E. Rieman; F. W. Allendorf

    2001-01-01

    Effective population size (Ne) is an important concept in the management of threatened species like bull trout Salvelinus confluentus. General guidelines suggest that effective population sizes of 50 or 500 are essential to minimize inbreeding effects or maintain adaptive genetic variation, respectively....

  12. Repeated Habitat Disturbances by Fire Decrease Local Effective Population Size.

    PubMed

    Schrey, Aaron W; Ragsdale, Alexandria K; McCoy, Earl D; Mushinsky, Henry R

    2016-07-01

    Effective population size is a fundamental parameter in population genetics, and factors that alter effective population size will shape the genetic characteristics of populations. Habitat disturbance may have a large effect on genetic characteristics of populations by influencing immigration and gene flow, particularly in fragmented habitats. We used the Florida Sand Skink (Plestiodon reynoldsi) to investigate the effect of fire-based habitat disturbances on the effective population size in the highly threatened, severely fragmented, and fire dependent Florida scrub habitat. We screened 7 microsatellite loci in 604 individuals collected from 12 locations at Archbold Biological Station. Archbold Biological Station has an active fire management plan and detailed records of fires dating to 1967. Our objective was to determine how the timing, number, and intervals between fires affect effective population size, focusing on multiple fires in the same location. Effective population size was higher in areas that had not been burned for more than 10 years and decreased with number of fires and shorter time between fires. A similar pattern was observed in abundance: increasing abundance with time-since-fire and decreasing abundance with number of fires. The ratio of effective population size to census size was higher at sites with more recent fires and tended to decrease with time-since-last-fire. These results suggest that habitat disturbances, such as fire, may have a large effect in the genetic characteristics of local populations and that Florida Sand Skinks are well adapted to the natural fire dynamics required to maintain Florida scrub.

  13. Inferring Past Effective Population Size from Distributions of Coalescent Times

    PubMed Central

    Gattepaille, Lucie; Günther, Torsten; Jakobsson, Mattias

    2016-01-01

    Inferring and understanding changes in effective population size over time is a major challenge for population genetics. Here we investigate some theoretical properties of random-mating populations with varying size over time. In particular, we present an exact solution to compute the population size as a function of time, Ne(t), based on distributions of coalescent times of samples of any size. This result reduces the problem of population size inference to a problem of estimating coalescent time distributions. To illustrate the analytic results, we design a heuristic method using a tree-inference algorithm and investigate simulated and empirical population-genetic data. We investigate the effects of a range of conditions associated with empirical data, for instance number of loci, sample size, mutation rate, and cryptic recombination. We show that our approach performs well with genomic data (≥ 10,000 loci) and that increasing the sample size from 2 to 10 greatly improves the inference of Ne(t) whereas further increase in sample size results in modest improvements, even under a scenario of exponential growth. We also investigate the impact of recombination and characterize the potential biases in inference of Ne(t). The approach can handle large sample sizes and the computations are fast. We apply our method to human genomes from four populations and reconstruct population size profiles that are coherent with previous finds, including the Out-of-Africa bottleneck. Additionally, we uncover a potential difference in population size between African and non-African populations as early as 400 KYA. In summary, we provide an analytic relationship between distributions of coalescent times and Ne(t), which can be incorporated into powerful approaches for inferring past population sizes from population-genomic data. PMID:27638421

  14. On the Meaning and Existence of an Effective Population Size

    PubMed Central

    Sjödin, P.; Kaj, I.; Krone, S.; Lascoux, M.; Nordborg, M.

    2005-01-01

    We investigate conditions under which a model with stochastic demography or population structure converges to the coalescent with a linear change in timescale. We argue that this is a necessary condition for the existence of a meaningful effective population size. We find that such a linear timescale change is obtained when demographic fluctuations and coalescence events occur on different timescales. Simple models of population structure and randomly fluctuating population size are used to exemplify the ideas and provide an intuitive feel for the meaning of the conditions. PMID:15489538

  15. The effective size of mixed sexually and asexually reproducing populations.

    PubMed Central

    Yonezawa, Katsuei; Ishii, Takuro; Nagamine, Tsukasa

    2004-01-01

    Using the transition matrix of inbreeding and coancestry coefficients, the inbreeding (N(eI)), variance (N(eV)), and asymptotic (N(e lambda)) effective sizes of mixed sexual and asexual populations are formulated in terms of asexuality rate (delta), variance of asexual (C) and sexual (K) reproductive contributions of individuals, correlation between asexual and sexual contributions (rho(ck)), selfing rate (beta), and census population size (N). The trajectory of N(eI) toward N(e lambda) changes crucially depending on delta, N, and beta, whereas that of N(eV) is rather consistent. With increasing asexuality, N(e lambda) either increases or decreases depending on C, K, and rho(ck). The parameter space in which a partially asexual population has a larger N(e lambda) than a fully sexual population is delineated. This structure is destroyed when N(1 - delta) < 1 or delta > 1 - 1/N. With such a high asexuality, tremendously many generations are required for the asymptotic size N(e lambda) to be established, and N(e lambda) is extremely large with any value of C, K, and rho(ck) because the population is dominated eventually by individuals of the same genotype and the allelic diversity within the individuals decays quite slowly. In reality, the asymptotic state would occur only occasionally, and instantaneous rather than asymptotic effective sizes should be practical when predicting evolutionary dynamics of highly asexual populations. PMID:15082566

  16. The effect of habitat patch size on small mammal populations

    Treesearch

    Mark D. Yates; Susan C. Loeb; David C. Guynn

    1997-01-01

    Habitat fragmentation is one of the greatest threats to the conservation of bio­diversity and has 3 components: habitat loss, patch isolation, and patch size. The authors tested the effects of forest-clearing size on small mammal populations in the Upper Coastal Plain of South Carolina. These clearings act as islands for many species of small mam­mals, particularly old...

  17. Sampling strategies for estimating brook trout effective population size

    Treesearch

    Andrew R. Whiteley; Jason A. Coombs; Mark Hudy; Zachary Robinson; Keith H. Nislow; Benjamin H. Letcher

    2012-01-01

    The influence of sampling strategy on estimates of effective population size (Ne) from single-sample genetic methods has not been rigorously examined, though these methods are increasingly used. For headwater salmonids, spatially close kin association among age-0 individuals suggests that sampling strategy (number of individuals and location from...

  18. Estimation of effective population size in continuously distributed populations: There goes the neighborhood

    Treesearch

    M. C. Neel; K. McKelvey; N. Ryman; M. W. Lloyd; R. Short Bull; F. W. Allendorf; M. K. Schwartz; R. S. Waples

    2013-01-01

    Use of genetic methods to estimate effective population size (Ne) is rapidly increasing, but all approaches make simplifying assumptions unlikely to be met in real populations. In particular, all assume a single, unstructured population, and none has been evaluated for use with continuously distributed species. We simulated continuous populations with local mating...

  19. gesp: A computer program for modelling genetic effective population size, inbreeding and divergence in substructured populations.

    PubMed

    Olsson, Fredrik; Laikre, Linda; Hössjer, Ola; Ryman, Nils

    2017-03-24

    The genetically effective population size (Ne ) is of key importance for quantifying rates of inbreeding and genetic drift and is often used in conservation management to set targets for genetic viability. The concept was developed for single, isolated populations and the mathematical means for analysing the expected Ne in complex, subdivided populations have previously not been available. We recently developed such analytical theory and central parts of that work have now been incorporated into a freely available software tool presented here. gesp (Genetic Effective population size, inbreeding and divergence in Substructured Populations) is R-based and designed to model short- and long-term patterns of genetic differentiation and effective population size of subdivided populations. The algorithms performed by gesp allow exact computation of global and local inbreeding and eigenvalue effective population size, predictions of genetic divergence among populations (GST ) as well as departures from random mating (FIS , FIT ) while varying (i) subpopulation census and effective size, separately or including trend of the global population size, (ii) rate and direction of migration between all pairs of subpopulations, (iii) degree of relatedness and divergence among subpopulations, (iv) ploidy (haploid or diploid) and (v) degree of selfing. Here, we describe gesp and exemplify its use in conservation genetics modelling. © 2017 John Wiley & Sons Ltd.

  20. Effects of body size and temperature on population growth.

    PubMed

    Savage, Van M; Gilloly, James F; Brown, James H; Charnov, Eric L

    2004-03-01

    For at least 200 years, since the time of Malthus, population growth has been recognized as providing a critical link between the performance of individual organisms and the ecology and evolution of species. We present a theory that shows how the intrinsic rate of exponential population growth, rmax, and the carrying capacity, K, depend on individual metabolic rate and resource supply rate. To do this, we construct equations for the metabolic rates of entire populations by summing over individuals, and then we combine these population-level equations with Malthusian growth. Thus, the theory makes explicit the relationship between rates of resource supply in the environment and rates of production of new biomass and individuals. These individual-level and population-level processes are inextricably linked because metabolism sets both the demand for environmental resources and the resource allocation to survival, growth, and reproduction. We use the theory to make explicit how and why rmax exhibits its characteristic dependence on body size and temperature. Data for aerobic eukaryotes, including algae, protists, insects, zooplankton, fishes, and mammals, support these predicted scalings for rmax. The metabolic flux of energy and materials also dictates that the carrying capacity or equilibrium density of populations should decrease with increasing body size and increasing temperature. Finally, we argue that body mass and body temperature, through their effects on metabolic rate, can explain most of the variation in fecundity and mortality rates. Data for marine fishes in the field support these predictions for instantaneous rates of mortality. This theory links the rates of metabolism and resource use of individuals to life-history attributes and population dynamics for a broad assortment of organisms, from unicellular organisms to mammals.

  1. Bacterial finite-size effects for population expansion under flow

    NASA Astrophysics Data System (ADS)

    Toschi, Federico; Tesser, Francesca; Zeegers, Jos C. H.; Clercx, Herman J. H.; Brunsveld, Luc

    2016-11-01

    For organisms living in a liquid ecosystem, flow and flow gradients have a dual role as they transport nutrient while, at the same time, dispersing the individuals. In absence of flow and under homogeneous conditions, the growth of a population towards an empty region is usually described by a reaction-diffusion equation. The effect of fluid flow is not yet well understood and the interplay between transport of individuals and growth opens a wide scenario of possible behaviors. In this work, we study experimentally the dynamics of non-motile E. coli bacteria colonies spreading inside rectangular channels, in PDMS microfluidic devices. By use of a fluorescent microscope we analyze the dynamics of the population density subjected to different co- and counter-flow conditions and shear rates. A simple model incorporating growth, dispersion and drift of finite size beads is able to explain the experimental findings. This indicates that models based on the Fisher-Kolmogorov-Petrovsky-Piscounov equation (FKPP) may have to be supplemented with bacterial finite-size effects in order to be able to accurately reproduce experimental results for population spatial growth.

  2. Family size and effective population size in a hatchery stock of coho salmon (Oncorhynchus kisutch)

    USGS Publications Warehouse

    Simon, R.C.; McIntyre, J.D.; Hemmingsen, A.R.

    1986-01-01

    Means and variances of family size measured in five year-classes of wire-tagged coho salmon (Oncorhynchus kisutch) were linearly related. Population effective size was calculated by using estimated means and variances of family size in a 25-yr data set. Although numbers of age 3 adults returning to the hatchery appeared to be large enough to avoid inbreeding problems (the 25-yr mean exceeded 4500), the numbers actually contributing to the hatchery production may be too low. Several strategies are proposed to correct the problem perceived. Argument is given to support the contention that the problem of effective size is fairly general and is not confined to the present study population.

  3. Small Effective Population Sizes and Rare Nonsynonymous Variants in Potyviruses

    PubMed Central

    Hughes, Austin L.

    2009-01-01

    Analysis of nucleotide sequence polymorphism in complete genomes of 12 species of potyviruses (single-stranded, positive-sense RNA viruses, family Potyviridae) revealed evidence that long-term effective population sizes of these viruses are on the order of 104. Comparison of nucleotide diversity in non-coding regions and at synonymous and nonsynonymous sites in coding regions showed that purifying selection has acted to eliminate numerous deleterious mutations both at nonsynonymous sites and in non-coding regions. The ratio of nonsynonymous to synonymous polymorphic sites increased as a function of the number of genomes sampled, whereas mean gene diversity at nonsynonymous polymorphic sites decreased with increasing sample size at a substantially faster rate than does mean gene diversity at synonymous polymorphic sites. Very similar relationships were observed both in available genomic sequences of 12 potyvirus species and in subsets created by randomly sampling from among 98 TuMV genomes. Taken together, these observations imply that a greater proportion of nonsynonymous than of synonymous variants are relatively rare as the result of ongoing purifying selection, and thus many nonsynonymous variants are unlikely to be discovered without extensive sampling. PMID:19695658

  4. Effective population size and inbreeding depression on litter size in rabbits. A case study.

    PubMed

    Ragab, M; Sánchez, J P; Baselga, M

    2015-02-01

    The purpose of this study is to use demographic and litter size data on four Spanish maternal lines of rabbits (A, V, H and LP), as a case study, in order to: (i) estimate the effective population size of the lines, as a measure of the rate of increase of inbreeding, and (ii) study whether the inbreeding effect on litter size traits depends on the pattern of its accumulation over time. The lines are being selected for litter size at weaning and are kept closed at the same selection nucleus under the same selection and management programme. The study considered 47,794 l and a pedigree of 14,622 animals. Some practices in mating and selection management allow an increase of the inbreeding coefficient lower than 0.01 per generation in these lines of around 25 males and 125 females. Their effective population size (Ne) was around 57.3, showing that the effect of selection, increasing the inbreeding, was counterbalanced by the management practices, intended to reduce the rate of inbreeding increase. The inbreeding of each individual was broken down into three components: old, intermediate and new inbreeding. The coefficients of regression of the old, intermediate and new inbreeding on total born (TB), number born alive (NBA) and number weaned (NW) per litter showed a decreasing trend from positive to negative values. Regression coefficients significantly different from zero were those for the old inbreeding on TB (6.79 ± 2.37) and NBA (5.92 ± 2.37). The contrast between the coefficients of regression between the old and new inbreeding were significant for the three litter size traits: 7.57 ± 1.72 for TB; 6.66 ± 1.73 for NBA and 5.13 ± 1.67 for NW. These results have been interpreted as the combined action of purging unfavourable genes and artificial selection favoured by the inbreeding throughout the generations of selection.

  5. Long-term effective population size dynamics of an intensively monitored vertebrate population

    PubMed Central

    Mueller, A-K; Chakarov, N; Krüger, O; Hoffman, J I

    2016-01-01

    Long-term genetic data from intensively monitored natural populations are important for understanding how effective population sizes (Ne) can vary over time. We therefore genotyped 1622 common buzzard (Buteo buteo) chicks sampled over 12 consecutive years (2002–2013 inclusive) at 15 microsatellite loci. This data set allowed us to both compare single-sample with temporal approaches and explore temporal patterns in the effective number of parents that produced each cohort in relation to the observed population dynamics. We found reasonable consistency between linkage disequilibrium-based single-sample and temporal estimators, particularly during the latter half of the study, but no clear relationship between annual Ne estimates () and census sizes. We also documented a 14-fold increase in between 2008 and 2011, a period during which the census size doubled, probably reflecting a combination of higher adult survival and immigration from further afield. Our study thus reveals appreciable temporal heterogeneity in the effective population size of a natural vertebrate population, confirms the need for long-term studies and cautions against drawing conclusions from a single sample. PMID:27553455

  6. Impacts of mutation effects and population size on mutation rate in asexual populations: a simulation study

    PubMed Central

    2010-01-01

    Background In any natural population, mutation is the primary source of genetic variation required for evolutionary novelty and adaptation. Nevertheless, most mutations, especially those with phenotypic effects, are harmful and are consequently removed by natural selection. For this reason, under natural selection, an organism will evolve to a lower mutation rate. Overall, the action of natural selection on mutation rate is related to population size and mutation effects. Although theoretical work has intensively investigated the relationship between natural selection and mutation rate, most of these studies have focused on individual competition within a population, rather than on competition among populations. The aim of the present study was to use computer simulations to investigate how natural selection adjusts mutation rate among asexually reproducing subpopulations with different mutation rates. Results The competition results for the different subpopulations showed that a population could evolve to an "optimum" mutation rate during long-term evolution, and that this rate was modulated by both population size and mutation effects. A larger population could evolve to a higher optimum mutation rate than could a smaller population. The optimum mutation rate depended on both the fraction and the effects of beneficial mutations, rather than on the effects of deleterious ones. The optimum mutation rate increased with either the fraction or the effects of beneficial mutations. When strongly favored mutations appeared, the optimum mutation rate was elevated to a much higher level. The competition time among the subpopulations also substantially shortened. Conclusions Competition at the population level revealed that the evolution of the mutation rate in asexual populations was determined by both population size and mutation effects. The most striking finding was that beneficial mutations, rather than deleterious mutations, were the leading force that modulated the

  7. Accurate Non-parametric Estimation of Recent Effective Population Size from Segments of Identity by Descent.

    PubMed

    Browning, Sharon R; Browning, Brian L

    2015-09-03

    Existing methods for estimating historical effective population size from genetic data have been unable to accurately estimate effective population size during the most recent past. We present a non-parametric method for accurately estimating recent effective population size by using inferred long segments of identity by descent (IBD). We found that inferred segments of IBD contain information about effective population size from around 4 generations to around 50 generations ago for SNP array data and to over 200 generations ago for sequence data. In human populations that we examined, the estimates of effective size were approximately one-third of the census size. We estimate the effective population size of European-ancestry individuals in the UK four generations ago to be eight million and the effective population size of Finland four generations ago to be 0.7 million. Our method is implemented in the open-source IBDNe software package.

  8. Accurate Non-parametric Estimation of Recent Effective Population Size from Segments of Identity by Descent

    PubMed Central

    Browning, Sharon R.; Browning, Brian L.

    2015-01-01

    Existing methods for estimating historical effective population size from genetic data have been unable to accurately estimate effective population size during the most recent past. We present a non-parametric method for accurately estimating recent effective population size by using inferred long segments of identity by descent (IBD). We found that inferred segments of IBD contain information about effective population size from around 4 generations to around 50 generations ago for SNP array data and to over 200 generations ago for sequence data. In human populations that we examined, the estimates of effective size were approximately one-third of the census size. We estimate the effective population size of European-ancestry individuals in the UK four generations ago to be eight million and the effective population size of Finland four generations ago to be 0.7 million. Our method is implemented in the open-source IBDNe software package. PMID:26299365

  9. Estimation of the variance effective population size in age structured populations.

    PubMed

    Olsson, Fredrik; Hössjer, Ola

    2015-05-01

    The variance effective population size for age structured populations is generally hard to estimate and the temporal method often gives biased estimates. Here, we give an explicit expression for a correction factor which, combined with estimates from the temporal method, yield approximately unbiased estimates. The calculation of the correction factor requires knowledge of the age specific offspring distribution and survival probabilities as well as possible correlation between survival and reproductive success. In order to relax these requirements, we show that only first order moments of these distributions need to be known if the time between samples is large, or individuals from all age classes which reproduce are sampled. A very explicit approximate expression for the asymptotic coefficient of standard deviation of the estimator is derived, and it can be used to construct confidence intervals and optimal ways of weighting information from different markers. The asymptotic coefficient of standard deviation can also be used to design studies and we show that in order to maximize the precision for a given sample size, individuals from older age classes should be sampled since their expected variance of allele frequency change is higher and easier to estimate. However, for populations with fluctuating age class sizes, the accuracy of the method is reduced when samples are taken from older age classes with high demographic variation. We also present a method for simultaneous estimation of the variance effective and census population size. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

  10. Adaptive evolution and effective population size in wild house mice.

    PubMed

    Phifer-Rixey, Megan; Bonhomme, François; Boursot, Pierre; Churchill, Gary A; Piálek, Jaroslav; Tucker, Priscilla K; Nachman, Michael W

    2012-10-01

    Estimates of the proportion of amino acid substitutions that have been fixed by selection (α) vary widely among taxa, ranging from zero in humans to over 50% in Drosophila. This wide range may reflect differences in the efficacy of selection due to differences in the effective population size (N(e)). However, most comparisons have been made among distantly related organisms that differ not only in N(e) but also in many other aspects of their biology. Here, we estimate α in three closely related lineages of house mice that have a similar ecology but differ widely in N(e): Mus musculus musculus (N(e) ∼ 25,000-120,000), M. m. domesticus (N(e) ∼ 58,000-200,000), and M. m. castaneus (N(e) ∼ 200,000-733,000). Mice were genotyped using a high-density single nucleotide polymorphism array, and the proportions of replacement and silent mutations within subspecies were compared with those fixed between each subspecies and an outgroup, Mus spretus. There was significant evidence of positive selection in M. m. castaneus, the lineage with the largest N(e), with α estimated to be approximately 40%. In contrast, estimates of α for M. m. domesticus (α = 13%) and for M. m. musculus (α = 12 %) were much smaller. Interestingly, the higher estimate of α for M. m. castaneus appears to reflect not only more adaptive fixations but also more effective purifying selection. These results support the hypothesis that differences in N(e) contribute to differences among species in the efficacy of selection.

  11. Population genomics of eusocial insects: the costs of a vertebrate-like effective population size.

    PubMed

    Romiguier, J; Lourenco, J; Gayral, P; Faivre, N; Weinert, L A; Ravel, S; Ballenghien, M; Cahais, V; Bernard, A; Loire, E; Keller, L; Galtier, N

    2014-03-01

    The evolution of reproductive division of labour and social life in social insects has lead to the emergence of several life-history traits and adaptations typical of larger organisms: social insect colonies can reach masses of several kilograms, they start reproducing only when they are several years old, and can live for decades. These features and the monopolization of reproduction by only one or few individuals in a colony should affect molecular evolution by reducing the effective population size. We tested this prediction by analysing genome-wide patterns of coding sequence polymorphism and divergence in eusocial vs. noneusocial insects based on newly generated RNA-seq data. We report very low amounts of genetic polymorphism and an elevated ratio of nonsynonymous to synonymous changes – a marker of the effective population size – in four distinct species of eusocial insects, which were more similar to vertebrates than to solitary insects regarding molecular evolutionary processes. Moreover, the ratio of nonsynonymous to synonymous substitutions was positively correlated with the level of social complexity across ant species. These results are fully consistent with the hypothesis of a reduced effective population size and an increased genetic load in eusocial insects, indicating that the evolution of social life has important consequences at both the genomic and population levels. © 2014 The Authors. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

  12. Genome-wide estimates of coancestry, inbreeding and effective population size in the Spanish Holstein population.

    PubMed

    Rodríguez-Ramilo, Silvia Teresa; Fernández, Jesús; Toro, Miguel Angel; Hernández, Delfino; Villanueva, Beatriz

    2015-01-01

    Estimates of effective population size in the Holstein cattle breed have usually been low despite the large number of animals that constitute this breed. Effective population size is inversely related to the rates at which coancestry and inbreeding increase and these rates have been high as a consequence of intense and accurate selection. Traditionally, coancestry and inbreeding coefficients have been calculated from pedigree data. However, the development of genome-wide single nucleotide polymorphisms has increased the interest of calculating these coefficients from molecular data in order to improve their accuracy. In this study, genomic estimates of coancestry, inbreeding and effective population size were obtained in the Spanish Holstein population and then compared with pedigree-based estimates. A total of 11,135 animals genotyped with the Illumina BovineSNP50 BeadChip were available for the study. After applying filtering criteria, the final genomic dataset included 36,693 autosomal SNPs and 10,569 animals. Pedigree data from those genotyped animals included 31,203 animals. These individuals represented only the last five generations in order to homogenise the amount of pedigree information across animals. Genomic estimates of coancestry and inbreeding were obtained from identity by descent segments (coancestry) or runs of homozygosity (inbreeding). The results indicate that the percentage of variance of pedigree-based coancestry estimates explained by genomic coancestry estimates was higher than that for inbreeding. Estimates of effective population size obtained from genome-wide and pedigree information were consistent and ranged from about 66 to 79. These low values emphasize the need of controlling the rate of increase of coancestry and inbreeding in Holstein selection programmes.

  13. Effective number of breeders, effective population size and their relationship with census size in an iteroparous species, Salvelinus fontinalis

    PubMed Central

    Ruzzante, Daniel E.; McCracken, Gregory R.; Parmelee, Samantha; Hill, Kristen; Corrigan, Amelia; MacMillan, John; Walde, Sandra J.

    2016-01-01

    The relationship between the effective number of breeders (Nb) and the generational effective size (Ne) has rarely been examined empirically in species with overlapping generations and iteroparity. Based on a suite of 11 microsatellite markers, we examine the relationship between Nb, Ne and census population size (Nc) in 14 brook trout (Salvelinus fontinalis) populations inhabiting 12 small streams in Nova Scotia and sampled at least twice between 2009 and 2015. Unbiased estimates of Nb obtained with individuals of a single cohort, adjusted on the basis of age at first maturation (α) and adult lifespan (AL), were from 1.66 to 0.24 times the average estimates of Ne obtained with random samples of individuals of mixed ages (i.e. ). In turn, these differences led to adjusted Ne estimates that were from nearly five to 0.7 times the estimates derived from mixed-aged individuals. These differences translate into the same range of variation in the ratio of effective to census population size within populations. Adopting as the more precise and unbiased estimates, we found that these brook trout populations differ markedly in their effective to census population sizes (range approx. 0.3 to approx. 0.01). Using AgeNe, we then showed that the variance in reproductive success or reproductive skew varied among populations by a factor of 40, from Vk/k ≈ 5 to 200. These results suggest wide differences in population dynamics, probably resulting from differences in productivity affecting the intensity of competition for access to mates or redds, and thus reproductive skew. Understanding the relationship between Ne, Nb and Nc, and how these relate to population dynamics and fluctuations in population size, are important for the design of robust conservation strategies in small populations with overlapping generations and iteroparity. PMID:26817773

  14. Empirical Bayes procedure for estimating genetic distance between populations and effective population size.

    PubMed Central

    Kitada, S; Hayashi, T; Kishino, H

    2000-01-01

    We developed an empirical Bayes procedure to estimate genetic distances between populations using allele frequencies. This procedure makes it possible to describe the skewness of the genetic distance while taking full account of the uncertainty of the sample allele frequencies. Dirichlet priors of the allele frequencies are specified, and the posterior distributions of the various composite parameters are obtained by Monte Carlo simulation. To avoid overdependence on subjective priors, we adopt a hierarchical model and estimate hyperparameters by maximizing the joint marginal-likelihood function. Taking advantage of the empirical Bayesian procedure, we extend the method to estimate the effective population size using temporal changes in allele frequencies. The method is applied to data sets on red sea bream, herring, northern pike, and ayu broodstock. It is shown that overdispersion overestimates the genetic distance and underestimates the effective population size, if it is not taken into account during the analysis. The joint marginal-likelihood function also estimates the rate of gene flow into island populations. PMID:11102396

  15. [Effects of food concentration on population growth, body size, and egg size of the freshwater rotifer Brachionus angularis].

    PubMed

    Hu, Haoyuan; Xi, Yilong; Geng, Hong

    2002-07-01

    With the food Chlorella pyrenoidosa and the method of population accumulative culture, the effects of food concentration on the population growth, body size, and egg size of the freshwater rotifer Brachionus angularis were studied. The results showed that there were very significant effects of food concentrations on the population growth rate, body size and egg size. The relationship between the population growth rate and the food concentration was curvilinear correlation. When the food concentration was 8.2453 x 10(6) cells.ml-1, the population growth rate reached it's maximum, 0.6085 d-1. Body size tended to enlarge with increasing food concentration. At the intermediate range of food levels between 6.0 x 10(6) cells.ml-1 and 9.0 x 10(6) cells.ml-1, the egg volume was larger than those at the other food concentrations.

  16. Comparative estimation of effective population sizes and temporal gene flow in two contrasting population systems.

    PubMed

    Fraser, Dylan J; Hansen, Michael M; Ostergaard, Siri; Tessier, Nathalie; Legault, Michel; Bernatchez, Louis

    2007-09-01

    Estimation of effective population sizes (N(e)) and temporal gene flow (N(e)m, m) has many implications for understanding population structure in evolutionary and conservation biology. However, comparative studies that gauge the relative performance of N(e), N(e)m or m methods are few. Using temporal genetic data from two salmonid fish population systems with disparate population structure, we (i) evaluated the congruence in estimates and precision of long- and short-term N(e), N(e)m and m from six methods; (ii) explored the effects of metapopulation structure on N(e) estimation in one system with spatiotemporally linked subpopulations, using three approaches; and (iii) determined to what degree interpopulation gene flow was asymmetric over time. We found that long-term N(e) estimates exceeded short-term N(e) within populations by 2-10 times; the two were correlated in the system with temporally stable structure (Atlantic salmon, Salmo salar) but not in the highly dynamic system (brown trout, Salmo trutta). Four temporal methods yielded short-term N(e) estimates within populations that were strongly correlated, and these were higher but more variable within salmon populations than within trout populations. In trout populations, however, these short-term N(e) estimates were always lower when assuming gene flow than when assuming no gene flow. Linkage disequilibrium data generally yielded short-term N(e) estimates of the same magnitude as temporal methods in both systems, but the two were uncorrelated. Correlations between long- and short-term geneflow estimates were inconsistent between methods, and their relative size varied up to eightfold within systems. While asymmetries in gene flow were common in both systems (58-63% of population-pair comparisons), they were only temporally stable in direction within certain salmon population pairs, suggesting that gene flow between particular populations is often intermittent and/or variable. Exploratory metapopulation N

  17. Effective size of density-dependent two-sex populations: the effect of mating systems.

    PubMed

    Myhre, A M; Engen, S; SAEther, B-E

    2017-08-01

    Density dependence in vital rates is a key feature affecting temporal fluctuations of natural populations. This has important implications for the rate of random genetic drift. Mating systems also greatly affect effective population sizes, but knowledge of how mating system and density regulation interact to affect random genetic drift is poor. Using theoretical models and simulations, we compare Ne in short-lived, density-dependent animal populations with different mating systems. We study the impact of a fluctuating, density-dependent sex ratio and consider both a stable and a fluctuating environment. We find a negative relationship between annual Ne /N and adult population size N due to density dependence, suggesting that loss of genetic variation is reduced at small densities. The magnitude of this decrease was affected by mating system and life history. A male-biased, density-dependent sex ratio reduces the rate of genetic drift compared to an equal, density-independent sex ratio, but a stochastic change towards male bias reduces the Ne /N ratio. Environmental stochasticity amplifies temporal fluctuations in population size and is thus vital to consider in estimation of effective population sizes over longer time periods. Our results on the reduced loss of genetic variation at small densities, particularly in polygamous populations, indicate that density regulation may facilitate adaptive evolution at small population sizes. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

  18. Estimation of census and effective population sizes: the increasing usefulness of DNA-based approaches

    Treesearch

    Gordon Luikart; Nils Ryman; David A. Tallmon; Michael K. Schwartz; Fred W. Allendorf

    2010-01-01

    Population census size (NC) and effective population sizes (Ne) are two crucial parameters that influence population viability, wildlife management decisions, and conservation planning. Genetic estimators of both NC and Ne are increasingly widely used because molecular markers are increasingly available, statistical methods are improving rapidly, and genetic estimators...

  19. Effective size of two feral domestic cat populations (Felis catus L): effect of the mating system.

    PubMed

    Kaeuffer, R; Pontier, D; Devillard, S; Perrin, N

    2004-02-01

    A variety of behavioural traits have substantial effects on the gene dynamics and genetic structure of local populations. The mating system is a plastic trait that varies with environmental conditions in the domestic cat (Felis catus) allowing an intraspecific comparison of the impact of this feature on genetic characteristics of the population. To assess the potential effect of the heterogenity of males' contribution to the next generation on variance effective size, we applied the ecological approach of Nunney & Elam (1994) based upon a demographic and behavioural study, and the genetic 'temporal methods' of Waples (1989) and Berthier et al. (2002) using microsatellite markers. The two cat populations studied were nearly closed, similar in size and survival parameters, but differed in their mating system. Immigration appeared extremely restricted in both cases due to environmental and social constraints. As expected, the ratio of effective size to census number (Ne/N) was higher in the promiscuous cat population (harmonic mean = 42%) than in the polygynous one (33%), when Ne was calculated from the ecological method. Only the genetic results based on Waples' estimator were consistent with the ecological results, but failed to evidence an effect of the mating system. Results based on the estimation of Berthier et al. (2002) were extremely variable, with Ne sometimes exceeding census size. Such low reliability in the genetic results should retain attention for conservation purposes.

  20. Effect of reference population size and available ancestor genotypes on imputation of Mexican Holstein genotypes

    USDA-ARS?s Scientific Manuscript database

    The effects of reference population size and the availability of information from genotyped ancestors on the accuracy of imputation of single nucleotide polymorphisms (SNPs) were investigated for Mexican Holstein cattle. Three scenarios for reference population size were examined: (1) a local popula...

  1. Estimation of the ancestral effective population sizes of African great apes under different selection regimes.

    PubMed

    Schrago, Carlos G

    2014-08-01

    Reliable estimates of ancestral effective population sizes are necessary to unveil the population-level phenomena that shaped the phylogeny and molecular evolution of the African great apes. Although several methods have previously been applied to infer ancestral effective population sizes, an analysis of the influence of the selective regime on the estimates of ancestral demography has not been thoroughly conducted. In this study, three independent data sets under different selective regimes were used were composed to tackle this issue. The results showed that selection had a significant impact on the estimates of ancestral effective population sizes of the African great apes. The inference of the ancestral demography of African great apes was affected by the selection regime. The effects, however, were not homogeneous along the ancestral populations of great apes. The effective population size of the ancestor of humans and chimpanzees was more impacted by the selection regime when compared to the same parameter in the ancestor of humans, chimpanzees and gorillas. Because the selection regime influenced the estimates of ancestral effective population size, it is reasonable to assume that a portion of the discrepancy found in previous studies that inferred the ancestral effective population size may be attributable to the differential action of selection on the genes sampled.

  2. Population genetic structure, linkage disequilibrium and effective population size of conserved and extensively raised village chicken populations of Southern Africa

    PubMed Central

    Khanyile, Khulekani S.; Dzomba, Edgar F.; Muchadeyi, Farai C.

    2015-01-01

    Extensively raised village chickens are considered a valuable source of biodiversity, with genetic variability developed over thousands of years that ought to be characterized and utilized. Surveys that can reveal a population's genetic structure and provide an insight into its demographic history will give valuable information that can be used to manage and conserve important indigenous animal genetic resources. This study reports population diversity and structure, linkage disequilibrium and effective population sizes of Southern African village chickens and conservation flocks from South Africa. DNA samples from 312 chickens from South African village and conservation flocks (n = 146), Malawi (n = 30) and Zimbabwe (n = 136) were genotyped using the Illumina iSelect chicken SNP60K BeadChip. Population genetic structure analysis distinguished the four conservation flocks from the village chicken populations. Of the four flocks, the Ovambo clustered closer to the village chickens particularly those sampled from South Africa. Clustering of the village chickens followed a geographic gradient whereby South African chickens were closer to those from Zimbabwe than to chickens from Malawi. Different conservation flocks seemed to have maintained different components of the ancestral genomes with a higher proportion of village chicken diversity found in the Ovambo population. Overall population LD averaged over chromosomes ranged from 0.03 ± 0.07 to 0.58 ± 0.41 and averaged 0.15 ± 0.16. Higher LD, ranging from 0.29 to 0.36, was observed between SNP markers that were less than 10 kb apart in the conservation flocks. LD in the conservation flocks steadily decreased to 0.15 (PK) and 0.24 (VD) at SNP marker interval of 500 kb. Genomewide LD decay in the village chickens from Malawi, Zimbabwe and South Africa followed a similar trend as the conservation flocks although the mean LD values for the investigated SNP intervals were lower. The results suggest low effective

  3. Population genetic structure, linkage disequilibrium and effective population size of conserved and extensively raised village chicken populations of Southern Africa.

    PubMed

    Khanyile, Khulekani S; Dzomba, Edgar F; Muchadeyi, Farai C

    2015-01-01

    Extensively raised village chickens are considered a valuable source of biodiversity, with genetic variability developed over thousands of years that ought to be characterized and utilized. Surveys that can reveal a population's genetic structure and provide an insight into its demographic history will give valuable information that can be used to manage and conserve important indigenous animal genetic resources. This study reports population diversity and structure, linkage disequilibrium and effective population sizes of Southern African village chickens and conservation flocks from South Africa. DNA samples from 312 chickens from South African village and conservation flocks (n = 146), Malawi (n = 30) and Zimbabwe (n = 136) were genotyped using the Illumina iSelect chicken SNP60K BeadChip. Population genetic structure analysis distinguished the four conservation flocks from the village chicken populations. Of the four flocks, the Ovambo clustered closer to the village chickens particularly those sampled from South Africa. Clustering of the village chickens followed a geographic gradient whereby South African chickens were closer to those from Zimbabwe than to chickens from Malawi. Different conservation flocks seemed to have maintained different components of the ancestral genomes with a higher proportion of village chicken diversity found in the Ovambo population. Overall population LD averaged over chromosomes ranged from 0.03 ± 0.07 to 0.58 ± 0.41 and averaged 0.15 ± 0.16. Higher LD, ranging from 0.29 to 0.36, was observed between SNP markers that were less than 10 kb apart in the conservation flocks. LD in the conservation flocks steadily decreased to 0.15 (PK) and 0.24 (VD) at SNP marker interval of 500 kb. Genomewide LD decay in the village chickens from Malawi, Zimbabwe and South Africa followed a similar trend as the conservation flocks although the mean LD values for the investigated SNP intervals were lower. The results suggest low effective

  4. Methods to estimate effective population size using pedigree data: Examples in dog, sheep, cattle and horse.

    PubMed

    Leroy, Grégoire; Mary-Huard, Tristan; Verrier, Etienne; Danvy, Sophie; Charvolin, Eleonore; Danchin-Burge, Coralie

    2013-01-02

    Effective population sizes of 140 populations (including 60 dog breeds, 40 sheep breeds, 20 cattle breeds and 20 horse breeds) were computed using pedigree information and six different computation methods. Simple demographical information (number of breeding males and females), variance of progeny size, or evolution of identity by descent probabilities based on coancestry or inbreeding were used as well as identity by descent rate between two successive generations or individual identity by descent rate. Depending on breed and method, effective population sizes ranged from 15 to 133 056, computation method and interaction between computation method and species showing a significant effect on effective population size (P < 0.0001). On average, methods based on number of breeding males and females and variance of progeny size produced larger values (4425 and 356, respectively), than those based on identity by descent probabilities (average values between 93 and 203). Since breeding practices and genetic substructure within dog breeds increased inbreeding, methods taking into account the evolution of inbreeding produced lower effective population sizes than those taking into account evolution of coancestry. The correlation level between the simplest method (number of breeding males and females, requiring no genealogical information) and the most sophisticated one ranged from 0.44 to 0.60 according to species. When choosing a method to compute effective population size, particular attention should be paid to the species and the specific genetic structure of the population studied.

  5. Early detection of population declines: high power of genetic monitoring using effective population size estimators

    PubMed Central

    Antao, Tiago; Pérez-Figueroa, Andrés; Luikart, Gordon

    2011-01-01

    Early detection of population declines is essential to prevent extinctions and to ensure sustainable harvest. We evaluated the performance of two Ne estimators to detect population declines: the two-sample temporal method and a one-sample method based on linkage disequilibrium (LD). We used simulated data representing a wide range of population sizes, sample sizes and number of loci. Both methods usually detect a population decline only one generation after it occurs if Ne drops to less than approximately 100, and 40 microsatellite loci and 50 individuals are sampled. However, the LD method often out performed the temporal method by allowing earlier detection of less severe population declines (Ne approximately 200). Power for early detection increased more rapidly with the number of individuals sampled than with the number of loci genotyped, primarily for the LD method. The number of samples available is therefore an important criterion when choosing between the LD and temporal methods. We provide guidelines regarding design of studies targeted at monitoring for population declines. We also report that 40 single nucleotide polymorphism (SNP) markers give slightly lower precision than 10 microsatellite markers. Our results suggest that conservation management and monitoring strategies can reliably use genetic based methods for early detection of population declines. PMID:25567959

  6. The Effective Population Size of Malaria Mosquitoes: Large Impact of Vector Control

    PubMed Central

    Athrey, Giridhar; Hodges, Theresa K.; Reddy, Michael R.; Overgaard, Hans J.; Matias, Abrahan; Ridl, Frances C.; Kleinschmidt, Immo; Caccone, Adalgisa; Slotman, Michel A.

    2012-01-01

    Malaria vectors in sub-Saharan Africa have proven themselves very difficult adversaries in the global struggle against malaria. Decades of anti-vector interventions have yielded mixed results—with successful reductions in transmission in some areas and limited impacts in others. These varying successes can be ascribed to a lack of universally effective vector control tools, as well as the development of insecticide resistance in mosquito populations. Understanding the impact of vector control on mosquito populations is crucial for planning new interventions and evaluating existing ones. However, estimates of population size changes in response to control efforts are often inaccurate because of limitations and biases in collection methods. Attempts to evaluate the impact of vector control on mosquito effective population size (Ne) have produced inconclusive results thus far. Therefore, we obtained data for 13–15 microsatellite markers for more than 1,500 mosquitoes representing multiple time points for seven populations of three important vector species—Anopheles gambiae, An. melas, and An. moucheti—in Equatorial Guinea. These populations were exposed to indoor residual spraying or long-lasting insecticidal nets in recent years. For comparison, we also analyzed data from two populations that have no history of organized vector control. We used Approximate Bayesian Computation to reconstruct their demographic history, allowing us to evaluate the impact of these interventions on the effective population size. In six of the seven study populations, vector control had a dramatic impact on the effective population size, reducing Ne between 55%–87%, the exception being a single An. melas population. In contrast, the two negative control populations did not experience a reduction in effective population size. This study is the first to conclusively link anti-vector intervention programs in Africa to sharply reduced effective population sizes of malaria vectors

  7. Effects of habitat quality and size on extinction in experimental populations.

    PubMed

    Griffen, Blaine D; Drake, John M

    2008-10-07

    Stochastic population theory makes clear predictions about the effects of reproductive potential and carrying capacity on characteristic time-scales of extinction. At the same time, the effects of habitat size and quality on reproduction and regulation have been hotly debated. To trace the causal relationships among these factors, we looked at the effects of habitat size and quality on extinction time in experimental populations of Daphnia magna. Replicate model systems representative of a broad-spectrum consumer foraging on a continuously supplied resource were established under crossed treatments of habitat size (two levels) and habitat quality (three levels) and monitored until eventual extinction of all populations. Using statistically derived estimates of key parameters, we related experimental treatments to persistence time through their effect on carrying capacity and the population growth rate. We found that carrying capacity and the intrinsic rate of increase were each influenced similarly by habitat size and quality, and that carrying capacity and the intrinsic rate of increase were in turn both correlated with time to population extinction. We expected habitat quality to have a greater influence on extinction. However, owing to an unexpected effect of habitat size on reproductive potential, habitat size and quality were similarly important for population persistence. These results support the idea that improving the population growth rate or carrying capacity will reduce extinction risk and demonstrate that both are possible by improving habitat quality or increasing habitat size.

  8. Effects of population size on singing behavior of a rare duetting songbird.

    PubMed

    Valderrama, Sandra V; Molles, Laura E; Waas, Joseph R

    2013-02-01

    Although the genetic and ecological effects of population declines in endangered species have been well studied, little is known of the social consequences. Changes in signaling behavior may result in disrupted communication and affect both reproductive and conflict-resolution activities. The North Island Kōkako (Callaeas wilsoni) is an endangered, duetting (i.e., alternating, coordinated singing by mated pairs) songbird endemic to New Zealand temperate rain forests. Scattered populations (approximately 1500 individuals in 13 surviving and 11 translocated populations) in isolated conservation areas of different sizes have been rescued from extirpation and are currently recovering. We examined key song attributes of the Kōkako to assess whether population size or growth rate are related to song complexity, the reduction of which may compromise effective communication. We analyzed song repertoire size and phrase-type sharing (i.e., Jaccard index of similarity), vocal performance (singing rates, song switching rates, and diversity of phrase types), and song syntactical characteristics (i.e., unpredictability in sequences of phrase types) in surviving and translocated populations (populations of approximately 19-250 territorial individuals). Population size was positively correlated with a population's song repertoire, song diversity, and switching of song phrase types and negatively correlated with shared phrase types and variation in syntactical structure of songs. Population growth rate correlated positively with pair repertoire size, population repertoire size, and singing rates during song bouts. As for solo-singing species in fragmented landscapes, songs in the fragmented populations of Kōkako appear to be undergoing microevolution as occurs in island colonization events. Our results suggest that vocal changes in small populations could affect population establishment and growth, particularly in multiple-source translocations. We believe measurement of vocal

  9. Using target population specification, effect size, and reach to estimate and compare the population impact of two PTSD preventive interventions.

    PubMed

    Zatzick, Douglas F; Koepsell, Thomas; Rivara, Frederick P

    2009-01-01

    The population impact of a preventive intervention depends on two factors: what proportion of the full population at risk receives the intervention and how large a reduction in risk occurs among those who receive it. We sought to illustrate how information from a cognitive behavioral psychotherapy (CBT) trial and stepped collaborative care (CC) trial could be used to estimate the population impact of two contrasting approaches to PTSD prevention. We first specified trauma center target populations represented by participants in each trial. Patient characteristics were compared, as were effect size and reach indices and population-level reductions in PTSD incidence. The CBT trial demonstrated a larger effect size (50% PTSD prevention), but minimal reach (27/10,000), while the CC trial demonstrated a smaller effect size (7% PTSD prevention) but greater reach (1762/10,000). Modeling of the population impact suggested that a 9.5-fold greater cumulative reduction in the incidence of PTSD would result from the dissemination of the CC broad reach prevention strategy. A reciprocal relationship between effect size and reach was evident in these two trials. By specifying a target population, effect size and reach could be combined to project the overall population impact of each PTSD prevention approach.

  10. Effects of population size and mutation rate on the evolution of mutational robustness.

    PubMed

    Elena, Santiago F; Wilke, Claus O; Ofria, Charles; Lenski, Richard E

    2007-03-01

    It is often assumed that the efficiency of selection for mutational robustness would be proportional to mutation rate and population size, thus being inefficient in small populations. However, Krakauer and Plotkin (2002) hypothesized that selection in small populations would favor robustness mechanisms, such as redundancy, that mask the effect of deleterious mutations. In large populations, by contrast, selection is more effective at removing deleterious mutants and fitness would be improved by eliminating mechanisms that mask the effect of deleterious mutations and thus impede their removal. Here, we test whether these predictions are supported in experiments with evolving populations of digital organisms. Digital organisms are self-replicating programs that inhabit a virtual world inside a computer. Like their organic counterparts, digital organisms mutate, compete, evolve, and adapt by natural selection to their environment. In this study, 160 populations evolved at different combinations of mutation rate and population size. After 10(4) generations, we measured the mutational robustness of the most abundant genotype in each population. Mutational robustness tended to increase with mutation rate and to decline with population size, although the dependence with population size was in part mediated by a negative relationship between fitness and robustness. These results are independent of whether genomes were constrained to their original length or allowed to change in size.

  11. Loss of microsatellite diversity and low effective population size in an overexploited population of New Zealand snapper (Pagrus auratus)

    PubMed Central

    Hauser, Lorenz; Adcock, Greg J.; Smith, Peter J.; Bernal Ramírez, Julio H.; Carvalho, Gary R.

    2002-01-01

    Although the effects of overfishing on species diversity and abundance are well documented, threats to the genetic diversity of marine fish populations have so far been largely neglected. Indeed, there seems to be little cause for concern, as even “collapsed” stocks usually consist of several million individuals, whereas population genetics theory suggests that only very small populations suffer significant loss of genetic diversity. On the other hand, in many marine species the genetically effective population size (Ne), which determines the genetic properties of a population, may be orders of magnitude smaller than the census population size (N). Here, microsatellite analyses of a time series of archived scales demonstrated a significant decline in genetic diversity in a New Zealand snapper population during its exploitation history. Effective population sizes estimated both from the decline in heterozygosity and from temporal fluctuations in allele frequency were five orders of magnitude smaller than census population sizes from fishery data. If such low Ne/N ratios are commonplace in marine species, many exploited marine fish stocks may be in danger of losing genetic variability, potentially resulting in reduced adaptability, population persistence, and productivity. PMID:12185245

  12. Effects of spatial structure of population size on the population dynamics of barnacles across their elevational range.

    PubMed

    Fukaya, Keiichi; Okuda, Takehiro; Nakaoka, Masahiro; Noda, Takashi

    2014-11-01

    Explanations for why population dynamics vary across the range of a species reflect two contrasting hypotheses: (i) temporal variability of populations is larger in the centre of the range compared to the margins because overcompensatory density dependence destabilizes population dynamics and (ii) population variability is larger near the margins, where populations are more susceptible to environmental fluctuations. In both of these hypotheses, positions within the range are assumed to affect population variability. In contrast, the fact that population variability is often related to mean population size implies that the spatial structure of the population size within the range of a species may also be a useful predictor of the spatial variation in temporal variability of population size over the range of the species. To explore how population temporal variability varies spatially and the underlying processes responsible for the spatial variation, we focused on the intertidal barnacle Chthamalus dalli and examined differences in its population dynamics along the tidal levels it inhabits. Changes in coverage of barnacle populations were monitored for 10.5 years at 25 plots spanning the elevational range of this species. Data were analysed by fitting a population dynamics model to estimate the effects of density-dependent and density-independent processes on population growth. We also examined the temporal mean-variance relationship of population size with parameters estimated from the population dynamics model. We found that the relative variability of populations tended to increase from the centre of the elevational range towards the margins because of an increase in the magnitude of stochastic fluctuations of growth rates. Thus, our results supported hypothesis (2). We also found that spatial variations in temporal population variability were well characterized by Taylor's power law, the relative population variability being inversely related to the mean

  13. Small effective population size and genetic homogeneity in the Val Borbera isolate

    PubMed Central

    Colonna, Vincenza; Pistis, Giorgio; Bomba, Lorenzo; Mona, Stefano; Matullo, Giuseppe; Boano, Rosa; Sala, Cinzia; Viganò, Fiammetta; Torroni, Antonio; Achilli, Alessandro; Hooshiar Kashani, Baharak; Malerba, Giovanni; Gambaro, Giovanni; Soranzo, Nicole; Toniolo, Daniela

    2013-01-01

    Population isolates are a valuable resource for medical genetics because of their reduced genetic, phenotypic and environmental heterogeneity. Further, extended linkage disequilibrium (LD) allows accurate haplotyping and imputation. In this study, we use nuclear and mitochondrial DNA data to determine to what extent the geographically isolated population of the Val Borbera valley also presents features of genetic isolation. We performed a comparative analysis of population structure and estimated effective population size exploiting LD data. We also evaluated haplotype sharing through the analysis of segments of autozygosity. Our findings reveal that the valley has features characteristic of a genetic isolate, including reduced genetic heterogeneity and reduced effective population size. We show that this population has been subject to prolonged genetic drift and thus we expect many variants that are rare in the general population to reach significant frequency values in the valley, making this population suitable for the identification of rare variants underlying complex traits. PMID:22713810

  14. The context-dependent effect of multiple paternity on effective population size.

    PubMed

    Lotterhos, Katie E; Lotterhos, Katic E

    2011-06-01

    Effective population size (N(e)) is important because it describes how evolutionary forces will affect a population. The effect of multiple sires per female on N(e) has been the subject of some debate, at the crux of which is the effects of monandry and multiple-paternity (MP) on male variance in reproductive success. In both mating systems, females mate with several males over their lifetimes, but sire offspring with one male at a time in the former and have several sires per clutch in the latter. First, I theoretically show that whether the annual male variance in reproductive success in an MP population is greater or less than that of a monandrous population depends on the distributions of within-clutch paternity. Then, I simulated different distributions of within-clutch paternity under a range of parameters that characterize natural populations to show that an MP population can have an N(e) smaller or larger than that of a monandrous population with otherwise equal dynamics. The N(e(MP)):N(e(Monandry)) ratio increased with mating frequency and female variance in reproductive success, was equalized by long generation times, and was affected by the distribution of within-clutch paternities. The results of this model provide a unifying framework for the debate. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.

  15. Effective population size is positively correlated with levels of adaptive divergence among annual sunflowers.

    PubMed

    Strasburg, Jared L; Kane, Nolan C; Raduski, Andrew R; Bonin, Aurélie; Michelmore, Richard; Rieseberg, Loren H

    2011-05-01

    The role of adaptation in the divergence of lineages has long been a central question in evolutionary biology, and as multilocus sequence data sets have become available for a wide range of taxa, empirical estimates of levels of adaptive molecular evolution are increasingly common. Estimates vary widely among taxa, with high levels of adaptive evolution in Drosophila, bacteria, and viruses but very little evidence of widespread adaptive evolution in hominids. Although estimates in plants are more limited, some recent work has suggested that rates of adaptive evolution in a range of plant taxa are surprisingly low and that there is little association between adaptive evolution and effective population size in contrast to patterns seen in other taxa. Here, we analyze data from 35 loci for six sunflower species that vary dramatically in effective population size. We find that rates of adaptive evolution are positively correlated with effective population size in these species, with a significant fraction of amino acid substitutions driven by positive selection in the species with the largest effective population sizes but little or no evidence of adaptive evolution in species with smaller effective population sizes. Although other factors likely contribute as well, in sunflowers effective population size appears to be an important determinant of rates of adaptive evolution.

  16. Effective Population Size Is Positively Correlated with Levels of Adaptive Divergence among Annual Sunflowers

    PubMed Central

    Strasburg, Jared L.; Kane, Nolan C.; Raduski, Andrew R.; Bonin, Aurélie; Michelmore, Richard; Rieseberg, Loren H.

    2011-01-01

    The role of adaptation in the divergence of lineages has long been a central question in evolutionary biology, and as multilocus sequence data sets have become available for a wide range of taxa, empirical estimates of levels of adaptive molecular evolution are increasingly common. Estimates vary widely among taxa, with high levels of adaptive evolution in Drosophila, bacteria, and viruses but very little evidence of widespread adaptive evolution in hominids. Although estimates in plants are more limited, some recent work has suggested that rates of adaptive evolution in a range of plant taxa are surprisingly low and that there is little association between adaptive evolution and effective population size in contrast to patterns seen in other taxa. Here, we analyze data from 35 loci for six sunflower species that vary dramatically in effective population size. We find that rates of adaptive evolution are positively correlated with effective population size in these species, with a significant fraction of amino acid substitutions driven by positive selection in the species with the largest effective population sizes but little or no evidence of adaptive evolution in species with smaller effective population sizes. Although other factors likely contribute as well, in sunflowers effective population size appears to be an important determinant of rates of adaptive evolution. PMID:20952500

  17. Finite population size effects in quasispecies models with single-peak fitness landscape

    NASA Astrophysics Data System (ADS)

    Saakian, David B.; Deem, Michael W.; Hu, Chin-Kun

    2012-04-01

    We consider finite population size effects for Crow-Kimura and Eigen quasispecies models with single-peak fitness landscape. We formulate accurately the iteration procedure for the finite population models, then derive the Hamilton-Jacobi equation (HJE) to describe the dynamic of the probability distribution. The steady-state solution of HJE gives the variance of the mean fitness. Our results are useful for understanding the population sizes of viruses in which the infinite population models can give reliable results for biological evolution problems.

  18. The impact of supplementation in winter-run chinook salmon on effective population size.

    PubMed

    Hedrick, P W; Hedgecock, D; Hamelberg, S; Croci, S J

    2000-01-01

    Supplementation of young raised at a protected site, such as a hatchery, may influence the effective population size of an endangered species. A supplementation program for the endangered winter-run chinook salmon from the Sacramento River, California, has been releasing fish since 1991. A breeding protocol, instituted in 1992, seeks to maximize the effective population size from the captive spawners by equaling their contributions to the released progeny. As a result, the releases in 1994 and 1995 appear not to have decreased the overall effective population size and may have increased it somewhat. However, mistaken use of non-winter-run chinook spawners resulted in artificial crosses between runs with a potential reduction in effective population size, and imprinting of the released fish on Battle Creek, the site of the hatchery, resulted in limiting the contribution of the released fish to the target mainstem population. Rapid genetic analysis of captured spawners and a new rearing facility on the Sacramento River should alleviate these problems and their negative effect on the effective population size in future years.

  19. Temporal variation in population size of European bird species: effects of latitude and marginality of distribution.

    PubMed

    Cuervo, José J; Møller, Anders P

    2013-01-01

    In the Northern Hemisphere, global warming has been shown to affect animal populations in different ways, with southern populations in general suffering more from increased temperatures than northern populations of the same species. However, southern populations are also often marginal populations relative to the entire breeding range, and marginality may also have negative effects on populations. To disentangle the effects of latitude (possibly due to global warming) and marginality on temporal variation in population size, we investigated European breeding bird species across a latitudinal gradient. Population size estimates were regressed on years, and from these regressions we obtained the slope (a proxy for population trend) and the standard error of the estimate (SEE) (a proxy for population fluctuations). The possible relationships between marginality or latitude on one hand and slopes or SEE on the other were tested among populations within species. Potentially confounding factors such as census method, sampling effort, density-dependence, habitat fragmentation and number of sampling years were controlled statistically. Population latitude was positively related to regression slopes independent of marginality, with more positive slopes (i.e., trends) in northern than in southern populations. The degree of marginality was positively related to SEE independent of latitude, with marginal populations showing larger SEE (i.e., fluctuations) than central ones. Regression slopes were also significantly related to our estimate of density-dependence and SEE was significantly affected by the census method. These results are consistent with a scenario in which southern and northern populations of European bird species are negatively affected by marginality, with southern populations benefitting less from global warming than northern populations, thus potentially making southern populations more vulnerable to extinction.

  20. Population Genetics with Fluctuating Population Sizes

    NASA Astrophysics Data System (ADS)

    Chotibut, Thiparat; Nelson, David R.

    2017-05-01

    Standard neutral population genetics theory with a strictly fixed population size has important limitations. An alternative model that allows independently fluctuating population sizes and reproduces the standard neutral evolution is reviewed. We then study a situation such that the competing species are neutral at the equilibrium population size but population size fluctuations nevertheless favor fixation of one species over the other. In this case, a separation of timescales emerges naturally and allows adiabatic elimination of a fast population size variable to deduce the fluctuation-induced selection dynamics near the equilibrium population size. The results highlight the incompleteness of the standard population genetics with a strictly fixed population size.

  1. Population Genetics with Fluctuating Population Sizes

    NASA Astrophysics Data System (ADS)

    Chotibut, Thiparat; Nelson, David R.

    2017-02-01

    Standard neutral population genetics theory with a strictly fixed population size has important limitations. An alternative model that allows independently fluctuating population sizes and reproduces the standard neutral evolution is reviewed. We then study a situation such that the competing species are neutral at the equilibrium population size but population size fluctuations nevertheless favor fixation of one species over the other. In this case, a separation of timescales emerges naturally and allows adiabatic elimination of a fast population size variable to deduce the fluctuation-induced selection dynamics near the equilibrium population size. The results highlight the incompleteness of the standard population genetics with a strictly fixed population size.

  2. Variation in the fitness effects of mutations with population density and size in Escherichia coli.

    PubMed

    Cao, Huansheng; Butler, Kevin; Hossain, Mithi; Lewis, James D

    2014-01-01

    The fitness effects of mutations are context specific and depend on both external (e.g., environment) and internal (e.g., cellular stress, genetic background) factors. The influence of population size and density on fitness effects are unknown, despite the central role population size plays in the supply and fixation of mutations. We addressed this issue by comparing the fitness of 92 Keio strains (Escherichia coli K12 single gene knockouts) at comparatively high (1.2×10(7) CFUs/mL) and low (2.5×10(2) CFUs/mL) densities, which also differed in population size (high: 1.2×10(8); low: 1.25×10(3)). Twenty-eight gene deletions (30%) exhibited a fitness difference, ranging from 5 to 174% (median: 35%), between the high and low densities. Our analyses suggest this variation among gene deletions in fitness responses reflected in part both gene orientation and function, of the gene properties we examined (genomic position, length, orientation, and function). Although we could not determine the relative effects of population density and size, our results suggest fitness effects of mutations vary with these two factors, and this variation is gene-specific. Besides being a mechanism for density-dependent selection (r-K selection), the dependence of fitness effects on population density and size has implications for any population that varies in size over time, including populations undergoing evolutionary rescue, species invasions into novel habitats, and cancer progression and metastasis. Further, combined with recent advances in understanding the roles of other context-specific factors in the fitness effects of mutations, our results will help address theoretical and applied biological questions more realistically.

  3. Accounting for missing data in the estimation of contemporary genetic effective population size (N(e) ).

    PubMed

    Peel, D; Waples, R S; Macbeth, G M; Do, C; Ovenden, J R

    2013-03-01

    Theoretical models are often applied to population genetic data sets without fully considering the effect of missing data. Researchers can deal with missing data by removing individuals that have failed to yield genotypes and/or by removing loci that have failed to yield allelic determinations, but despite their best efforts, most data sets still contain some missing data. As a consequence, realized sample size differs among loci, and this poses a problem for unbiased methods that must explicitly account for random sampling error. One commonly used solution for the calculation of contemporary effective population size (N(e) ) is to calculate the effective sample size as an unweighted mean or harmonic mean across loci. This is not ideal because it fails to account for the fact that loci with different numbers of alleles have different information content. Here we consider this problem for genetic estimators of contemporary effective population size (N(e) ). To evaluate bias and precision of several statistical approaches for dealing with missing data, we simulated populations with known N(e) and various degrees of missing data. Across all scenarios, one method of correcting for missing data (fixed-inverse variance-weighted harmonic mean) consistently performed the best for both single-sample and two-sample (temporal) methods of estimating N(e) and outperformed some methods currently in widespread use. The approach adopted here may be a starting point to adjust other population genetics methods that include per-locus sample size components.

  4. Recombination gives a new insight in the effective population size and the history of the old world human populations.

    PubMed

    Melé, Marta; Javed, Asif; Pybus, Marc; Zalloua, Pierre; Haber, Marc; Comas, David; Netea, Mihai G; Balanovsky, Oleg; Balanovska, Elena; Jin, Li; Yang, Yajun; Pitchappan, R M; Arunkumar, G; Parida, Laxmi; Calafell, Francesc; Bertranpetit, Jaume

    2012-01-01

    The information left by recombination in our genomes can be used to make inferences on our recent evolutionary history. Specifically, the number of past recombination events in a population sample is a function of its effective population size (Ne). We have applied a method, Identifying Recombination in Sequences (IRiS), to detect specific past recombination events in 30 Old World populations to infer their Ne. We have found that sub-Saharan African populations have an Ne that is approximately four times greater than those of non-African populations and that outside of Africa, South Asian populations had the largest Ne. We also observe that the patterns of recombinational diversity of these populations correlate with distance out of Africa if that distance is measured along a path crossing South Arabia. No such correlation is found through a Sinai route, suggesting that anatomically modern humans first left Africa through the Bab-el-Mandeb strait rather than through present Egypt.

  5. [Effects of food component and concentration on population growth, body size, and egg size of freshwater rotifer Brachionus rubens].

    PubMed

    Geng, Hong; Xi, Yilong; Hu, Haoyuan

    2003-05-01

    The effects of food component and concentration on the population growth, body size, and egg size of freshwater rotifer Brachionus rubens were studied using population accumulative culture method. The results showed that there were very significant effects of food component and concentration on the population growth rate, body volume and egg volume. Among three types of algal food, the population growth rate of rotifers fed with Chlorella pyrenoidosa was lowest, and that fed with Scenedesmus obliquus was the highest. Rotifers fed with C. pyrenoidosa had the smallest body volume, but there were no significant difference between the two others. The relationship between population growth rate and food concentrations was curvilinear, and it could be described as Y = -0.0040X2 + 0.0409X + 0.4471. The body and egg volumes tended to be smaller, when the food concentrations were higher than 6.0 x 10(6) cells.ml-1 and or lower than 3.0 x 10(6) cells.ml-1.

  6. Metapopulation effective size and conservation genetic goals for the Fennoscandian wolf (Canis lupus) population

    PubMed Central

    Laikre, L; Olsson, F; Jansson, E; Hössjer, O; Ryman, N

    2016-01-01

    The Scandinavian wolf population descends from only five individuals, is isolated, highly inbred and exhibits inbreeding depression. To meet international conservation goals, suggestions include managing subdivided wolf populations over Fennoscandia as a metapopulation; a genetically effective population size of Ne⩾500, in line with the widely accepted long-term genetic viability target, might be attainable with gene flow among subpopulations of Scandinavia, Finland and Russian parts of Fennoscandia. Analytical means for modeling Ne of subdivided populations under such non-idealized situations have been missing, but we recently developed new mathematical methods for exploring inbreeding dynamics and effective population size of complex metapopulations. We apply this theory to the Fennoscandian wolves using empirical estimates of demographic parameters. We suggest that the long-term conservation genetic target for metapopulations should imply that inbreeding rates in the total system and in the separate subpopulations should not exceed Δf=0.001. This implies a meta-Ne of NeMeta⩾500 and a realized effective size of each subpopulation of NeRx⩾500. With current local effective population sizes and one migrant per generation, as recommended by management guidelines, the meta-Ne that can be reached is ~250. Unidirectional gene flow from Finland to Scandinavia reduces meta-Ne to ~130. Our results indicate that both local subpopulation effective sizes and migration among subpopulations must increase substantially from current levels to meet the conservation target. Alternatively, immigration from a large (Ne⩾500) population in northwestern Russia could support the Fennoscandian metapopulation, but immigration must be substantial (5–10 effective immigrants per generation) and migration among Fennoscandian subpopulations must nevertheless increase. PMID:27328654

  7. Metapopulation effective size and conservation genetic goals for the Fennoscandian wolf (Canis lupus) population.

    PubMed

    Laikre, L; Olsson, F; Jansson, E; Hössjer, O; Ryman, N

    2016-10-01

    The Scandinavian wolf population descends from only five individuals, is isolated, highly inbred and exhibits inbreeding depression. To meet international conservation goals, suggestions include managing subdivided wolf populations over Fennoscandia as a metapopulation; a genetically effective population size of Ne⩾500, in line with the widely accepted long-term genetic viability target, might be attainable with gene flow among subpopulations of Scandinavia, Finland and Russian parts of Fennoscandia. Analytical means for modeling Ne of subdivided populations under such non-idealized situations have been missing, but we recently developed new mathematical methods for exploring inbreeding dynamics and effective population size of complex metapopulations. We apply this theory to the Fennoscandian wolves using empirical estimates of demographic parameters. We suggest that the long-term conservation genetic target for metapopulations should imply that inbreeding rates in the total system and in the separate subpopulations should not exceed Δf=0.001. This implies a meta-Ne of NeMeta⩾500 and a realized effective size of each subpopulation of NeRx⩾500. With current local effective population sizes and one migrant per generation, as recommended by management guidelines, the meta-Ne that can be reached is ~250. Unidirectional gene flow from Finland to Scandinavia reduces meta-Ne to ~130. Our results indicate that both local subpopulation effective sizes and migration among subpopulations must increase substantially from current levels to meet the conservation target. Alternatively, immigration from a large (Ne⩾500) population in northwestern Russia could support the Fennoscandian metapopulation, but immigration must be substantial (5-10 effective immigrants per generation) and migration among Fennoscandian subpopulations must nevertheless increase.

  8. Can estimates of genetic effective population size contribute to fisheries stock assessments?

    PubMed

    Ovenden, J R; Leigh, G M; Blower, D C; Jones, A T; Moore, A; Bustamante, C; Buckworth, R C; Bennett, M B; Dudgeon, C L

    2016-12-01

    Sustainable exploitation of fisheries populations is challenging to achieve when the size of the population prior to exploitation and the actual numbers removed over time and across fishing zones are not clearly known. Quantitative fisheries' modeling is able to address this problem, but accurate and reliable model outcomes depend on high quality input data. Much of this information is obtained through the operation of the fishery under consideration, but while this seems appropriate, biases may occur. For example, poorly quantified changes in fishing methods that increase catch rates can erroneously suggest that the overall population size is increasing. Hence, the incorporation of estimates of abundance derived from independent data sources is preferable. We review and evaluate a fisheries-independent method of indexing population size; inferring adult abundance from estimates of the genetic effective size of a population (Ne ). Recent studies of elasmobranch species have shown correspondence between Ne and ecologically determined estimates of the population size (N). Simulation studies have flagged the possibility that the range of Ne /N ratios across species may be more restricted than previously thought, and also show that declines in Ne track declines in the abundance of model fisheries species. These key developments bring this new technology closer to implementation in fisheries science, particularly for data-poor fisheries or species of conservation interest. © 2016 The Fisheries Society of the British Isles.

  9. The Effect of Nonindependent Mate Pairing on the Effective Population Size

    PubMed Central

    Evans, Ben J.; Charlesworth, Brian

    2013-01-01

    The effective population size (Ne) quantifies the effectiveness of genetic drift in finite populations. When generations overlap, theoretical expectations for Ne typically assume that the sampling of offspring genotypes from a given individual is independent among successive breeding events, even though this is not true in many species, including humans. To explore the effects on Ne of nonindependent mate pairing across breeding events, we simulated the genetic drift of mitochondrial DNA, autosomal DNA, and sex chromosome DNA under three mating systems. Nonindependent mate pairing across breeding seasons has no effect when all adults mate pair for life, a small or moderate effect when females reuse stored sperm, and a large effect when there is intense male–male competition for reproduction in a harem social system. If adult females reproduce at a constant rate irrespective of the type of mate pairing, the general effect of nonindependent mate pairing is to decrease Ne for paternally inherited components of the genome. These findings have significant implications for the relative Ne values of different genomic regions, and hence for the expected levels of DNA sequence diversity in these regions. PMID:23183666

  10. Effective population size of natural populations of Drosophila buzzatii, with a comparative evaluation of nine methods of estimation.

    PubMed

    Barker, J S F

    2011-11-01

    Allozyme and microsatellite data from numerous populations of Drosophila buzzatii have been used (i) to determine to what degree N(e) varies among generations within populations, and among populations, and (ii) to evaluate the congruence of four temporal and five single-sample estimators of N(e) . Effective size of different populations varied over two orders of magnitude, most populations are not temporally stable in genetic composition, and N(e) showed large variation over generations in some populations. Short-term N(e) estimates from the temporal methods were highly correlated, but the smallest estimates were the most precise for all four methods, and the most consistent across methods. Except for one population, N(e) estimates were lower when assuming gene flow than when assuming populations that were closed. However, attempts to jointly estimate N(e) and immigration rate were of little value because the source of migrants was unknown. Correlations among the estimates from the single-sample methods generally were not significant although, as for the temporal methods, estimates were most consistent when they were small. These single-sample estimates of current N(e) are generally smaller than the short-term temporal estimates. Nevertheless, population genetic variation is not being depleted, presumably because of past or ongoing migration. A clearer picture of current and short-term effective population sizes will only follow with better knowledge of migration rates between populations. Different methods are not necessarily estimating the same N(e) , they are subject to different bias, and the biology, demography and history of the population(s) may affect different estimators differently.

  11. Effective Size and F-Statistics of Subdivided Populations. I. Monoecious Species with Partial Selfing

    PubMed Central

    Wang, J.

    1997-01-01

    Assuming discrete generations and autosomal inheritance involving genes that do not affect viability or reproductive ability, we have derived recurrence equations for the inbreeding coefficient and coancestry between individuals within and among subpopulations for a subdivided monoecious population with arbitrary distributions of male and female gametes per family, variable pollen and seed migration rates, and partial selfing. From the equations, formulas for effective size and expressions for F-statistics are obtained. For the special case of a single unsubdivided population, our equations reduce to the simple expressions derived by previous authors. It is shown that population structure (subdivision and migration) is important in determining the inbreeding coefficient and effective size. Failure to recognize internal structures of populations may lead to considerable bias in predicting effective size. Inbreeding coefficient, coancestry between individuals within and among subpopulations accrue at different and variable rates over initial generations before they converge to the same asymptotic rate of increase. For a given population, the smaller the pollen and seed migration rates, the more generations are required to attain the asymptotic rate and the larger the asymptotic effective size. The equations presented herein can be used for the study of evolutionary biology and conservation genetics. PMID:9258687

  12. cloncase: Estimation of sex frequency and effective population size by clonemate resampling in partially clonal organisms.

    PubMed

    Ali, Sajid; Soubeyrand, Samuel; Gladieux, Pierre; Giraud, Tatiana; Leconte, Marc; Gautier, Angélique; Mboup, Mamadou; Chen, Wanquan; de Vallavieille-Pope, Claude; Enjalbert, Jérôme

    2016-07-01

    Inferring reproductive and demographic parameters of populations is crucial to our understanding of species ecology and evolutionary potential but can be challenging, especially in partially clonal organisms. Here, we describe a new and accurate method, cloncase, for estimating both the rate of sexual vs. asexual reproduction and the effective population size, based on the frequency of clonemate resampling across generations. Simulations showed that our method provides reliable estimates of sex frequency and effective population size for a wide range of parameters. The cloncase method was applied to Puccinia striiformis f.sp. tritici, a fungal pathogen causing stripe/yellow rust, an important wheat disease. This fungus is highly clonal in Europe but has been suggested to recombine in Asia. Using two temporally spaced samples of P. striiformis f.sp. tritici in China, the estimated sex frequency was 75% (i.e. three-quarter of individuals being sexually derived during the yearly sexual cycle), indicating strong contribution of sexual reproduction to the life cycle of the pathogen in this area. The inferred effective population size of this partially clonal organism (Nc  = 998) was in good agreement with estimates obtained using methods based on temporal variations in allelic frequencies. The cloncase estimator presented herein is the first method allowing accurate inference of both sex frequency and effective population size from population data without knowledge of recombination or mutation rates. cloncase can be applied to population genetic data from any organism with cyclical parthenogenesis and should in particular be very useful for improving our understanding of pest and microbial population biology. © 2016 John Wiley & Sons Ltd.

  13. Joint Prediction of the Effective Population Size and the Rate of Fixation of Deleterious Mutations.

    PubMed

    Santiago, Enrique; Caballero, Armando

    2016-11-01

    Mutation, genetic drift, and selection are considered the main factors shaping genetic variation in nature. There is a lack, however, of general predictions accounting for the mutual interrelation between these factors. In the context of the background selection model, we provide a set of equations for the joint prediction of the effective population size and the rate of fixation of deleterious mutations, which are applicable both to sexual and asexual species. For a population of N haploid individuals and a model of deleterious mutations with effect s appearing with rate U in a genome L Morgans long, the asymptotic effective population size (Ne) and the average number of generations (T) between consecutive fixations can be approximated by [Formula: see text] and [Formula: see text] The solution is applicable to Muller's ratchet, providing satisfactory approximations to the rate of accumulation of mutations for a wide range of parameters. We also obtain predictions of the effective size accounting for the expected nucleotide diversity. Predictions for sexual populations allow for outlining the general conditions where mutational meltdown occurs. The equations can be extended to any distribution of mutational effects and the consideration of hotspots of recombination, showing that Ne is rather insensitive and not proportional to changes in N for many combinations of parameters. This could contribute to explain the observed small differences in levels of polymorphism between species with very different census sizes.

  14. Quantifying the Variation in the Effective Population Size Within a Genome

    PubMed Central

    Gossmann, Toni I.; Woolfit, Megan; Eyre-Walker, Adam

    2011-01-01

    The effective population size (Ne) is one of the most fundamental parameters in population genetics. It is thought to vary across the genome as a consequence of differences in the rate of recombination and the density of selected sites due to the processes of genetic hitchhiking and background selection. Although it is known that there is intragenomic variation in the effective population size in some species, it is not known whether this is widespread or how much variation in the effective population size there is. Here, we test whether the effective population size varies across the genome, between protein-coding genes, in 10 eukaryotic species by considering whether there is significant variation in neutral diversity, taking into account differences in the mutation rate between loci by using the divergence between species. In most species we find significant evidence of variation. We investigate whether the variation in Ne is correlated to recombination rate and the density of selected sites in four species, for which these data are available. We find that Ne is positively correlated to recombination rate in one species, Drosophila melanogaster, and negatively correlated to a measure of the density of selected sites in two others, humans and Arabidopsis thaliana. However, much of the variation remains unexplained. We use a hierarchical Bayesian analysis to quantify the amount of variation in the effective population size and show that it is quite modest in all species—most genes have an Ne that is within a few fold of all other genes. Nonetheless we show that this modest variation in Ne is sufficient to cause significant differences in the efficiency of natural selection across the genome, by demonstrating that the ratio of the number of nonsynonymous to synonymous polymorphisms is significantly correlated to synonymous diversity and estimates of Ne, even taking into account the obvious nonindependence between these measures. PMID:21954163

  15. Detecting population recovery using gametic disequilibrium-based effective population size estimates

    Treesearch

    David A. Tallmon; Robin S. Waples; Dave Gregovich; Michael K. Schwartz

    2012-01-01

    Recovering populations often must meet specific growth rate or abundance targets before their legal status can be changed from endangered or threatened. While the efficacy, power, and performance of population metrics to infer trends in declining populations has received considerable attention, how these same metrics perform when populations are increasing is less...

  16. Estimation of effective population size of HIV-1 within a host: a pseudomaximum-likelihood approach.

    PubMed Central

    Seo, Tae-Kun; Thorne, Jeffrey L; Hasegawa, Masami; Kishino, Hirohisa

    2002-01-01

    Using pseudomaximum-likelihood approaches to phylogenetic inference and coalescent theory, we develop a computationally tractable method of estimating effective population size from serially sampled viral data. We show that the variance of the maximum-likelihood estimator of effective population size depends on the serial sampling design only because internal node times on a coalescent genealogy can be better estimated with some designs than with others. Given the internal node times and the number of sequences sampled, the variance of the maximum-likelihood estimator is independent of the serial sampling design. We then estimate the effective size of the HIV-1 population within nine hosts. If we assume that the mutation rate is 2.5 x 10(-5) substitutions/generation and is the same in all patients, estimated generation lengths vary from 0.73 to 2.43 days/generation and the mean (1.47) is similar to the generation lengths estimated by other researchers. If we assume that generation length is 1.47 days and is the same in all patients, mutation rate estimates vary from 1.52 x 10(-5) to 5.02 x 10(-5). Our results indicate that effective viral population size and evolutionary rate per year are negatively correlated among HIV-1 patients. PMID:11973287

  17. Joint effects of population size and isolation on genetic erosion in fragmented populations: finding fragmentation thresholds for management

    PubMed Central

    Méndez, María; Vögeli, Matthias; Tella, José L; Godoy, José A

    2014-01-01

    Size and isolation of local populations are main parameters of interest when assessing the genetic consequences of habitat fragmentation. However, their relative influence on the genetic erosion of local populations remains unclear. In this study, we first analysed how size and isolation of habitat patches influence the genetic variation of local populations of the Dupont's lark (Chersophilus duponti), an endangered songbird. An information-theoretic approach to model selection allowed us to address the importance of interactions between habitat variables, an aspect seldom considered in fragmentation studies, but which explained up to 65% of the variance in genetic parameters. Genetic diversity and inbreeding were influenced by the size of local populations depending on their degree of isolation, and genetic differentiation was positively related to isolation. We then identified a minimum local population of 19 male territories and a maximum distance of 30 km to the nearest population as thresholds from which genetic erosion becomes apparent. Our results alert on possibly misleading conclusions and suboptimal management recommendations when only additive effects are taken into account and encourage the use of most explanatory but easy-to-measure variables for the evaluation of genetic risks in conservation programmes. PMID:24822084

  18. Joint effects of population size and isolation on genetic erosion in fragmented populations: finding fragmentation thresholds for management.

    PubMed

    Méndez, María; Vögeli, Matthias; Tella, José L; Godoy, José A

    2014-04-01

    Size and isolation of local populations are main parameters of interest when assessing the genetic consequences of habitat fragmentation. However, their relative influence on the genetic erosion of local populations remains unclear. In this study, we first analysed how size and isolation of habitat patches influence the genetic variation of local populations of the Dupont's lark (Chersophilus duponti), an endangered songbird. An information-theoretic approach to model selection allowed us to address the importance of interactions between habitat variables, an aspect seldom considered in fragmentation studies, but which explained up to 65% of the variance in genetic parameters. Genetic diversity and inbreeding were influenced by the size of local populations depending on their degree of isolation, and genetic differentiation was positively related to isolation. We then identified a minimum local population of 19 male territories and a maximum distance of 30 km to the nearest population as thresholds from which genetic erosion becomes apparent. Our results alert on possibly misleading conclusions and suboptimal management recommendations when only additive effects are taken into account and encourage the use of most explanatory but easy-to-measure variables for the evaluation of genetic risks in conservation programmes.

  19. Historical analysis of genetic variation reveals low effective population size in a northern pike (Esox lucius) population.

    PubMed

    Miller, L M; Kapuscinski, A R

    1997-11-01

    Effective population size (Ne) of a natural fish population was estimated from temporal changes in allele frequencies at seven microsatellite loci. Use of a historical collection of fish scales made it possible to increase the precision of estimates by increasing the time interval between samples and to use an equation developed for discrete generations without correcting for demographic parameters. Estimates of Ne for the time intervals 1961-1977 and 1977-1993 were 35 and 72, respectively. For the entire interval, 1961-1993, the estimate of Ne was 48 when based on a weighted mean derived from the above two estimates or 125 when calculated from 1961 and 1993 samples only. Corresponding ratios of effective size to adult census size ranged from 0.03 to 0.14. An Ne of 48 over a 32-year period would imply that this population lost as much as 8% of its heterozygosity in that time. Results suggest the potential for using genetic methods based on microsatellite loci data to compare historical trends in Ne with population dynamic parameters. Such comparisons will help to evaluate the relationship between genetic diversity and long-term persistence of natural populations.

  20. Historical Analysis of Genetic Variation Reveals Low Effective Population Size in a Northern Pike (Esox Lucius) Population

    PubMed Central

    Miller, L. M.; Kapuscinski, A. R.

    1997-01-01

    Effective population size (N(e)) of a natural fish population was estimated from temporal changes in allele frequencies at seven microsatellite loci. Use of a historical collection of fish scales made it possible to increase the precision of estimates by increasing the time interval between samples and to use an equation developed for discrete generations without correcting for demographic parameters. Estimates of N(e) for the time intervals 1961-1977 and 1977-1993 were 35 and 72, respectively. For the entire interval, 1961-1993, the estimate of N(e) was 48 when based on a weighted mean derived from the above two estimates or 125 when calculated from 1961 and 1993 samples only. Corresponding ratios of effective size to adult census size ranged from 0.03 to 0.14. An N(e) of 48 over a 32-year period would imply that this population lost as much as 8% of its heterozygosity in that time. Results suggest the potential for using genetic methods based on microsatellite loci data to compare historical trends in N(e) with population dynamic parameters. Such comparisons will help to evaluate the relationship between genetic diversity and long-term persistence of natural populations. PMID:9383067

  1. The influence of persistent individual differences and age at maturity on effective population size

    PubMed Central

    Lee, Aline Magdalena; Engen, Steinar; Sæther, Bernt-Erik

    2011-01-01

    Ratios of effective populations size, Ne, to census population size, N, are used as a measure of genetic drift in populations. Several life-history parameters have been shown to affect these ratios, including mating system and age at sexual maturation. Using a stochastic matrix model, we examine how different levels of persistent individual differences in mating success among males may affect Ne/N, and how this relates to generation time. Individual differences of this type are shown to cause a lower Ne/N ratio than would be expected when mating is independent among seasons. Examining the way in which age at maturity affects Ne/N, we find that both the direction and magnitude of the effect depends on the survival rate of juveniles in the population. In particular, when maturation is delayed, lowered juvenile survival causes higher levels of genetic drift. In addition, predicted shifts in Ne/N with changing age at maturity are shown to be dependent on which of the commonly used definitions of census population size, N, is employed. Our results demonstrate that patterns of mating success, as well as juvenile survival probabilities, have substantial effects on rates of genetic drift. PMID:21436183

  2. Assessing the effect of sequencing depth and sample size in population genetics inferences.

    PubMed

    Fumagalli, Matteo

    2013-01-01

    Next-Generation Sequencing (NGS) technologies have dramatically revolutionised research in many fields of genetics. The ability to sequence many individuals from one or multiple populations at a genomic scale has greatly enhanced population genetics studies and made it a data-driven discipline. Recently, researchers have proposed statistical modelling to address genotyping uncertainty associated with NGS data. However, an ongoing debate is whether it is more beneficial to increase the number of sequenced individuals or the per-sample sequencing depth for estimating genetic variation. Through extensive simulations, I assessed the accuracy of estimating nucleotide diversity, detecting polymorphic sites, and predicting population structure under different experimental scenarios. Results show that the greatest accuracy for estimating population genetics parameters is achieved by employing a large sample size, despite single individuals being sequenced at low depth. Under some circumstances, the minimum sequencing depth for obtaining accurate estimates of allele frequencies and to identify polymorphic sites is [Formula: see text], where both alleles are more likely to have been sequenced. On the other hand, inferences of population structure are more accurate at very large sample sizes, even with extremely low sequencing depth. This all points to the conclusion that under various experimental scenarios, in cost-limited population genetics studies, large sample sizes at low sequencing depth are desirable to achieve high accuracy. These findings will help researchers design their experimental set-ups and guide further investigation on the effect of protocol design for genetic research.

  3. Demographic and genetic estimates of effective population size (Ne) reveals genetic compensation in steelhead trout.

    PubMed

    Ardren, William R; Kapuscinski, Anne R

    2003-01-01

    Estimates of effective population size (Ne) are required to predict the impacts of genetic drift and inbreeding on the evolutionary dynamics of populations. How the ratio of Ne to the number of sexually mature adults (N) varies in natural vertebrate populations has not been addressed. We examined the sensitivity of Ne/N to fluctuations of N and determined the major variables responsible for changing the ratio over a period of 17 years in a population of steelhead trout (Oncorhynchus mykiss) from Washington State. Demographic and genetic methods were used to estimate Ne. Genetic estimates of Ne were gained via temporal and linkage disequilibrium methods using data from eight microsatellite loci. DNA for genetic analysis was amplified from archived smolt scales. The Ne/N from 1977 to 1994, estimated using the temporal method, was 0.73 and the comprehensive demographic estimate of Ne/N over the same time period was 0.53. Demographic estimates of Ne indicated that variance in reproductive success had the most substantial impact on reducing Ne in this population, followed by fluctuations in population size. We found increased Ne/N ratios at low N, which we identified as genetic compensation. Combining the information from the demographic and genetic methods of estimating Ne allowed us to determine that a reduction in variance in reproductive success must be responsible for this compensation effect. Understanding genetic compensation in natural populations will be valuable for predicting the effects of changes in N (i.e. periods of high population density and bottlenecks) on the fitness and genetic variation of natural populations.

  4. Effects of Overlapping Generations on Linkage Disequilibrium Estimates of Effective Population Size

    PubMed Central

    Waples, Robin S.; Antao, Tiago; Luikart, Gordon

    2014-01-01

    Use of single-sample genetic methods to estimate effective population size has skyrocketed in recent years. Although the underlying models assume discrete generations, they are widely applied to age-structured species. We simulated genetic data for 21 iteroparous animal and plant species to evaluate two untested hypotheses regarding performance of the single-sample method based on linkage disequilibrium (LD): (1) estimates based on single-cohort samples reflect the effective number of breeders in one reproductive cycle (Nb), and (2) mixed-age samples reflect the effective size per generation (Ne). We calculated true Ne and Nb, using the model species’ vital rates, and verified these with individual-based simulations. We show that single-cohort samples should be equally influenced by Nb and Ne and confirm this with simulated results: N^b was a linear (r2 = 0.98) function of the harmonic mean of Ne and Nb. We provide a quantitative bias correction for raw N^b based on the ratio Nb/Ne, which can be estimated from two or three simple life history traits. Bias-adjusted estimates were within 5% of true Nb for all 21 study species and proved robust when challenged with new data. Mixed-age adult samples produced downwardly biased estimates in all species, which we attribute to a two-locus Wahlund effect (mixture LD) caused by combining parents from different cohorts in a single sample. Results from this study will facilitate interpretation of rapidly accumulating genetic estimates in terms of both Ne (which influences long-term evolutionary processes) and Nb (which is more important for understanding eco-evolutionary dynamics and mating systems). PMID:24717176

  5. Extent of linkage disequilibrium and effective population size in Finnish Landrace and Finnish Yorkshire pig breeds.

    PubMed

    Uimari, P; Tapio, M

    2011-03-01

    The extent of linkage disequilibrium (LD) and effective population size in Finnish Landrace and Finnish Yorkshire pig populations were studied using a whole genome SNP panel (Illumina PorcineSNP60 BeadChip) and pedigree data. Genotypic data included 86 Finnish Landrace and 32 Finnish Yorkshire boars. Pedigree data included 608,138 Finnish Landrace 554,237 and Finnish Yorkshire pigs, and on average 15 ancestral generations were known for the reference animals, born in 2005 to 2009. The breeding animals of the 2 populations have been kept separate in the breeding programs. Based on the pedigree data, the current effective population size for Finnish Landrace is 91 and for Finnish Yorkshire 61. Linkage disequilibrium measures (D' and r(2)) were estimated for over 1.5 million pairs of SNP. Average r(2) for SNP 30 kb apart was 0.47 and 0.49 and for SNP 5 Mb apart 0.09 and 0.12 for Finnish Landrace and Finnish Yorkshire, respectively. Average LD (r(2)) between adjacent SNP in the Illumina PorcineSNP60 BeadChip was 0.43 (57% of the adjacent SNP pairs had r(2) > 0.2) for Finnish Landrace and 0.46 (60% of the adjacent SNP pairs had r(2) > 0.2) for Finnish Yorkshire, and average r(2) > 0.2 extended to 1.0 and 1.5 Mb for Finnish Landrace and Finnish Yorkshire, respectively. Effective population size estimates based on the decay of r(2) with distance were similar to those based on the pedigree data: 80 and 55 for Finnish Landrace and Finnish Yorkshire, respectively. Thus, the results indicate that the effective population size of Finnish Yorkshire is smaller than of Finnish Landrace and has a clear effect on the extent of LD. The current effective population size of both breeds is above the recommended minimum of 50 but may get smaller than that in the near future, if no action is taken to balance the inbreeding rate and selection response. Because a moderate level of LD extends over a long distance, selection based on whole genome SNP markers (genomic selection) is expected

  6. Estimation of effective population size using single-nucleotide polymorphism (SNP) data in Jeju horse.

    PubMed

    Do, Kyoung-Tag; Lee, Joon-Ho; Lee, Hak-Kyo; Kim, Jun; Park, Kyung-Do

    2014-01-01

    This study was conducted to estimate the effective population size using SNPs data of 240 Jeju horses that had raced at the Jeju racing park. Of the total 61,746 genotyped autosomal SNPs, 17,320 (28.1%) SNPs (missing genotype rate of >10%, minor allele frequency of <0.05 and Hardy-Weinberg equilibrium test P-value of <10(-6)) were excluded after quality control processes. SNPs on the X and Y chromosomes and genotyped individuals with missing genotype rate over 10% were also excluded, and finally, 44,426 (71.9%) SNPs were selected and used for the analysis. The measures of the LD, square of correlation coefficient (r(2)) between SNP pairs, were calculated for each allele and the effective population size was determined based on r(2) measures. The polymorphism information contents (PIC) and expected heterozygosity (HE) were 0.27 and 0.34, respectively. In LD, the most rapid decline was observed over the first 1 Mb. But r(2) decreased more slowly with increasing distance and was constant after 2 Mb of distance and the decline was almost linear with log-transformed distance. The average r(2) between adjacent SNP pairs ranged from 0.20 to 0.31 in each chromosome and whole average was 0.26, while the whole average r(2) between all SNP pairs was 0.02. We observed an initial pattern of decreasing Ne and estimated values were closer to 41 at 1 ~ 5 generations ago. The effective population size (41 heads) estimated in this study seems to be large considering Jeju horse's population size (about 2,000 heads), but it should be interpreted with caution because of the technical limitations of the methods and sample size.

  7. Sexual dimorphism in human cranial trait scores: effects of population, age, and body size.

    PubMed

    Garvin, Heather M; Sholts, Sabrina B; Mosca, Laurel A

    2014-06-01

    Sex estimation from the skull is commonly performed by physical and forensic anthropologists using a five-trait scoring system developed by Walker. Despite the popularity of this method, validation studies evaluating its accuracy across a variety of samples are lacking. Furthermore, it remains unclear what other intrinsic or extrinsic variables are related to the expression of these traits. In this study, cranial trait scores and postcranial measurements were collected from four diverse population groups (U.S. Whites, U.S. Blacks, medieval Nubians, and Arikara Native Americans) following Walker's protocols (total n = 499). Univariate and multivariate analyses were utilized to evaluate the accuracy of these traits in sex estimation, and to test for the effects of population, age, and body size on trait expressions. Results revealed significant effects of population on all trait scores. Sample-specific correct sex classification rates ranged from 74% to 94%, with an overall accuracy of 85% for the pooled sample. Classification performance varied among the traits (best for glabella and mastoid scores and worst for nuchal scores). Furthermore, correlations between traits were weak or nonsignificant, suggesting that different factors may influence individual traits. Some traits displayed correlations with age and/or postcranial size that were significant but weak, and within-population analyses did not reveal any consistent relationships between these traits across all groups. These results indicate that neither age nor body size plays a large role in trait expression, and thus does not need to be incorporated into sex estimation methods.

  8. Inexpensive Computation of the Inverse of the Genomic Relationship Matrix in Populations with Small Effective Population Size

    PubMed Central

    Misztal, Ignacy

    2016-01-01

    Many computations with SNP data including genomic evaluation, parameter estimation, and genome-wide association studies use an inverse of the genomic relationship matrix. The cost of a regular inversion is cubic and is prohibitively expensive for large matrices. Recent studies in cattle demonstrated that the inverse can be computed in almost linear time by recursion on any subset of ∼10,000 individuals. The purpose of this study is to present a theory of why such a recursion works and its implication for other populations. Assume that, because of a small effective population size, the additive information in a genotyped population has a small dimensionality, even with a very large number of SNP markers. That dimensionality is visible as a limited number of effective SNP effects, independent chromosome segments, or the rank of the genomic relationship matrix. Decompose a population arbitrarily into core and noncore individuals, with the number of core individuals equal to that dimensionality. Then, breeding values of noncore individuals can be derived by recursions on breeding values of core individuals, with coefficients of the recursion computed from the genomic relationship matrix. A resulting algorithm for the inversion called “algorithm for proven and young” (APY) has a linear computing and memory cost for noncore animals. Noninfinitesimal genetic architecture can be accommodated through a trait-specific genomic relationship matrix, possibly derived from Bayesian regressions. For populations with small effective population size, the inverse of the genomic relationship matrix can be computed inexpensively for a very large number of genotyped individuals. PMID:26584903

  9. Linkage Disequilibrium Estimation of Effective Population Size with Immigrants from Divergent Populations: A Case Study on Spanish Mackerel (Scomberomorus commerson).

    PubMed

    Macbeth, Gilbert Michael; Broderick, Damien; Buckworth, Rik C; Ovenden, Jennifer R

    2013-04-09

    Estimates of genetic effective population size (Ne) using molecular markers are a potentially useful tool for the management of endangered through to commercial species. However, pitfalls are predicted when the effective size is large because estimates require large numbers of samples from wild populations for statistical validity. Our simulations showed that linkage disequilibrium estimates of Ne up to 10,000 with finite confidence limits can be achieved with sample sizes of approximately 5000. This number was deduced from empirical allele frequencies of seven polymorphic microsatellite loci in a commercially harvested fisheries species, the narrow-barred Spanish mackerel (Scomberomorus commerson). As expected, the smallest SD of Ne estimates occurred when low-frequency alleles were excluded. Additional simulations indicated that the linkage disequilibrium method was sensitive to small numbers of genotypes from cryptic species or conspecific immigrants. A correspondence analysis algorithm was developed to detect and remove outlier genotypes that could possibly be inadvertently sampled from cryptic species or nonbreeding immigrants from genetically separate populations. Simulations demonstrated the value of this approach in Spanish mackerel data. When putative immigrants were removed from the empirical data, 95% of the Ne estimates from jacknife resampling were greater than 24,000.

  10. Linkage Disequilibrium Estimation of Effective Population Size with Immigrants from Divergent Populations: A Case Study on Spanish Mackerel (Scomberomorus commerson)

    PubMed Central

    Macbeth, Gilbert Michael; Broderick, Damien; Buckworth, Rik C.; Ovenden, Jennifer R.

    2013-01-01

    Estimates of genetic effective population size (Ne) using molecular markers are a potentially useful tool for the management of endangered through to commercial species. However, pitfalls are predicted when the effective size is large because estimates require large numbers of samples from wild populations for statistical validity. Our simulations showed that linkage disequilibrium estimates of Ne up to 10,000 with finite confidence limits can be achieved with sample sizes of approximately 5000. This number was deduced from empirical allele frequencies of seven polymorphic microsatellite loci in a commercially harvested fisheries species, the narrow-barred Spanish mackerel (Scomberomorus commerson). As expected, the smallest SD of Ne estimates occurred when low-frequency alleles were excluded. Additional simulations indicated that the linkage disequilibrium method was sensitive to small numbers of genotypes from cryptic species or conspecific immigrants. A correspondence analysis algorithm was developed to detect and remove outlier genotypes that could possibly be inadvertently sampled from cryptic species or nonbreeding immigrants from genetically separate populations. Simulations demonstrated the value of this approach in Spanish mackerel data. When putative immigrants were removed from the empirical data, 95% of the Ne estimates from jacknife resampling were greater than 24,000. PMID:23550119

  11. Evaluating methods for estimating local effective population size with and without migration.

    PubMed

    Gilbert, Kimberly J; Whitlock, Michael C

    2015-08-01

    Effective population size is a fundamental parameter in population genetics, evolutionary biology, and conservation biology, yet its estimation can be fraught with difficulties. Several methods to estimate Ne from genetic data have been developed that take advantage of various approaches for inferring Ne . The ability of these methods to accurately estimate Ne , however, has not been comprehensively examined. In this study, we employ seven of the most cited methods for estimating Ne from genetic data (Colony2, CoNe, Estim, MLNe, ONeSAMP, TMVP, and NeEstimator including LDNe) across simulated datasets with populations experiencing migration or no migration. The simulated population demographies are an isolated population with no immigration, an island model metapopulation with a sink population receiving immigrants, and an isolation by distance stepping stone model of populations. We find considerable variance in performance of these methods, both within and across demographic scenarios, with some methods performing very poorly. The most accurate estimates of Ne can be obtained by using LDNe, MLNe, or TMVP; however each of these approaches is outperformed by another in a differing demographic scenario. Knowledge of the approximate demography of population as well as the availability of temporal data largely improves Ne estimates.

  12. Low effective population size and evidence for inbreeding in an overexploited flatfish, plaice (Pleuronectes platessa L.)

    PubMed Central

    Hoarau, Galice; Boon, Eva; Jongma, Dorris N; Ferber, Steven; Palsson, Jonbjorn; Van der Veer, Henk W; Rijnsdorp, Adriaan D; Stam, Wytze T; Olsen, Jeanine L

    2005-01-01

    Overexploitation and subsequent collapse of major worldwide fisheries has made it clear that marine stocks are not inexhaustible. Unfortunately, the perception remains that marine fishes are resilient to large population reductions, as even a commercially ‘collapsed’ stock will still consist of millions of individuals. Coupled with this notion is the idea that fisheries can, therefore, have little effect on the genetic diversity of stocks. We used DNA from archived otoliths collected between 1924 and 1972 together with 2002 juvenile's tissue to estimate effective population size (Ne) in plaice (Pleuronectes platessa). Ne was estimated at 20 000 in the North Sea and 2000 in Iceland. These values are five orders of magnitude smaller than the estimated census size for the two locations. Populations examined between 1924 and 1960 were in Hardy–Weinberg equilibrium, whereas populations examined after approximately 1970 were not. Extensive testing was performed to rule out genotyping artefacts and Wahlund effects. The significant heterozygote deficiencies found from 1970 onward were attributed to inbreeding. The emergence of inbreeding between 1950 and 1970 coincides with the increase in fishing mortality after World War II. Although the biological mechanisms remain speculative, our demonstration of inbreeding signals the need for understanding the social and mating behaviour in commercially important fishes. PMID:15799945

  13. Description and validation of a method for simultaneous estimation of effective population size and mutation rate from human population data.

    PubMed Central

    Chakraborty, R; Neel, J V

    1989-01-01

    A method is presented for utilizing population data on electrophoretic variants of proteins to estimate simultaneously the effective sizes (Ne values) of the populations in question and the rate of mutation resulting in electromorphs at the loci whose products were surveyed. The method is applied to data from 12 relatively unacculturated Amerindian tribes for whom census data and independent estimates of the number of different electrophoretic variants at 27 loci are available. Because of tribal demographic structure, Ne should be less than the current number of reproductive-aged adults. In fact, it is substantially greater for 7 tribes, most likely due to intertribal migration and a recent decrease in tribal size. Estimates of locus mutation rates for the 27 loci vary by more than a factor of 20, with an average of 1.1 x 10(-5) per locus per generation. This latter estimate is in satisfactory agreement with the results of other indirect approaches to the estimation of mutation rates in these tribes but about two times higher than the results of direct estimates based on these same loci in studies on civilized populations. This discrepancy could be due to the above-hypothesized migration and to decreases in tribal size. PMID:2594777

  14. Effect of reference population size and available ancestor genotypes on imputation of Mexican Holstein genotypes.

    PubMed

    García-Ruiz, A; Ruiz-Lopez, F J; Wiggans, G R; Van Tassell, C P; Montaldo, H H

    2015-05-01

    The effects of reference population size and the availability of information from genotyped ancestors on the accuracy of imputation of single nucleotide polymorphisms (SNP) were investigated for Mexican Holstein cattle. Three scenarios for reference population size were examined: (1) a local population of 2,011 genotyped Mexican Holsteins, (2) animals in scenario 1 plus 866 Holsteins in the US genotype database (GDB) with genotyped Mexican daughters, and (3) animals in scenario 1 and all US GDB Holsteins (338,073). Genotypes from 4 chip densities (2 low density, 1 mid density, and 1 high density) were imputed using findhap (version 3) to the 45,195 markers on the mid-density chip. Imputation success was determined by comparing the numbers of SNP with 1 or 2 alleles missing and the numbers of differently predicted SNP (conflicts) among the 3 scenarios. Imputation accuracy improved as chip density and numbers of genotyped ancestors increased, and the percentage of SNP with 1 missing allele was greater than that for 2 missing alleles for all scenarios. The largest numbers of conflicts were found between scenarios 1 and 3. The inclusion of information from direct ancestors (dam or sire) with US GDB genotypes in the imputation of Mexican Holstein genotypes increased imputation accuracy by 1 percentage point for low-density genotypes and by 0.5 percentage points for high-density genotypes, which was about half the gain found with information from all US GDB Holsteins. A larger reference population and the availability of genotyped ancestors improved imputation; animals with genotyped parents in a large reference population had higher imputation accuracy than those with no or few genotyped relatives in a small reference population. For small local populations, including genotypes from other related populations can aid in improving imputation accuracy.

  15. The evolution of harm--effect of sexual conflicts and population size.

    PubMed

    Gay, Laurène; Hosken, David J; Eady, Paul; Vasudev, Ram; Tregenza, Tom

    2011-03-01

    Conflicts of interest between mates can promote the evolution of male traits that reduce female fitness and that drive coevolution between the sexes. The rate of adaptation depends on the intensity of selection and its efficiency, which depends on drift and genetic variability. This leads to the largely untested prediction that coevolutionary adaptations such as those driven by sexual conflict should evolve faster in large populations. We tested this using the bruchid beetle Callosobruchus maculatus, a species where harm inflicted by males is well documented. Although most experimental evolution studies remove sexual conflict, we reintroduced it in populations in which it had been experimentally removed. Both population size and standing genetic variability were manipulated in a factorial experimental design. After 90 generations of relaxed conflict (monogamy), the reintroduction of sexual conflicts for 30 generations favored males that harmed females and females that were more resistant to the genital damage inflicted by males. Males evolved to become more harmful when population size was large rather than when initial genetic variation was enriched. Our study shows that sexual selection can create conditions in which males can benefit from harming females and that selection may tend to be more intense and effective in larger populations. © 2010 The Author(s). Evolution© 2010 The Society for the Study of Evolution.

  16. Short-Term Genetic Changes: Evaluating Effective Population Size Estimates in a Comprehensively Described Brown Trout (Salmo trutta) Population

    PubMed Central

    Serbezov, Dimitar; Jorde, Per Erik; Bernatchez, Louis; Olsen, Esben Moland; Vøllestad, L. Asbjørn

    2012-01-01

    The effective population size (Ne) is notoriously difficult to accurately estimate in wild populations as it is influenced by a number of parameters that are difficult to delineate in natural systems. The different methods that are used to estimate Ne are affected variously by different processes at the population level, such as the life-history characteristics of the organism, gene flow, and population substructure, as well as by the frequency patterns of genetic markers used and the sampling design. Here, we compare Ne estimates obtained by different genetic methods and from demographic data and elucidate how the estimates are affected by various factors in an exhaustively sampled and comprehensively described natural brown trout (Salmo trutta) system. In general, the methods yielded rather congruent estimates, and we ascribe that to the adequate genotyping and exhaustive sampling. Effects of violating the assumptions of the different methods were nevertheless apparent. In accordance with theoretical studies, skewed allele frequencies would underestimate temporal allele frequency changes and thereby upwardly bias Ne if not accounted for. Overlapping generations and iteroparity would also upwardly bias Ne when applied to temporal samples taken over short time spans. Gene flow from a genetically not very dissimilar source population decreases temporal allele frequency changes and thereby acts to increase estimates of Ne. Our study reiterates the importance of adequate sampling, quantification of life-history parameters and gene flow, and incorporating these data into the Ne estimation. PMID:22466040

  17. Quantitative ultrasound estimates from populations of scatterers with continuous size distributions - Effects of the size estimator algorithm

    PubMed Central

    Oelze, Michael

    2012-01-01

    Quantitative ultrasonic techniques using backscatter coefficients (BSCs) may fail to produce physically meaningful estimates of effective scatterer diameter (ESD) when the analysis media contains scatterers of different sizes. In this work, three different estimator algorithms were used to produce estimates of ESD. The performance of the three estimators was compared over different frequency bands using simulations and experiments with physical phantoms. All estimators produced ESD estimates by comparing the estimated BSCs with a scattering model based on the backscattering cross-section of a single spherical fluid scatterer. The first estimator consisted of minimizing the average square deviation of the ratio between the estimated BSCs and the scattering model with both expressed in decibels. The second and third estimators consisted of minimizing the mean square error between the estimated BSCs and a linear transformation of the scattering model with and without considering an intercept, respectively. Simulations were conducted over several analysis bandwidths between 1 and 40 MHz from populations of scatterers with either a uniform size distribution or a distribution based on the inverse cubic of the size. Diameters of the distributions ranged between [25, 100], [25, 50], [50, 100], and [50, 75] μm. Experimental results were obtained from two gelatin phantoms containing Sephadex spheres ranging in diameter from 28 to 130 μm and 70 to 130 μm, respectively, and 5, 7.5, 10, and 13 MHz focused transducers. Significant differences in the performances of the ESD estimator algorithms as a function of the analysis frequency were observed. Specifically, the third estimator exhibited potential to produce physically meaningful ESD estimates even for large ka values when using a single-size scattering model if sufficient analysis bandwidth was available. PMID:23007782

  18. Quantitative ultrasound estimates from populations of scatterers with continuous size distributions: effects of the size estimator algorithm.

    PubMed

    Lavarello, Roberto; Oelze, Michael

    2012-09-01

    Quantitative ultrasonic techniques using backscatter coefficients (BSCs) may fail to produce physically meaningful estimates of effective scatterer diameter (ESD) when the analysis media contains scatterers of different sizes. In this work, three different estimator algorithms were used to produce estimates of ESD. The performance of the three estimators was compared over different frequency bands using simulations and experiments with physical phantoms. All estimators produced ESD estimates by comparing the estimated BSCs with a scattering model based on the backscattering cross section of a single spherical fluid scatterer. The first estimator consisted of minimizing the average square deviation of the logarithmically compressed ratio between the estimated BSCs and the scattering model. The second and third estimators consisted of minimizing the mean square error between the estimated BSCs and a linear transformation of the scattering model with and without considering an intercept, respectively. Simulations were conducted over several analysis bandwidths between 1 and 40 MHz from populations of scatterers with either a uniform size distribution or a distribution based on the inverse cubic of the size. Diameters of the distributions ranged between [25, 100], [25, 50], [50, 100], and [50, 75] μm. Experimental results were obtained from two gelatin phantoms containing cross-linked dextran gel spheres ranging in diameter from 28 to 130 μm and 70 to 130 μm, respectively, and 5-, 7.5-, 10-, and 13-MHz focused transducers. Significant differences in the performances of the ESD estimator algorithms as a function of the analysis frequency were observed. Specifically, the third estimator exhibited potential to produce physically meaningful ESD estimates even for large ka values when using a single-size scattering model if sufficient analysis bandwidth was available.

  19. Extent of Linkage Disequilibrium and Effective Population Size in Four South African Sanga Cattle Breeds.

    PubMed

    Makina, Sithembile O; Taylor, Jeremy F; van Marle-Köster, Este; Muchadeyi, Farai C; Makgahlela, Mahlako L; MacNeil, Michael D; Maiwashe, Azwihangwisi

    2015-01-01

    Knowledge on the extent of linkage disequilibrium (LD) in livestock populations is essential to determine the minimum distance between markers required for effective coverage when conducting genome-wide association studies (GWAS). This study evaluated the extent of LD, persistence of allelic phase and effective population size (Ne) for four Sanga cattle breeds in South Africa including the Afrikaner (n = 44), Nguni (n = 54), Drakensberger (n = 47), and Bonsmara breeds (n = 46), using Angus (n = 31) and Holstein (n = 29) as reference populations. We found that moderate LD extends up to inter-marker distances of 40-60 kb in Angus (0.21) and Holstein (0.21) and up to 100 kb in Afrikaner (0.20). This suggests that genomic selection and association studies performed within these breeds using an average inter-marker r (2)≥ 0.20 would require about 30,000-50,000 SNPs. However, r (2)≥ 0.20 extended only up to 10-20 kb in the Nguni and Drakensberger and 20-40 kb in the Bonsmara indicating that 75,000 to 150,000 SNPs would be necessary for GWAS in these breeds. Correlation between alleles at contiguous loci indicated that phase was not strongly preserved between breeds. This suggests the need for breed-specific reference populations in which a much greater density of markers should be scored to identify breed specific haplotypes which may then be imputed into multi-breed commercial populations. Analysis of effective population size based on the extent of LD, revealed Ne = 95 (Nguni), Ne = 87 (Drakensberger), Ne = 77 (Bonsmara), and Ne = 41 (Afrikaner). Results of this study form the basis for implementation of genomic selection programs in the Sanga breeds of South Africa.

  20. Extent of Linkage Disequilibrium and Effective Population Size in Four South African Sanga Cattle Breeds

    PubMed Central

    Makina, Sithembile O.; Taylor, Jeremy F.; van Marle-Köster, Este; Muchadeyi, Farai C.; Makgahlela, Mahlako L.; MacNeil, Michael D.; Maiwashe, Azwihangwisi

    2015-01-01

    Knowledge on the extent of linkage disequilibrium (LD) in livestock populations is essential to determine the minimum distance between markers required for effective coverage when conducting genome-wide association studies (GWAS). This study evaluated the extent of LD, persistence of allelic phase and effective population size (Ne) for four Sanga cattle breeds in South Africa including the Afrikaner (n = 44), Nguni (n = 54), Drakensberger (n = 47), and Bonsmara breeds (n = 46), using Angus (n = 31) and Holstein (n = 29) as reference populations. We found that moderate LD extends up to inter-marker distances of 40–60 kb in Angus (0.21) and Holstein (0.21) and up to 100 kb in Afrikaner (0.20). This suggests that genomic selection and association studies performed within these breeds using an average inter-marker r2≥ 0.20 would require about 30,000–50,000 SNPs. However, r2≥ 0.20 extended only up to 10–20 kb in the Nguni and Drakensberger and 20–40 kb in the Bonsmara indicating that 75,000 to 150,000 SNPs would be necessary for GWAS in these breeds. Correlation between alleles at contiguous loci indicated that phase was not strongly preserved between breeds. This suggests the need for breed-specific reference populations in which a much greater density of markers should be scored to identify breed specific haplotypes which may then be imputed into multi-breed commercial populations. Analysis of effective population size based on the extent of LD, revealed Ne = 95 (Nguni), Ne = 87 (Drakensberger), Ne = 77 (Bonsmara), and Ne = 41 (Afrikaner). Results of this study form the basis for implementation of genomic selection programs in the Sanga breeds of South Africa. PMID:26648975

  1. Preferred habitat and effective population size drive landscape genetic patterns in an endangered species

    PubMed Central

    Weckworth, Byron V.; Musiani, Marco; DeCesare, Nicholas J.; McDevitt, Allan D.; Hebblewhite, Mark; Mariani, Stefano

    2013-01-01

    Landscape genetics provides a framework for pinpointing environmental features that determine the important exchange of migrants among populations. These studies usually test the significance of environmental variables on gene flow, yet ignore one fundamental driver of genetic variation in small populations, effective population size, Ne. We combined both approaches in evaluating genetic connectivity of a threatened ungulate, woodland caribou. We used least-cost paths to calculate matrices of resistance distance for landscape variables (preferred habitat, anthropogenic features and predation risk) and population-pairwise harmonic means of Ne, and correlated them with genetic distances, FST and Dc. Results showed that spatial configuration of preferred habitat and Ne were the two best predictors of genetic relationships. Additionally, controlling for the effect of Ne increased the strength of correlations of environmental variables with genetic distance, highlighting the significant underlying effect of Ne in modulating genetic drift and perceived spatial connectivity. We therefore have provided empirical support to emphasize preventing increased habitat loss and promoting population growth to ensure metapopulation viability. PMID:24004939

  2. Effective size of a wild salmonid population is greatly reduced by hatchery supplementation

    PubMed Central

    Christie, M R; Marine, M L; French, R A; Waples, R S; Blouin, M S

    2012-01-01

    Many declining and commercially important populations are supplemented with captive-born individuals that are intentionally released into the wild. These supplementation programs often create large numbers of offspring from relatively few breeding adults, which can have substantial population-level effects. We examined the genetic effects of supplementation on a wild population of steelhead (Oncorhynchus mykiss) from the Hood River, Oregon, by matching 12 run-years of hatchery steelhead back to their broodstock parents. We show that the effective number of breeders producing the hatchery fish (broodstock parents; Nb) was quite small (harmonic mean Nb=25 fish per brood-year vs 373 for wild fish), and was exacerbated by a high variance in broodstock reproductive success among individuals within years. The low Nb caused hatchery fish to have decreased allelic richness, increased average relatedness, more loci in linkage disequilibrium and substantial levels of genetic drift in comparison with their wild-born counterparts. We also documented a substantial Ryman–Laikre effect whereby the additional hatchery fish doubled the total number of adult fish on the spawning grounds each year, but cut the effective population size of the total population (wild and hatchery fish combined) by nearly two-thirds. We further demonstrate that the Ryman–Laikre effect is most severe in this population when (1) >10% of fish allowed onto spawning grounds are from hatcheries and (2) the hatchery fish have high reproductive success in the wild. These results emphasize the trade-offs that arise when supplementation programs attempt to balance disparate goals (increasing production while maintaining genetic diversity and fitness). PMID:22805657

  3. Complex Genetics of Type 2 Diabetes and Effect Size: What have We Learned from Isolated Populations?

    PubMed Central

    Nair, Anup K.; Baier, Leslie J.

    2015-01-01

    Genetic studies in large outbred populations have documented a complex, highly polygenic basis for type 2 diabetes (T2D). Most of the variants currently known to be associated with T2D risk have been identified in large studies that included tens of thousands of individuals who are representative of a single major ethnic group such as European, Asian, or African. However, most of these variants have only modest effects on the risk for T2D; identification of definitive 'causal variant' or 'causative loci' is typically lacking. Studies in isolated populations offer several advantages over outbred populations despite being, on average, much smaller in sample size. For example, reduced genetic variability, enrichment of rare variants, and a more uniform environment and lifestyle, which are hallmarks of isolated populations, can reduce the complexity of identifying disease-associated genes. To date, studies in isolated populations have provided valuable insight into the genetic basis of T2D by providing both a deeper understanding of previously identified T2D-associated variants (e.g. demonstrating that variants in KCNQ1 have a strong parent-of-origin effect) or providing novel variants (e.g. ABCC8 in Pima Indians, TBC1D4 in the Greenlandic population, HNF1A in Canadian Oji-Cree). This review summarizes advancements in genetic studies of T2D in outbred and isolated populations, and provides information on whether the difference in the prevalence of T2D in different populations (Pima Indians vs. non-Hispanic Whites and non-Hispanic Whites vs. non-Hispanic Blacks) can be explained by the difference in risk allele frequencies of established T2D variants. PMID:27111117

  4. Recent Evolution in Rattus norvegicus Is Shaped by Declining Effective Population Size.

    PubMed

    Deinum, Eva E; Halligan, Daniel L; Ness, Rob W; Zhang, Yao-Hua; Cong, Lin; Zhang, Jian-Xu; Keightley, Peter D

    2015-10-01

    The brown rat, Rattus norvegicus, is both a notorious pest and a frequently used model in biomedical research. By analyzing genome sequences of 12 wild-caught brown rats from their presumed ancestral range in NE China, along with the sequence of a black rat, Rattus rattus, we investigate the selective and demographic forces shaping variation in the genome. We estimate that the recent effective population size (Ne) of this species = [Formula: see text], based on silent site diversity. We compare patterns of diversity in these genomes with patterns in multiple genome sequences of the house mouse (Mus musculus castaneus), which has a much larger Ne. This reveals an important role for variation in the strength of genetic drift in mammalian genome evolution. By a Pairwise Sequentially Markovian Coalescent analysis of demographic history, we infer that there has been a recent population size bottleneck in wild rats, which we date to approximately 20,000 years ago. Consistent with this, wild rat populations have experienced an increased flux of mildly deleterious mutations, which segregate at higher frequencies in protein-coding genes and conserved noncoding elements. This leads to negative estimates of the rate of adaptive evolution (α) in proteins and conserved noncoding elements, a result which we discuss in relation to the strongly positive estimates observed in wild house mice. As a consequence of the population bottleneck, wild rats also show a markedly slower decay of linkage disequilibrium with physical distance than wild house mice.

  5. Estimating Effective Population Size from Linkage Disequilibrium between Unlinked Loci: Theory and Application to Fruit Fly Outbreak Populations

    PubMed Central

    Sved, John A; Cameron, Emilie C.; Gilchrist, A. Stuart

    2013-01-01

    There is a substantial literature on the use of linkage disequilibrium (LD) to estimate effective population size using unlinked loci. The estimates are extremely sensitive to the sampling process, and there is currently no theory to cope with the possible biases. We derive formulae for the analysis of idealised populations mating at random with multi-allelic (microsatellite) loci. The ‘Burrows composite index’ is introduced in a novel way with a ‘composite haplotype table’. We show that in a sample of diploid size , the mean value of or from the composite haplotype table is biased by a factor of , rather than the usual factor for a conventional haplotype table. But analysis of population data using these formulae leads to estimates that are unrealistically low. We provide theory and simulation to show that this bias towards low estimates is due to null alleles, and introduce a randomised permutation correction to compensate for the bias. We also consider the effect of introducing a within-locus disequilibrium factor to , and find that this factor leads to a bias in the estimate. However this bias can be overcome using the same randomised permutation correction, to yield an altered with lower variance than the original , and one that is also insensitive to null alleles. The resulting formulae are used to provide estimates on 40 samples of the Queensland fruit fly, Bactrocera tryoni, from populations with widely divergent expectations. Linkage relationships are known for most of the microsatellite loci in this species. We find that there is little difference in the estimated values from using known unlinked loci as compared to using all loci, which is important for conservation studies where linkage relationships are unknown. PMID:23894410

  6. Effective population size dynamics and the demographic collapse of Bornean orang-utans.

    PubMed

    Sharma, Reeta; Arora, Natasha; Goossens, Benoit; Nater, Alexander; Morf, Nadja; Salmona, Jordi; Bruford, Michael W; Van Schaik, Carel P; Krützen, Michael; Chikhi, Lounès

    2012-01-01

    Bornean orang-utans experienced a major demographic decline and local extirpations during the Pleistocene and Holocene due to climate change, the arrival of modern humans, of farmers and recent commercially-driven habitat loss and fragmentation. The recent loss of habitat and its dramatic fragmentation has affected the patterns of genetic variability and differentiation among the remaining populations and increased the extinction risk of the most isolated ones. However, the contribution of recent demographic events to such genetic patterns is still not fully clear. Indeed, it can be difficult to separate the effects of recent anthropogenic fragmentation from the genetic signature of prehistoric demographic events. Here, we investigated the genetic structure and population size dynamics of orang-utans from different sites. Altogether 126 individuals were analyzed and a full-likelihood Bayesian approach was applied. All sites exhibited clear signals of population decline. Population structure is known to generate spurious bottleneck signals and we found that it does indeed contribute to the signals observed. However, population structure alone does not easily explain the observed patterns. The dating of the population decline varied across sites but was always within the 200-2000 years period. This suggests that in some sites at least, orang-utan populations were affected by demographic events that started before the recent anthropogenic effects that occurred in Borneo. These results do not mean that the recent forest exploitation did not leave its genetic mark on orang-utans but suggests that the genetic pool of orang-utans is also impacted by more ancient events. While we cannot identify the main cause for this decline, our results suggests that the decline may be related to the arrival of the first farmers or climatic events, and that more theoretical work is needed to understand how multiple demographic events impact the genome of species and how we can assess

  7. Effective Population Size Dynamics and the Demographic Collapse of Bornean Orang-Utans

    PubMed Central

    Goossens, Benoit; Nater, Alexander; Morf, Nadja; Salmona, Jordi; Bruford, Michael W.; Van Schaik, Carel P.; Krützen, Michael; Chikhi, Lounès

    2012-01-01

    Bornean orang-utans experienced a major demographic decline and local extirpations during the Pleistocene and Holocene due to climate change, the arrival of modern humans, of farmers and recent commercially-driven habitat loss and fragmentation. The recent loss of habitat and its dramatic fragmentation has affected the patterns of genetic variability and differentiation among the remaining populations and increased the extinction risk of the most isolated ones. However, the contribution of recent demographic events to such genetic patterns is still not fully clear. Indeed, it can be difficult to separate the effects of recent anthropogenic fragmentation from the genetic signature of prehistoric demographic events. Here, we investigated the genetic structure and population size dynamics of orang-utans from different sites. Altogether 126 individuals were analyzed and a full-likelihood Bayesian approach was applied. All sites exhibited clear signals of population decline. Population structure is known to generate spurious bottleneck signals and we found that it does indeed contribute to the signals observed. However, population structure alone does not easily explain the observed patterns. The dating of the population decline varied across sites but was always within the 200–2000 years period. This suggests that in some sites at least, orang-utan populations were affected by demographic events that started before the recent anthropogenic effects that occurred in Borneo. These results do not mean that the recent forest exploitation did not leave its genetic mark on orang-utans but suggests that the genetic pool of orang-utans is also impacted by more ancient events. While we cannot identify the main cause for this decline, our results suggests that the decline may be related to the arrival of the first farmers or climatic events, and that more theoretical work is needed to understand how multiple demographic events impact the genome of species and how we can assess

  8. Single-gene speciation with pleiotropy: effects of allele dominance, population size, and delayed inheritance.

    PubMed

    Yamamichi, Masato; Sasaki, Akira

    2013-07-01

    Single-gene speciation is considered to be unlikely, but an excellent example is found in land snails, in which a gene for left-right reversal has given rise to new species multiple times. This reversal might be facilitated by their small population sizes and maternal effect (i.e., "delayed inheritance," in which an individual's phenotype is determined by the genotype of its mother). Recent evidence suggests that a pleiotropic effect of the speciation gene on antipredator survival may also promote speciation. Here we theoretically demonstrate that, without a pleiotropic effect, in small populations the fixation probability of a recessive mutant is higher than a dominant mutant, but they are identical for large populations and sufficiently weak selection. With a pleiotropic effect that increases mutant viability, a dominant mutant has a higher fixation probability if the strength of viability selection is sufficiently greater than that of reproductive incompatibility, whereas a recessive mutant has a higher fixation probability otherwise. Delayed inheritance increases the fixation probability of a mutant if viability selection is sufficiently weaker than reproductive incompatibility. Our results clarify the conflicting effects of viability selection and positive frequency-dependent selection due to reproductive incompatibility and provide a new perspective to single-gene speciation theory.

  9. Effect of distance-related heterogeneity on population size estimates from point counts

    USGS Publications Warehouse

    Efford, Murray G.; Dawson, Deanna K.

    2009-01-01

    Point counts are used widely to index bird populations. Variation in the proportion of birds counted is a known source of error, and for robust inference it has been advocated that counts be converted to estimates of absolute population size. We used simulation to assess nine methods for the conduct and analysis of point counts when the data included distance-related heterogeneity of individual detection probability. Distance from the observer is a ubiquitous source of heterogeneity, because nearby birds are more easily detected than distant ones. Several recent methods (dependent double-observer, time of first detection, time of detection, independent multiple-observer, and repeated counts) do not account for distance-related heterogeneity, at least in their simpler forms. We assessed bias in estimates of population size by simulating counts with fixed radius w over four time intervals (occasions). Detection probability per occasion was modeled as a half-normal function of distance with scale parameter sigma and intercept g(0) = 1.0. Bias varied with sigma/w; values of sigma inferred from published studies were often 50% for a 100-m fixed-radius count. More critically, the bias of adjusted counts sometimes varied more than that of unadjusted counts, and inference from adjusted counts would be less robust. The problem was not solved by using mixture models or including distance as a covariate. Conventional distance sampling performed well in simulations, but its assumptions are difficult to meet in the field. We conclude that no existing method allows effective estimation of population size from point counts.

  10. Adaptive Protein Evolution in Animals and the Effective Population Size Hypothesis

    PubMed Central

    Galtier, Nicolas

    2016-01-01

    The rate at which genomes adapt to environmental changes and the prevalence of adaptive processes in molecular evolution are two controversial issues in current evolutionary genetics. Previous attempts to quantify the genome-wide rate of adaptation through amino-acid substitution have revealed a surprising diversity of patterns, with some species (e.g. Drosophila) experiencing a very high adaptive rate, while other (e.g. humans) are dominated by nearly-neutral processes. It has been suggested that this discrepancy reflects between-species differences in effective population size. Published studies, however, were mainly focused on model organisms, and relied on disparate data sets and methodologies, so that an overview of the prevalence of adaptive protein evolution in nature is currently lacking. Here we extend existing estimators of the amino-acid adaptive rate by explicitly modelling the effect of favourable mutations on non-synonymous polymorphism patterns, and we apply these methods to a newly-built, homogeneous data set of 44 non-model animal species pairs. Data analysis uncovers a major contribution of adaptive evolution to the amino-acid substitution process across all major metazoan phyla—with the notable exception of humans and primates. The proportion of adaptive amino-acid substitution is found to be positively correlated to species effective population size. This relationship, however, appears to be primarily driven by a decreased rate of nearly-neutral amino-acid substitution because of more efficient purifying selection in large populations. Our results reveal that adaptive processes dominate the evolution of proteins in most animal species, but do not corroborate the hypothesis that adaptive substitutions accumulate at a faster rate in large populations. Implications regarding the factors influencing the rate of adaptive evolution and positive selection detection in humans vs. other organisms are discussed. PMID:26752180

  11. Effective/census population size ratio estimation: a compendium and appraisal

    PubMed Central

    Palstra, Friso P; Fraser, Dylan J

    2012-01-01

    With an ecological-evolutionary perspective increasingly applied toward the conservation and management of endangered or exploited species, the genetic estimation of effective population size (Ne) has proliferated. Based on a comprehensive analysis of empirical literature from the past two decades, we asked: (i) how often do studies link Ne to the adult census population size (N)? (ii) To what extent is Ne correctly linked to N? (iii) How readily is uncertainty accounted for in both Ne and N when quantifying Ne/N ratios? and (iv) how frequently and to what degree might errors in the estimation of Ne or N affect inferences of Ne/N ratios? We found that only 20% of available Ne estimates (508 of 2617; 233 studies) explicitly attempted to link Ne and N; of these, only 31% (160 of 508) correctly linked Ne and N. Moreover, only 7% (41 of 508) of Ne/N ratios (correctly linked or not) reported confidence intervals for both Ne and N; for those cases where confidence intervals were reported for Ne only, 31% of Ne/N ratios overlapped with 1, of which more than half also reached below Ne/N = 0.01. Uncertainty in Ne/N ratios thus sometimes spanned at least two orders of magnitude. We conclude that the estimation of Ne/N ratios in natural populations could be significantly improved, discuss several options for doing so, and briefly outline some future research directions. PMID:23139893

  12. Effective Population Size, Extended Linkage Disequilibrium and Signatures of Selection in the Rare Dog Breed Lundehund

    PubMed Central

    Pfahler, Sophia; Distl, Ottmar

    2015-01-01

    The Lundehund is an old dog breed with remarkable anatomical features including polydactyly in all four limbs and extraordinary flexibility of the spine. We genotyped 28 Lundehund using the canine Illumina high density beadchip to estimate the effective population size (Ne) and inbreeding coefficients as well as to identify potential regions of positive selection. The decay of linkage disequilibrium was slow with r2 = 0.95 in 50 kb distance. The last 7-200 generations ago, Ne was at 10-13. An increase of Ne was noted in the very recent generations with a peak value of 19 for Ne at generation 4. The FROH estimated for 50-, 65- and 358-SNP windows were 0.87, 087 and 0.81, respectively. The most likely estimates for FROH after removing identical-by-state segments due to linkage disequilibria were at 0.80-0.81. The extreme loss of heterozygosity has been accumulated through continued inbreeding over 200 generations within a probably closed population with a small effective population size. The mean inbreeding coefficient based on pedigree data for the last 11 generations (FPed = 0.10) was strongly biased downwards due to the unknown coancestry of the founders in this pedigree data. The long-range haplotype test identified regions with genes involved in processes of immunity, olfaction, woundhealing and neuronal development as potential targets of selection. The genes QSOX2, BMPR1B and PRRX2 as well as MYOM1 are candidates for selection on the Lundehund characteristics small body size, increased number of digits per paw and extraordinary mobility, respectively. PMID:25860808

  13. Effect of population size on the estimation of QTL: a test using resistance to barley stripe rust.

    PubMed

    Vales, M I; Schön, C C; Capettini, F; Chen, X M; Corey, A E; Mather, D E; Mundt, C C; Richardson, K L; Sandoval-Islas, J S; Utz, H F; Hayes, P M

    2005-11-01

    The limited population sizes used in many quantitative trait locus (QTL) detection experiments can lead to underestimation of QTL number, overestimation of QTL effects, and failure to quantify QTL interactions. We used the barley/barley stripe rust pathosystem to evaluate the effect of population size on the estimation of QTL parameters. We generated a large (n = 409) population of doubled haploid lines derived from the cross of two inbred lines, BCD47 and Baronesse. This population was evaluated for barley stripe rust severity in the Toluca Valley, Mexico, and in Washington State, USA, under field conditions. BCD47 was the principal donor of resistance QTL alleles, but the susceptible parent also contributed some resistance alleles. The major QTL, located on the long arm of chromosome 4H, close to the Mlo gene, accounted for up to 34% of the phenotypic variance. Subpopulations of different sizes were generated using three methods-resampling, selective genotyping, and selective phenotyping-to evaluate the effect of population size on the estimation of QTL parameters. In all cases, the number of QTL detected increased with population size. QTL with large effects were detected even in small populations, but QTL with small effects were detected only by increasing population size. Selective genotyping and/or selective phenotyping approaches could be effective strategies for reducing the costs associated with conducting QTL analysis in large populations. The method of choice will depend on the relative costs of genotyping versus phenotyping.

  14. Glossina swynnertoni Austen: effective population size and breeding structure estimated by mitochondrial diversity

    PubMed Central

    Marquez, J G; Malele, I I; Ouma, J O; Krafsur, E S

    2006-01-01

    Nucleotide diversity was examined at mitochondrial COI and r16S2 loci in eight Glossina swynnertoni collections from northern Tanzania and from a culture maintained by the International Atomic Energy Agency. Eighteen composite haplotypes were observed among 149 flies, two of which were common to all samples and 10 were private. Mean haplotype diversity was 0.59 and nucleotide diversity was 0.0013. There were excess singular haplotypes and mutation-drift disequilibrium suggesting that populations had experienced an earlier bottleneck and subsequent expansion. Factorial correspondence analysis showed that haplotype frequencies varied much more temporally (GST = 0.18) than spatially (GST = 0.04). The estimate of effective population size Ne in Tarangire was a harmonic mean ~ 50 reproductive flies averaged over ~ 47 generations. The mean rate of gene flow was estimated to be ~ 5 ± 1 reproducing females per generation but inflated because of mutation-drift disequilibrium arising from likely earlier bottlenecks. PMID:16923202

  15. Estimates of linkage disequilibrium and effective population size in rainbow trout.

    PubMed

    Rexroad, Caird E; Vallejo, Roger L

    2009-12-14

    The use of molecular genetic technologies for broodstock management and selective breeding of aquaculture species is becoming increasingly more common with the continued development of genome tools and reagents. Several laboratories have produced genetic maps for rainbow trout to aid in the identification of loci affecting phenotypes of interest. These maps have resulted in the identification of many quantitative/qualitative trait loci affecting phenotypic variation in traits associated with albinism, disease resistance, temperature tolerance, sex determination, embryonic development rate, spawning date, condition factor and growth. Unfortunately, the elucidation of the precise allelic variation and/or genes underlying phenotypic diversity has yet to be achieved in this species having low marker densities and lacking a whole genome reference sequence. Experimental designs which integrate segregation analyses with linkage disequilibrium (LD) approaches facilitate the discovery of genes affecting important traits. To date the extent of LD has been characterized for humans and several agriculturally important livestock species but not for rainbow trout. We observed that the level of LD between syntenic loci decayed rapidly at distances greater than 2 cM which is similar to observations of LD in other agriculturally important species including cattle, sheep, pigs and chickens. However, in some cases significant LD was also observed up to 50 cM. Our estimate of effective population size based on genome wide estimates of LD for the NCCCWA broodstock population was 145, indicating that this population will respond well to high selection intensity. However, the range of effective population size based on individual chromosomes was 75.51 - 203.35, possibly indicating that suites of genes on each chromosome are disproportionately under selection pressures. Our results indicate that large numbers of markers, more than are currently available for this species, will be required

  16. Population structure and effective/census population size ratio in threatened three-spined stickleback populations from an isolated river basin in northwest Spain.

    PubMed

    Pérez-Figueroa, A; Fernández, C; Amaro, R; Hermida, M; San Miguel, E

    2015-08-01

    Variability at 20 microsatellite loci was examined to assess the population genetic structure, gene flow, and effective population size (N(e)) in three populations of three-spined stickleback (Gasterosteus aculeatus) from the upper basin of the Miño River in Galicia, NW Spain, where this species is threatened. The three populations showed similar levels of genetic diversity. There is a significant genetic differentiation between the three populations, but also significant gene flow. N(e) estimates based on linkage disequilibrium yielded values of 355 for the Miño River population and 241 and 311 for the Rato and Guisande Rivers, respectively, although we expect that these are overestimates. N(e) estimates based on temporal methods, considering gene flow or not, for the tributaries yielded values of 30-56 and 47-56 for the Rato and Guisande Rivers, respectively. Estimated census size (N(c)) for the Rato River was 880 individuals. This yielded a N(e)/N(c) estimate of 3-6 % for temporal estimation of N(e), which is within the empirical range observed in freshwater fishes. We suggest that the three populations analyzed have a sufficient level of genetic diversity with some genetic structure. Additionally, the absence of physical barriers suggests that conservation efforts and monitoring should focus in the whole basin as a unit.

  17. Effects of Insecticide Exposure on Movement and Population Size Estimates of Predatory Ground Beetles (Coleoptera: Carabidae)

    USDA-ARS?s Scientific Manuscript database

    Population size estimates of arthropod predators and parasitoids may paradoxically increase following insecticide applications. Previous research with ground beetles (Coleoptera: Carabidae) suggests such unusual results reflect increased arthropod movement and capture in traps rather than real chang...

  18. Founder representation and effective population size in old versus young breeds-genetic diversity of Finnish and Nordic Spitz.

    PubMed

    Kumpulainen, M; Anderson, H; Svevar, T; Kangasvuo, I; Donner, J; Pohjoismäki, J

    2017-10-01

    Finnish Spitz is 130-year-old breed and has been highly popular in Finland throughout its history. Nordic Spitz is very similar to Finnish Spitz by origin and use, but is a relatively recent breed with much smaller population size. To see how breed age and breeding history have influenced the current population, we performed comprehensive population genetic analysis using pedigree data of 28,119 Finnish and 9,009 Nordic Spitzes combined with genomewide single nucleotide polymorphism (SNP) data from 135 Finnish and 110 Nordic Spitzes. We found that the Finnish Spitz has undergone repeated male bottlenecks resulting in dramatic loss of genetic diversity, reflected by 20 effective founders (fa ) and mean heterozygosity (Hz) of 0.313. The realized effective population size in the breed based on pedigree analysis (N¯ec) is 168, whereas the genetic effective population size (Neg ) computed the decay of linkage disequilibrium (r(2) ) is only 57 individuals. Nordic Spitz, although once been near extinction, has not been exposed to similar repeated bottlenecks than Finnish Spitz and had fa of 27 individuals. However, due to the smaller total population size, the breed has also smaller effective population size than Finnish Spitz (N¯ec = 98 and Neg  = 49). Interestingly, the r(2) data show that the effective population size has contracted dramatically since the establishment of the breed, emphasizing the role of breed standards as constrains for the breeding population. Despite the small population size, Nordic Spitz still maintains SNP heterozygosity levels similar to mixed breed dogs (mean Hz = 0.409). Our study demonstrates that although pedigree analyses cannot provide estimates of the present diversity within a breed, the effective population sizes inferred from them correlate with the genotyping results. The genetic relationships of the northern Spitz breeds and the benefits of the open breed registry are discussed. © 2017 Blackwell Verlag GmbH.

  19. Genome-wide linkage disequilibrium and past effective population size in three Korean cattle breeds.

    PubMed

    Sudrajad, P; Seo, D W; Choi, T J; Park, B H; Roh, S H; Jung, W Y; Lee, S S; Lee, J H; Kim, S; Lee, S H

    2017-02-01

    The routine collection and use of genomic data are useful for effectively managing breeding programs for endangered populations. Linkage disequilibrium (LD) using high-density DNA markers has been widely used to determine population structures and predict the genomic regions that are associated with economic traits in beef cattle. The extent of LD also provides information about historical events, including past effective population size (Ne ), and it allows inferences on the genetic diversity of breeds. The objective of this study was to estimate the LD and Ne in three Korean cattle breeds that are genetically similar but have different coat colors (Brown, Brindle and Jeju Black Hanwoo). Brindle and Jeju Black are endangered breeds with small populations, whereas Brown Hanwoo is the main breeding population in Korea. DNA samples from these cattle breeds were genotyped using the Illumina BovineSNP50 Bead Chip. We examined 13 cattle breeds, including European taurines, African taurines and indicines, and hybrids to compare their LD values. Brown Hanwoo consistently had the lowest mean LD compared to Jeju Black, Brindle and the other 13 cattle breeds (0.13, 0.19, 0.21 and 0.15-0.22 respectively). The high LD values of Brindle and Jeju Black contributed to small Ne values (53 and 60 respectively), which were distinct from that of Brown Hanwoo (531) for 11 generations ago. The differences in LD and Ne for each breed reflect the breeding strategy applied. The Ne for these endangered cattle breeds remain low; thus, effort is needed to bring them back to a sustainable tract. © 2016 Stichting International Foundation for Animal Genetics.

  20. Effective size and polymorphism of linked neutral loci in populations under directional selection.

    PubMed Central

    Santiago, E; Caballero, A

    1998-01-01

    The general theory of the effective size (Ne) for populations under directional selection is extended to cover linkage. Ne is a function of the association between neutral and selected genes generated by finite sampling. This association is reduced by three factors: the recombination rate, the reduction of genetic variance due to drift, and the reduction of genetic variance of the selected genes due to selection. If the genetic size of the genome (L in Morgans) is not extremely small the equation for Ne is [formula, see text] where N is the number of reproductive individuals, C 2 is the genetic variance for fitness scaled by the squared mean fitness, (1 - Z) = Vm/C2 is the rate of reduction of genetic variation per generation and Vm is the mutational input of genetic variation for fitness. The above predictive equation of Ne is valid for the infinitesimal model and for a model of detrimental mutations. The principles of the theory are also applicable to favorable mutation models if there is a continuous flux of advantageous mutations. The predictions are tested by simulation, and the connection with previous results is found and discussed. The reduction of effective size associated with a neutral mutation is progressive over generations until the asymptotic value (the above expression) is reached after a number of generations. The magnitude of the drift process is, therefore, smaller for recent neutral mutations than for old ones. This produces equilibrium values of average heterozygosity and proportion of segregating sites that cannot be formally predicted from the asymptotic Ne, but both parameters can still be predicted by following the drift along the lineage of genes. The spectrum of gene frequencies in a given generation can also be predicted by considering the overlapping of distributions corresponding to mutations that arose in different generations and with different associated effective sizes. PMID:9691062

  1. Z chromosome divergence, polymorphism and relative effective population size in a genus of lekking birds

    USGS Publications Warehouse

    Oyler-McCance, Sara J.; Cornman, Robert S.; Kenneth L. Jones,; Fike, Jennifer

    2015-01-01

    Sex chromosomes contribute disproportionately to species boundaries as they diverge faster than autosomes and often have reduced diversity. Their hemizygous nature contributes to faster divergence and reduced diversity, as do some types of selection. In birds, other factors (mating system and bottlenecks) can further decrease the effective population size of Z-linked loci and accelerate divergence (Fast-Z). We assessed Z-linked divergence and effective population sizes for two polygynous sage-grouse species and compared them to estimates from birds with various mating systems. We found lower diversity and higher FST for Z-linked loci than for autosomes, as expected. The πZ/πA ratio was 0.38 in Centrocercus minimus, 0.48 in Centrocercus urophasianus and 0.59 in a diverged, parapatric population of C. urophasianus, a broad range given the mating system among these groups is presumably equivalent. The full data set had unequal males and females across groups, so we compared an equally balanced reduced set of C. minimus and individuals pooled from both C. urophasianus subgroups recovering similar estimates: 0.54 for C. urophasianus and 0.38 for C. minimus. We provide further evidence that NeZ/NeA in birds is often lower than expected under random mating or monogamy. The lower ratio in C. minimus could be a consequence of stronger selection or drift acting on Z loci during speciation, as this species differs strongly from C. urophasianus in sexually selected characters with minimal mitochondrial divergence. As C. minimus also exhibited lower genomic diversity, it is possible that a more severe demographic history may contribute to its lower ratio.

  2. Z chromosome divergence, polymorphism and relative effective population size in a genus of lekking birds

    PubMed Central

    Oyler-McCance, S J; Cornman, R S; Jones, K L; Fike, J A

    2015-01-01

    Sex chromosomes contribute disproportionately to species boundaries as they diverge faster than autosomes and often have reduced diversity. Their hemizygous nature contributes to faster divergence and reduced diversity, as do some types of selection. In birds, other factors (mating system and bottlenecks) can further decrease the effective population size of Z-linked loci and accelerate divergence (Fast-Z). We assessed Z-linked divergence and effective population sizes for two polygynous sage-grouse species and compared them to estimates from birds with various mating systems. We found lower diversity and higher FST for Z-linked loci than for autosomes, as expected. The πZ/πA ratio was 0.38 in Centrocercus minimus, 0.48 in Centrocercus urophasianus and 0.59 in a diverged, parapatric population of C. urophasianus, a broad range given the mating system among these groups is presumably equivalent. The full data set had unequal males and females across groups, so we compared an equally balanced reduced set of C. minimus and individuals pooled from both C. urophasianus subgroups recovering similar estimates: 0.54 for C. urophasianus and 0.38 for C. minimus. We provide further evidence that NeZ/NeA in birds is often lower than expected under random mating or monogamy. The lower ratio in C. minimus could be a consequence of stronger selection or drift acting on Z loci during speciation, as this species differs strongly from C. urophasianus in sexually selected characters with minimal mitochondrial divergence. As C. minimus also exhibited lower genomic diversity, it is possible that a more severe demographic history may contribute to its lower ratio. PMID:26014526

  3. Z chromosome divergence, polymorphism and relative effective population size in a genus of lekking birds.

    PubMed

    Oyler-McCance, S J; Cornman, R S; Jones, K L; Fike, J A

    2015-11-01

    Sex chromosomes contribute disproportionately to species boundaries as they diverge faster than autosomes and often have reduced diversity. Their hemizygous nature contributes to faster divergence and reduced diversity, as do some types of selection. In birds, other factors (mating system and bottlenecks) can further decrease the effective population size of Z-linked loci and accelerate divergence (Fast-Z). We assessed Z-linked divergence and effective population sizes for two polygynous sage-grouse species and compared them to estimates from birds with various mating systems. We found lower diversity and higher FST for Z-linked loci than for autosomes, as expected. The π(Z)/π(A) ratio was 0.38 in Centrocercus minimus, 0.48 in Centrocercus urophasianus and 0.59 in a diverged, parapatric population of C. urophasianus, a broad range given the mating system among these groups is presumably equivalent. The full data set had unequal males and females across groups, so we compared an equally balanced reduced set of C. minimus and individuals pooled from both C. urophasianus subgroups recovering similar estimates: 0.54 for C. urophasianus and 0.38 for C. minimus. We provide further evidence that N(eZ)/N(eA) in birds is often lower than expected under random mating or monogamy. The lower ratio in C. minimus could be a consequence of stronger selection or drift acting on Z loci during speciation, as this species differs strongly from C. urophasianus in sexually selected characters with minimal mitochondrial divergence. As C. minimus also exhibited lower genomic diversity, it is possible that a more severe demographic history may contribute to its lower ratio.

  4. Quasi equilibrium, variance effective size and fixation index for populations with substructure.

    PubMed

    Hössjer, Ola; Ryman, Nils

    2014-11-01

    In this paper, we develop a method for computing the variance effective size N eV, the fixation index F ST and the coefficient of gene differentiation G ST of a structured population under equilibrium conditions. The subpopulation sizes are constant in time, with migration and reproduction schemes that can be chosen with great flexibility. Our quasi equilibrium approach is conditional on non-fixation of alleles. This is of relevance when migration rates are of a larger order of magnitude than the mutation rates, so that new mutations can be ignored before equilibrium balance between genetic drift and migration is obtained. The vector valued time series of subpopulation allele frequencies is divided into two parts; one corresponding to genetic drift of the whole population and one corresponding to differences in allele frequencies among subpopulations. We give conditions under which the first two moments of the latter, after a simple standardization, are well approximated by quantities that can be explicitly calculated. This enables us to compute approximations of the quasi equilibrium values of N eV, F ST and G ST. Our findings are illustrated for several reproduction and migration scenarios, including the island model, stepping stone models and a model where one subpopulation acts as a demographic reservoir. We also make detailed comparisons with a backward approach based on coalescence probabilities.

  5. Differences in the effective population sizes of males and females do not require differences in their distribution of offspring number.

    PubMed

    Mendez, Fernando L

    2017-04-01

    Difference in male and female effective population sizes has, at times, been attributed to both sexes having unequal variance in their number of offspring. Such difference is paralleled by the relative effective sizes of autosomes, sex chromosomes, and mitochondrial DNA. I develop a simple framework to calculate the inbreeding effective population sizes for loci with different modes of inheritance. In this framework, I separate the effects due to mating strategy and those due to genetic transmission. I then show that, in addition to differences in the variance in offspring number, skew in the male/female effective sizes can also be caused by family composition. This approach can be used to illustrate the effect of induced behaviors on the relative male and female effective population sizes. In particular, I show the impact of the one-child policy formerly implemented in the People's Republic of China on the relative male and female effective population sizes. Furthermore, I argue that, under some strong constraints on family structure, the concepts of male and female effective population sizes are invalid. Copyright © 2016 The Author. Published by Elsevier Inc. All rights reserved.

  6. Census (N C) and genetically effective (N e) population size in a lake-resident population of brown trout Salmo trutta.

    PubMed

    Charlier, J; Palmé, A; Laikre, L; Andersson, J; Ryman, N

    2011-12-01

    Census (N(C)) and effective population size (N(e)) were estimated for a lake-resident population of brown trout Salmo trutta as 576 and 63, respectively. The point estimate of the ratio of effective to census population size (N(e):N(C)) for this population is 0.11 with a range of 0.06-0.26, suggesting that N(e):N(C) ratio for lake-resident populations agree more with estimates for fishes with anadromous life histories than the small ratios observed in many marine fishes. © 2011 The Authors. Journal of Fish Biology © 2011 The Fisheries Society of the British Isles.

  7. Effects of population size and isolation on heterosis, mean fitness, and inbreeding depression in a perennial plant.

    PubMed

    Oakley, Christopher G; Winn, Alice A

    2012-10-01

    • In small isolated populations, genetic drift is expected to increase chance fixation of partly recessive, mildly deleterious mutations, reducing mean fitness and inbreeding depression within populations and increasing heterosis in outcrosses between populations. • We estimated relative effective sizes and migration among populations and compared mean fitness, heterosis, and inbreeding depression for eight large and eight small populations of a perennial plant on the basis of fitness of progeny produced by hand pollinations within and between populations. • Migration was limited, and, consistent with expectations for drift, mean fitness was 68% lower in small populations; heterosis was significantly greater for small (mean = 70%, SE = 14) than for large populations (mean = 7%, SE = 27); and inbreeding depression was lower, although not significantly so, in small (mean = -0.29%, SE = 28) than in large (mean = 0.28%, SE = 23) populations. • Genetic drift promotes fixation of deleterious mutations in small populations, which could threaten their persistence. Limited migration will exacerbate drift, but data on migration and effective population sizes in natural populations are scarce. Theory incorporating realistic variation in population size and patterns of migration could better predict genetic threats to small population persistence.

  8. Effects of feed intake on composition of sheep rumen contents and their microbial population size.

    PubMed

    Rodríguez, C A; González, J; Alvir, M R; Redondo, R; Cajarville, C

    2003-01-01

    The present study was conducted to determine the effect of feed intake on the composition of the rumen contents of sheep and on their bacterial densities. Whole rumen contents were sampled after a period of continuous inter-rumen infusion of 15NH3 from four rumen-cannulated wethers successively fed on a hay-concentrate diet (2:1, w/w on a DM basis) at two rates of feed intake: 40 and 80 g DM/kg body weight0.75. Total weight and chemical composition of rumen contents, as well as the distribution by size and chemical composition of particles, were determined. The populations of bacteria associated with the liquid (liquid-associated bacteria, LAB) and solid (solid-associated bacteria, SAB) fractions of rumen digesta and the distribution of SAB according to feed particle size were also examined. The greater feed intake caused an increase in the mass of the rumen contents, while its chemical composition did not change, except for a higher content of organic matter (P=0.023). The distribution of feed particles by size was similar at both levels of intake. The concentrations of neutral- and acid-detergent fibre in feed particles decreased and those of total, dietary, and microbial N increased, both with a quadratic response (P=0.001), as particle size decreased. The proportion of LAB in the microbial biomass of rumen digesta reached only 8.0 %. This proportion and the density of LAB were unaffected by the level of feed intake, whereas an apparent reduction (10.4 %) occurred with the SAB biomass in whole rumen contents. A systematic, but not significant, reduction (mean value 11.9 %) in the level of microbial colonisation in the different particle fractions with the increase of feed intake was also observed.

  9. Finite-size effects on bacterial population expansion under controlled flow conditions

    NASA Astrophysics Data System (ADS)

    Tesser, Francesca; Zeegers, Jos C. H.; Clercx, Herman J. H.; Brunsveld, Luc; Toschi, Federico

    2017-03-01

    The expansion of biological species in natural environments is usually described as the combined effect of individual spatial dispersal and growth. In the case of aquatic ecosystems flow transport can also be extremely relevant as an extra, advection induced, dispersal factor. We designed and assembled a dedicated microfluidic device to control and quantify the expansion of populations of E. coli bacteria under both co-flowing and counter-flowing conditions, measuring the front speed at varying intensity of the imposed flow. At variance with respect to the case of classic advective-reactive-diffusive chemical fronts, we measure that almost irrespective of the counter-flow velocity, the front speed remains finite at a constant positive value. A simple model incorporating growth, dispersion and drift on finite-size hard beads allows to explain this finding as due to a finite volume effect of the bacteria. This indicates that models based on the Fisher-Kolmogorov-Petrovsky-Piscounov equation (FKPP) that ignore the finite size of organisms may be inaccurate to describe the physics of spatial growth dynamics of bacteria.

  10. Finite-size effects on bacterial population expansion under controlled flow conditions.

    PubMed

    Tesser, Francesca; Zeegers, Jos C H; Clercx, Herman J H; Brunsveld, Luc; Toschi, Federico

    2017-03-06

    The expansion of biological species in natural environments is usually described as the combined effect of individual spatial dispersal and growth. In the case of aquatic ecosystems flow transport can also be extremely relevant as an extra, advection induced, dispersal factor. We designed and assembled a dedicated microfluidic device to control and quantify the expansion of populations of E. coli bacteria under both co-flowing and counter-flowing conditions, measuring the front speed at varying intensity of the imposed flow. At variance with respect to the case of classic advective-reactive-diffusive chemical fronts, we measure that almost irrespective of the counter-flow velocity, the front speed remains finite at a constant positive value. A simple model incorporating growth, dispersion and drift on finite-size hard beads allows to explain this finding as due to a finite volume effect of the bacteria. This indicates that models based on the Fisher-Kolmogorov-Petrovsky-Piscounov equation (FKPP) that ignore the finite size of organisms may be inaccurate to describe the physics of spatial growth dynamics of bacteria.

  11. Finite-size effects on bacterial population expansion under controlled flow conditions

    PubMed Central

    Tesser, Francesca; Zeegers, Jos C. H.; Clercx, Herman J. H.; Brunsveld, Luc; Toschi, Federico

    2017-01-01

    The expansion of biological species in natural environments is usually described as the combined effect of individual spatial dispersal and growth. In the case of aquatic ecosystems flow transport can also be extremely relevant as an extra, advection induced, dispersal factor. We designed and assembled a dedicated microfluidic device to control and quantify the expansion of populations of E. coli bacteria under both co-flowing and counter-flowing conditions, measuring the front speed at varying intensity of the imposed flow. At variance with respect to the case of classic advective-reactive-diffusive chemical fronts, we measure that almost irrespective of the counter-flow velocity, the front speed remains finite at a constant positive value. A simple model incorporating growth, dispersion and drift on finite-size hard beads allows to explain this finding as due to a finite volume effect of the bacteria. This indicates that models based on the Fisher-Kolmogorov-Petrovsky-Piscounov equation (FKPP) that ignore the finite size of organisms may be inaccurate to describe the physics of spatial growth dynamics of bacteria. PMID:28262769

  12. Effects of recruitment, growth, and exploitation on walleye population size structure in northern Wisconsin lakes

    USGS Publications Warehouse

    Hansen, Michael J.; Nate, Nancy A.

    2014-01-01

    We evaluated the dynamics of walleye Sander vitreus population size structure, as indexed by the proportional size distribution (PSD) of quality-length fish, in Escanaba Lake during 1967–2003 and in 204 other lakes in northern Wisconsin during 1990–2011. We estimated PSD from angler-caught walleyes in Escanaba Lake and from spring electrofishing in 204 other lakes, and then related PSD to annual estimates of recruitment to age-3, length at age 3, and annual angling exploitation rate. In Escanaba Lake during 1967–2003, annual estimates of PSD were highly dynamic, growth (positively) explained 35% of PSD variation, recruitment explained only 3% of PSD variation, and exploitation explained only 7% of PSD variation. In 204 other northern Wisconsin lakes during 1990–2011, PSD varied widely among lakes, recruitment (negatively) explained 29% of PSD variation, growth (positively) explained 21% of PSD variation, and exploitation explained only 4% of PSD variation. We conclude that population size structure was most strongly driven by recruitment and growth, rather than exploitation, in northern Wisconsin walleye populations. Studies of other species over wide spatial and temporal ranges of recruitment, growth, and mortality are needed to determine which dynamic rate most strongly influences population size structure of other species. Our findings indicate a need to be cautious about assuming exploitation is a strong driver of walleye population size structure.

  13. Population size, center-periphery, and seed dispersers' effects on the genetic diversity and population structure of the Mediterranean relict shrub Cneorum tricoccon.

    PubMed

    Lázaro-Nogal, Ana; Matesanz, Silvia; García-Fernández, Alfredo; Traveset, Anna; Valladares, Fernando

    2017-09-01

    The effect of population size on population genetic diversity and structure has rarely been studied jointly with other factors such as the position of a population within the species' distribution range or the presence of mutualistic partners influencing dispersal. Understanding these determining factors for genetic variation is critical for conservation of relict plants that are generally suffering from genetic deterioration. Working with 16 populations of the vulnerable relict shrub Cneorum tricoccon throughout the majority of its western Mediterranean distribution range, and using nine polymorphic microsatellite markers, we examined the effects of periphery (peripheral vs. central), population size (large vs. small), and seed disperser (introduced carnivores vs. endemic lizards) on the genetic diversity and population structure of the species. Contrasting genetic variation (HE: 0.04-0.476) was found across populations. Peripheral populations showed lower genetic diversity, but this was dependent on population size. Large peripheral populations showed high levels of genetic diversity, whereas small central populations were less diverse. Significant isolation by distance was detected, indicating that the effect of long-distance gene flow is limited relative to that of genetic drift, probably due to high selfing rates (FIS = 0.155-0.887), restricted pollen flow, and ineffective seed dispersal. Bayesian clustering also supported the strong population differentiation and highly fragmented structure. Contrary to expectations, the type of disperser showed no significant effect on either population genetic diversity or structure. Our results challenge the idea of an effect of periphery per se that can be mainly explained by population size, drawing attention to the need of integrative approaches considering different determinants of genetic variation. Furthermore, the very low genetic diversity observed in several small populations and the strong among-population

  14. A simple method of removing the effect of a bottleneck and unequal population sizes on pairwise genetic distances.

    PubMed Central

    Gaggiotti, O E; Excoffier, L

    2000-01-01

    In this paper, we derive the expectation of two popular genetic distances under a model of pure population fission allowing for unequal population sizes. Under the model, we show that conventional genetic distances are not proportional to the divergence time and generally overestimate it due to unequal genetic drift and to a bottleneck effect at the divergence time. This bias cannot be totally removed even if the present population sizes are known. Instead, we present a method to estimate the divergence times between populations which is based on the average number of nucleotide differences within and between populations. The method simultaneously estimates the divergence time, the ancestral population size and the relative sizes of the derived populations. A simulation study revealed that this method is essentially unbiased and that it leads to better estimates than traditional approaches for a very wide range of parameter values. Simulations also indicated that moderate population growth after divergence has little effect on the estimates of all three estimated parameters. An application of our method to a comparison of humans and chimpanzee mitochondrial DNA diversity revealed that common chimpanzees have a significantly larger female population size than humans. PMID:10670957

  15. Quantitative trait loci in pepper control the effective population size of two RNA viruses at inoculation.

    PubMed

    Tamisier, Lucie; Rousseau, Elsa; Barraillé, Sebastien; Nemouchi, Ghislaine; Szadkowski, Marion; Mailleret, Ludovic; Grognard, Frederic; Fabre, Frederic; Moury, Benoit; Palloix, Alain

    2017-07-01

    Infection of plants by viruses is a complex process involving several steps: inoculation into plant cells, replication in inoculated cells and plant colonization. The success of the different steps depends, in part, on the viral effective population size (Ne), defined as the number of individuals passing their genes to the next generation. During infection, the virus population will undergo bottlenecks, leading to drastic reductions in Ne and, potentially, to the loss of the fittest variants. Therefore, it is crucial to better understand how plants affect Ne. We aimed to (i) identify the plant genetic factors controlling Ne during inoculation, (ii) understand the mechanisms used by the plant to control Ne and (iii) compare these genetic factors with the genes controlling plant resistance to viruses. Ne was measured in a doubled-haploid population of Capsicum annuum. Plants were inoculated with either a Potato virus Y (PVY) construct expressing the green fluorescent protein or a necrotic variant of Cucumber mosaic virus (CMV). Newas assessed by counting the number of primary infection foci on cotyledons for PVY or the number of necrotic local lesions on leaves for CMV. The number of foci and lesions was correlated (r=0.57) and showed a high heritability (h2=0.93 for PVY and h2=0.98 for CMV). The Ne of the two viruses was controlled by both common quantitative trait loci (QTLs) and virus-specific QTLs, indicating the contribution of general and specific mechanisms. The PVY-specific QTL colocalizes with a QTL that reduces PVY accumulation and the capacity to break down a major-effect resistance gene.

  16. Effects of social organization, trap arrangement and density, sampling scale, and population density on bias in population size estimation using some common mark-recapture estimators

    PubMed Central

    Joshi, Amitabh; Vidya, T. N. C.

    2017-01-01

    Mark-recapture estimators are commonly used for population size estimation, and typically yield unbiased estimates for most solitary species with low to moderate home range sizes. However, these methods assume independence of captures among individuals, an assumption that is clearly violated in social species that show fission-fusion dynamics, such as the Asian elephant. In the specific case of Asian elephants, doubts have been raised about the accuracy of population size estimates. More importantly, the potential problem for the use of mark-recapture methods posed by social organization in general has not been systematically addressed. We developed an individual-based simulation framework to systematically examine the potential effects of type of social organization, as well as other factors such as trap density and arrangement, spatial scale of sampling, and population density, on bias in population sizes estimated by POPAN, Robust Design, and Robust Design with detection heterogeneity. In the present study, we ran simulations with biological, demographic and ecological parameters relevant to Asian elephant populations, but the simulation framework is easily extended to address questions relevant to other social species. We collected capture history data from the simulations, and used those data to test for bias in population size estimation. Social organization significantly affected bias in most analyses, but the effect sizes were variable, depending on other factors. Social organization tended to introduce large bias when trap arrangement was uniform and sampling effort was low. POPAN clearly outperformed the two Robust Design models we tested, yielding close to zero bias if traps were arranged at random in the study area, and when population density and trap density were not too low. Social organization did not have a major effect on bias for these parameter combinations at which POPAN gave more or less unbiased population size estimates. Therefore, the

  17. Effects of social organization, trap arrangement and density, sampling scale, and population density on bias in population size estimation using some common mark-recapture estimators.

    PubMed

    Gupta, Manan; Joshi, Amitabh; Vidya, T N C

    2017-01-01

    Mark-recapture estimators are commonly used for population size estimation, and typically yield unbiased estimates for most solitary species with low to moderate home range sizes. However, these methods assume independence of captures among individuals, an assumption that is clearly violated in social species that show fission-fusion dynamics, such as the Asian elephant. In the specific case of Asian elephants, doubts have been raised about the accuracy of population size estimates. More importantly, the potential problem for the use of mark-recapture methods posed by social organization in general has not been systematically addressed. We developed an individual-based simulation framework to systematically examine the potential effects of type of social organization, as well as other factors such as trap density and arrangement, spatial scale of sampling, and population density, on bias in population sizes estimated by POPAN, Robust Design, and Robust Design with detection heterogeneity. In the present study, we ran simulations with biological, demographic and ecological parameters relevant to Asian elephant populations, but the simulation framework is easily extended to address questions relevant to other social species. We collected capture history data from the simulations, and used those data to test for bias in population size estimation. Social organization significantly affected bias in most analyses, but the effect sizes were variable, depending on other factors. Social organization tended to introduce large bias when trap arrangement was uniform and sampling effort was low. POPAN clearly outperformed the two Robust Design models we tested, yielding close to zero bias if traps were arranged at random in the study area, and when population density and trap density were not too low. Social organization did not have a major effect on bias for these parameter combinations at which POPAN gave more or less unbiased population size estimates. Therefore, the

  18. GONe: software for estimating effective population size in species with generational overlap.

    PubMed

    Coombs, J A; Letcher, B H; Nislow, K H

    2012-01-01

    GONe is a user-friendly, Windows-based program for estimating effective size (N(e) ) in populations with overlapping generations. It uses the Jorde-Ryman modification to the temporal method to account for age structure in populations. This method requires estimates of age-specific survival and birth rate and allele frequencies measured in two or more consecutive cohorts. Allele frequencies are acquired by reading in genotypic data from files formatted for either GENEPOP or TEMPOFS. For each interval between consecutive cohorts, N(e) is estimated at each locus and over all loci. Furthermore, N(e) estimates are output for three different genetic drift estimators (F(s) , F(c) and F(k) ). Confidence intervals are derived from a chi-square distribution with degrees of freedom equal to the number of independent alleles. GONe has been validated over a wide range of N(e) values, and for scenarios where survival and birth rates differ between sexes, sex ratios are unequal and reproductive variances differ. GONe is freely available for download at https://bcrc.bio.umass.edu/pedigreesoftware/.

  19. GONe: Software for estimating effective population size in species with generational overlap

    USGS Publications Warehouse

    Coombs, J.A.; Letcher, B.H.; Nislow, K.H.

    2012-01-01

    GONe is a user-friendly, Windows-based program for estimating effective size (N e) in populations with overlapping generations. It uses the Jorde-Ryman modification to the temporal method to account for age structure in populations. This method requires estimates of age-specific survival and birth rate and allele frequencies measured in two or more consecutive cohorts. Allele frequencies are acquired by reading in genotypic data from files formatted for either GENEPOP or TEMPOFS. For each interval between consecutive cohorts, N e is estimated at each locus and over all loci. Furthermore, N e estimates are output for three different genetic drift estimators (F s, F c and F k). Confidence intervals are derived from a chi-square distribution with degrees of freedom equal to the number of independent alleles. GONe has been validated over a wide range of N e values, and for scenarios where survival and birth rates differ between sexes, sex ratios are unequal and reproductive variances differ. GONe is freely available for download at. ?? 2011 Blackwell Publishing Ltd.

  20. Effects of population size and selection intensity on responses to disruptive selection in Drosophila melangaster.

    PubMed

    Barker, J S; Karlsson, L J

    1974-10-01

    Disruptive selection for sternopleural bristle number with opportunity for random mating was done in the four treatment combinations of two population sizes (40 pairs and 8 pairs of selected parents) and two selection intensities (1 in 40 and 1 in 2). In each generation, matings among selected parents were observed in a mating chamber, and progeny collected separately from each female parent. In the high number, high selection intensity treatment, divergence between the high and low parts ceased about generation 11. The isolation index increased rapidly to generation 3, but then fluctuated to termination of the population at generation 17. The overall isolation index was significant, indicating a real tendency to assortative mating. The failure of the isolation index to increase after generation 3 was attributed to lower average mating fitness of high males (due to inbreeding) and reduced receptivity of low females (due to a homozygous lethal gene with a large effect on sternopleural bristle number in heterozygotes). In the two low number treatments, isolation indices fluctuated from generation to generation with no obvious trends, and none of the overall isolation indices were significantly different from zero. The high number, low selection intensity treatment showed very little divergence, and one of the replicates showed, in contrast with expectation and the high number, high selection intensity treatment, a significant tendency to disassortative mating. Intense disruptive selection may lead to assortative mating.

  1. Population bottleneck and effective size in Bonamia ostreae-resistant populations of Ostrea edulis as inferred by microsatellite markers.

    PubMed

    Launey, S; Barre, M; Gerard, A; Naciri-Graven, Y

    2001-12-01

    Genetic variability at five microsatellite loci was analysed in three hatchery-propagated populations of the flat oyster, Ostrea edulis. These populations were part of a selection programme for resistance to the protozoan parasite Bonamia ostreae and were produced by mass spawns, without control of the genealogy. Evidence for population bottlenecks and inbreeding was sought. A reduction in the number of alleles, mainly due to the loss of rare alleles, was observed in all selected populations, relative to the natural population from which they were derived. Heterozygote excesses were observed in two populations, and were attributed to substructuring of the population into a small number of families. Pedigree reconstruction showed that these two populations were produced by at most two spawning events involving a limited number of parents. Most individuals within these populations are half or full-sib, as shown by relatedness coefficients. The occurrence of population bottlenecks was supported by estimates of effective number of breeders derived by three methods: temporal variance in allelic frequencies, heterozygote excess, and a new method based on reduction in the number of alleles. The estimates from the different methods were consistent. The evidence for bottleneck and small effective number of breeders are expected to lead to increasing inbreeding, and have important consequences for the future management of the three O. edulis selected populations.

  2. Estimation of historical effective population size using linkage disequilibria with marker data.

    PubMed

    Corbin, L J; Liu, A Y H; Bishop, S C; Woolliams, J A

    2012-08-01

    Theory hypothesizes that the rate of decline in linkage disequilibrium (LD) as a function of distance between markers, measured by r(2), can be used to estimate effective population size (N(e)) and how it varies over time. The development of high-density genotyping makes feasible the application of this theory and has provided an impetus to improve predictions. This study considers the impact of several developments on the estimation of N(e) using both simulated and equine high-density single-nucleotide polymorphism data, when N(e) is assumed to be constant a priori and when it is not. In all models, estimates of N(e) were highly sensitive to thresholds imposed upon minor allele frequency (MAF) and to a priori assumptions on the expected r(2) for adjacent markers. Where constant N(e) was assumed a priori, then estimates with the lowest mean square error were obtained with MAF thresholds between 0.05 and 0.10, adjustment of r(2) for finite sample size, estimation of a [the limit for r(2) as recombination frequency (c) approaches 0] and relating N(e) to c (1 - c/2). The findings for predicting N(e) from models allowing variable N(e) were much less clear, apart from the desirability of correcting for finite sample size, and the lack of consistency in estimating recent N(e) (<7 generations) where estimates use data with large c. The theoretical conflicts over how estimation should proceed and uncertainty over where predictions might be expected to fit well suggest that the estimation of N(e) when it varies be carried out with extreme caution.

  3. On effect size.

    PubMed

    Kelley, Ken; Preacher, Kristopher J

    2012-06-01

    The call for researchers to report and interpret effect sizes and their corresponding confidence intervals has never been stronger. However, there is confusion in the literature on the definition of effect size, and consequently the term is used inconsistently. We propose a definition for effect size, discuss 3 facets of effect size (dimension, measure/index, and value), outline 10 corollaries that follow from our definition, and review ideal qualities of effect sizes. Our definition of effect size is general and subsumes many existing definitions of effect size. We define effect size as a quantitative reflection of the magnitude of some phenomenon that is used for the purpose of addressing a question of interest. Our definition of effect size is purposely more inclusive than the way many have defined and conceptualized effect size, and it is unique with regard to linking effect size to a question of interest. Additionally, we review some important developments in the effect size literature and discuss the importance of accompanying an effect size with an interval estimate that acknowledges the uncertainty with which the population value of the effect size has been estimated. We hope that this article will facilitate discussion and improve the practice of reporting and interpreting effect sizes. (c) 2012 APA, all rights reserved)

  4. Effect of sampling methods, effective population size and migration rate estimation in Glossina palpalis palpalis from Cameroon.

    PubMed

    Mélachio, Tanekou Tito Trésor; Njiokou, Flobert; Ravel, Sophie; Simo, Gustave; Solano, Philippe; De Meeûs, Thierry

    2015-07-01

    Human and animal trypanosomiases are two major constraints to development in Africa. These diseases are mainly transmitted by tsetse flies in particular by Glossina palpalis palpalis in Western and Central Africa. To set up an effective vector control campaign, prior population genetics studies have proved useful. Previous studies on population genetics of G. p. palpalis using microsatellite loci showed high heterozygote deficits, as compared to Hardy-Weinberg expectations, mainly explained by the presence of null alleles and/or the mixing of individuals belonging to several reproductive units (Wahlund effect). In this study we implemented a system of trapping, consisting of a central trap and two to four satellite traps around the central one to evaluate a possible role of the Wahlund effect in tsetse flies from three Cameroon human and animal African trypanosomiases foci (Campo, Bipindi and Fontem). We also estimated effective population sizes and dispersal. No difference was observed between the values of allelic richness, genetic diversity and Wright's FIS, in the samples from central and from satellite traps, suggesting an absence of Wahlund effect. Partitioning of the samples with Bayesian methods showed numerous clusters of 2-3 individuals as expected from a population at demographic equilibrium with two expected offspring per reproducing female. As previously shown, null alleles appeared as the most probable factor inducing these heterozygote deficits in these populations. Effective population sizes varied from 80 to 450 individuals while immigration rates were between 0.05 and 0.43, showing substantial genetic exchanges between different villages within a focus. These results suggest that the "suppression" with establishment of physical barriers may be the best strategy for a vector control campaign in this forest context.

  5. The effect of EIF dynamics on the cryopreservation process of a size distributed cell population.

    PubMed

    Fadda, S; Briesen, H; Cincotti, A

    2011-06-01

    Typical mathematical modeling of cryopreservation of cell suspensions assumes a thermodynamic equilibrium between the ice and liquid water in the extracellular solution. This work investigates the validity of this assumption by introducing a population balance approach for dynamic extracellular ice formation (EIF) in the absence of any cryo-protectant agent (CPA). The population balance model reflects nucleation and diffusion-limited growth in the suspending solution whose driving forces are evaluated in the relevant phase diagram. This population balance description of the extracellular compartment has been coupled to a model recently proposed in the literature [Fadda et al., AIChE Journal, 56, 2173-2185, (2010)], which is capable of quantitatively describing and predicting internal ice formation (IIF) inside the cells. The cells are characterized by a size distribution (i.e. through another population balance), thus overcoming the classic view of a population of identically sized cells. From the comparison of the system behavior in terms of the dynamics of the cell size distribution it can be concluded that the assumption of a thermodynamic equilibrium in the extracellular compartment is not always justified. Depending on the cooling rate, the dynamics of EIF needs to be considered. Copyright © 2011 Elsevier Inc. All rights reserved.

  6. Estimating the Effective Population Size from Temporal Allele Frequency Changes in Experimental Evolution

    PubMed Central

    Jónás, Ágnes; Taus, Thomas; Kosiol, Carolin; Schlötterer, Christian; Futschik, Andreas

    2016-01-01

    The effective population size (Ne) is a major factor determining allele frequency changes in natural and experimental populations. Temporal methods provide a powerful and simple approach to estimate short-term Ne. They use allele frequency shifts between temporal samples to calculate the standardized variance, which is directly related to Ne. Here we focus on experimental evolution studies that often rely on repeated sequencing of samples in pools (Pool-seq). Pool-seq is cost-effective and often outperforms individual-based sequencing in estimating allele frequencies, but it is associated with atypical sampling properties: Additional to sampling individuals, sequencing DNA in pools leads to a second round of sampling, which increases the variance of allele frequency estimates. We propose a new estimator of Ne, which relies on allele frequency changes in temporal data and corrects for the variance in both sampling steps. In simulations, we obtain accurate Ne estimates, as long as the drift variance is not too small compared to the sampling and sequencing variance. In addition to genome-wide Ne estimates, we extend our method using a recursive partitioning approach to estimate Ne locally along the chromosome. Since the type I error is controlled, our method permits the identification of genomic regions that differ significantly in their Ne estimates. We present an application to Pool-seq data from experimental evolution with Drosophila and provide recommendations for whole-genome data. The estimator is computationally efficient and available as an R package at https://github.com/ThomasTaus/Nest. PMID:27542959

  7. Effective population size does not predict codon usage bias in mammals

    PubMed Central

    Kessler, Michael D; Dean, Matthew D

    2014-01-01

    Synonymous codons are not used at equal frequency throughout the genome, a phenomenon termed codon usage bias (CUB). It is often assumed that interspecific variation in the intensity of CUB is related to species differences in effective population sizes (Ne), with selection on CUB operating less efficiently in species with small Ne. Here, we specifically ask whether variation in Ne predicts differences in CUB in mammals and report two main findings. First, across 41 mammalian genomes, CUB was not correlated with two indirect proxies of Ne (body mass and generation time), even though there was statistically significant evidence of selection shaping CUB across all species. Interestingly, autosomal genes showed higher codon usage bias compared to X-linked genes, and high-recombination genes showed higher codon usage bias compared to low recombination genes, suggesting intraspecific variation in Ne predicts variation in CUB. Second, across six mammalian species with genetic estimates of Ne (human, chimpanzee, rabbit, and three mouse species: Mus musculus, M. domesticus, and M. castaneus), Ne and CUB were weakly and inconsistently correlated. At least in mammals, interspecific divergence in Ne does not strongly predict variation in CUB. One hypothesis is that each species responds to a unique distribution of selection coefficients, confounding any straightforward link between Ne and CUB. PMID:25505518

  8. Effect of group size on parasitism in a natural population of the Baltimore checkerspot Euphydryas phaeton.

    PubMed

    Stamp, Nancy E

    1981-05-01

    The effect of group size of early instars on parasitism of Euphydryas phaeton (Nymphalidae) was examined. Different numbers of larvae were stocked per web to determine the effect of group size on parasitism. Larval aggregations of moderate size (the size occurring naturally) had the least parasitism. Larger larval groups had a disproportionately high rate of parasitism. The major larval parasitoids located vulnerable larvae within webs, instead of attacking larvae available on the outside of webs. Parasitism rates were similar for larvae of damaged and undamaged webs, a consequence of the behavior and location of larvae in the webs. Lower limit to group size was a function of facilitation of larval numbers in reaching the first feeding site, the top of the host plant. Feeding facilitation by larval aggregations was not a factor in larval survival or growth.

  9. Estimating Divergence Time and Ancestral Effective Population Size of Bornean and Sumatran Orangutan Subspecies Using a Coalescent Hidden Markov Model

    PubMed Central

    Mailund, Thomas; Dutheil, Julien Y.; Hobolth, Asger; Lunter, Gerton; Schierup, Mikkel H.

    2011-01-01

    Due to genetic variation in the ancestor of two populations or two species, the divergence time for DNA sequences from two populations is variable along the genome. Within genomic segments all bases will share the same divergence—because they share a most recent common ancestor—when no recombination event has occurred to split them apart. The size of these segments of constant divergence depends on the recombination rate, but also on the speciation time, the effective population size of the ancestral population, as well as demographic effects and selection. Thus, inference of these parameters may be possible if we can decode the divergence times along a genomic alignment. Here, we present a new hidden Markov model that infers the changing divergence (coalescence) times along the genome alignment using a coalescent framework, in order to estimate the speciation time, the recombination rate, and the ancestral effective population size. The model is efficient enough to allow inference on whole-genome data sets. We first investigate the power and consistency of the model with coalescent simulations and then apply it to the whole-genome sequences of the two orangutan sub-species, Bornean (P. p. pygmaeus) and Sumatran (P. p. abelii) orangutans from the Orangutan Genome Project. We estimate the speciation time between the two sub-species to be thousand years ago and the effective population size of the ancestral orangutan species to be , consistent with recent results based on smaller data sets. We also report a negative correlation between chromosome size and ancestral effective population size, which we interpret as a signature of recombination increasing the efficacy of selection. PMID:21408205

  10. Effects of season and population size on pollination and reproductive output in a Mediterranean shrub.

    PubMed

    Sánchez, A M; Rodríguez, M; Albert, M J; Escudero, A

    2017-05-01

    Pollinator guilds may change throughout extended flowering periods, affecting plant reproductive output, especially in seasonal climates. We hypothesised a seasonal shift in pollinator guild and an autumn reduction in pollinator abundance, especially in small and sparse populations. We recorded pollinator identity, abundance and behaviour in relation to flower density from plant to population throughout the extended flowering of Ononis tridentata. We evaluated female reproductive output by recording pollination success and pre-dispersal seed predation in eight populations of contrasting size and density. Offspring quality was also characterised through seed weight and germination. A diverse guild of insects visited O. tridentata in spring, while only Apis mellifera was observed in autumn. Visitation frequency did not vary seasonally, but the number of flowers per foraging bout was lower, and seeds were heavier and had a higher germination rate in autumn. Plant and neighbourhood flowering display were not related to pollinator visitation frequency or behaviour. However, the rate of fertilised ovules, seed set and autumn flowering display size were positively related to population density. The maintenance of pollination in autumn enhances the reproductive performance of O. tridentata due to higher quality of autumn seed, and to a large reduction in seed predator pressure. We also suggest that observed changes in pollinator behaviour could be one of the processes behind seasonal variation in seed performance, since geitonogamous crosses were less likely to occur in autumn.

  11. The history of effective population size and genetic diversity in the Yellowstone grizzly (Ursus arctos): implications for conservation.

    PubMed

    Miller, Craig R; Waits, Lisette P

    2003-04-01

    Protein, mtDNA, and nuclear microsatellite DNA analyses have demonstrated that the Yellowstone grizzly bear has low levels of genetic variability compared with other Ursus arctos populations. Researchers have attributed this difference to inbreeding during a century of anthropogenic isolation and population size reduction. We test this hypothesis and assess the seriousness of genetic threats by generating microsatellite data for 110 museum specimens collected between 1912 and 1981. A loss of variability is detected, but it is much less severe than hypothesized. Variance in allele frequencies over time is used to estimate an effective population size of approximately 80 across the 20th century and >100 currently. The viability of the population is unlikely to be substantially reduced by genetic factors in the next several generations. However, gene flow from outside populations will be beneficial in avoiding inbreeding and the erosion of genetic diversity in the future.

  12. Effective population sizes in cattle, sheep, horses, pigs and goats estimated from census and herdbook data.

    PubMed

    Hall, S J G

    2016-11-01

    Accurate measures of effective population sizes (Ne ) in livestock require good quality data and specialized skills for their computation and analysis. Ne can be estimated by Wright's equation Ne =4MF/(M+ F) (M, F being sires and dams, respectively), but this requires assumptions which are often not met. Total census sizes Nc of livestock breeds are collated globally. This paper investigates whether estimates of Ne can be made from Nc ; this would facilitate conservation monitoring. Some Ne methodologies avoid the assumptions of Wright's equation and permit measurement, rather than estimation, of Ne . Those considered here employ, respectively, linkage disequilibrium (LD) of single-nucleotide polymorphisms (yielding Ne (LD)), and genealogical analysis (rate of increase of inbreeding, DF), yielding Ne (DF). Considering breeds of cattle, sheep, horses, pigs and goats for which Nc and either Ne (LD) or N e(DF) are known (totals of 203 breeds and 321 breeds, respectively), proportionality has been investigated between Nc and these measures of Ne . Ne (LD) was found to increase with Nc , significantly in sheep and horses, less so in cattle, but not at all in pigs. Ne (DF) was correlated with log10(Nc ) in cattle, sheep and horses (53, 56, 43 breeds, respectively). Ne (LD) was correlated in cattle (73 breeds) and pigs (31 breeds) with the log10 transformation of Ne as calculated by Wright's equation. Further verification and refinement are needed, particularly of census data, but credible predictions of Ne are obtainable by applying the following multipliers to log10(Nc ): cattle 17.61, sheep 97.72, horse 70.78. For cattle and pigs, multiplying log10(Ne (Wright)) by, respectively, 40.69 and 60.09, also gives credible predictions. Such census-based estimates of Ne could in principle be generated by non-specialists and are likely to be suited to audits of conservation activity when financial resources or availability of data are limiting. The ratio Ne /Nc varied among

  13. New Nuclear SNP Markers Unravel the Genetic Structure and Effective Population Size of Albacore Tuna (Thunnus alalunga)

    PubMed Central

    Laconcha, Urtzi; Iriondo, Mikel; Arrizabalaga, Haritz; Manzano, Carmen; Markaide, Pablo; Montes, Iratxe; Zarraonaindia, Iratxe; Velado, Igor; Bilbao, Eider; Goñi, Nicolas; Santiago, Josu; Domingo, Andrés; Karakulak, Saadet; Oray, Işık; Estonba, Andone

    2015-01-01

    In the present study we have investigated the population genetic structure of albacore (Thunnus alalunga, Bonnaterre 1788) and assessed the loss of genetic diversity, likely due to overfishing, of albacore population in the North Atlantic Ocean. For this purpose, 1,331 individuals from 26 worldwide locations were analyzed by genotyping 75 novel nuclear SNPs. Our results indicated the existence of four genetically homogeneous populations delimited within the Mediterranean Sea, the Atlantic Ocean, the Indian Ocean and the Pacific Ocean. Current definition of stocks allows the sustainable management of albacore since no stock includes more than one genetic entity. In addition, short- and long-term effective population sizes were estimated for the North Atlantic Ocean albacore population, and results showed no historical decline for this population. Therefore, the genetic diversity and, consequently, the adaptive potential of this population have not been significantly affected by overfishing. PMID:26090851

  14. New Nuclear SNP Markers Unravel the Genetic Structure and Effective Population Size of Albacore Tuna (Thunnus alalunga).

    PubMed

    Laconcha, Urtzi; Iriondo, Mikel; Arrizabalaga, Haritz; Manzano, Carmen; Markaide, Pablo; Montes, Iratxe; Zarraonaindia, Iratxe; Velado, Igor; Bilbao, Eider; Goñi, Nicolas; Santiago, Josu; Domingo, Andrés; Karakulak, Saadet; Oray, Işık; Estonba, Andone

    2015-01-01

    In the present study we have investigated the population genetic structure of albacore (Thunnus alalunga, Bonnaterre 1788) and assessed the loss of genetic diversity, likely due to overfishing, of albacore population in the North Atlantic Ocean. For this purpose, 1,331 individuals from 26 worldwide locations were analyzed by genotyping 75 novel nuclear SNPs. Our results indicated the existence of four genetically homogeneous populations delimited within the Mediterranean Sea, the Atlantic Ocean, the Indian Ocean and the Pacific Ocean. Current definition of stocks allows the sustainable management of albacore since no stock includes more than one genetic entity. In addition, short- and long-term effective population sizes were estimated for the North Atlantic Ocean albacore population, and results showed no historical decline for this population. Therefore, the genetic diversity and, consequently, the adaptive potential of this population have not been significantly affected by overfishing.

  15. Effect of reaction-step-size noise on the switching dynamics of stochastic populations

    NASA Astrophysics Data System (ADS)

    Be'er, Shay; Heller-Algazi, Metar; Assaf, Michael

    2016-05-01

    In genetic circuits, when the messenger RNA lifetime is short compared to the cell cycle, proteins are produced in geometrically distributed bursts, which greatly affects the cellular switching dynamics between different metastable phenotypic states. Motivated by this scenario, we study a general problem of switching or escape in stochastic populations, where influx of particles occurs in groups or bursts, sampled from an arbitrary distribution. The fact that the step size of the influx reaction is a priori unknown and, in general, may fluctuate in time with a given correlation time and statistics, introduces an additional nondemographic reaction-step-size noise into the system. Employing the probability-generating function technique in conjunction with Hamiltonian formulation, we are able to map the problem in the leading order onto solving a stationary Hamilton-Jacobi equation. We show that compared to the "usual case" of single-step influx, bursty influx exponentially decreases the population's mean escape time from its long-lived metastable state. In particular, close to bifurcation we find a simple analytical expression for the mean escape time which solely depends on the mean and variance of the burst-size distribution. Our results are demonstrated on several realistic distributions and compare well with numerical Monte Carlo simulations.

  16. Discriminating the effects of spatial extent and population size in cyclic competition among species.

    PubMed

    Lamouroux, D; Eule, S; Geisel, T; Nagler, J

    2012-08-01

    We introduce a population model for species under cyclic competition. This model allows individuals to coexist and interact on single cells while migration takes place between adjacent cells. In contrast to the model introduced by Reichenbach, Mobilia, and Frey [Reichenbach, Mobilia, and Frey, Nature (London) 448, 1046 (2007)], we find that the emergence of spirals results in an ambiguous behavior regarding the stability of coexistence. The typical time until extinction exhibits, however, a qualitatively opposite dependence on the newly introduced nonunit carrying capacity in the spiraling and the nonspiraling regimes. This allows us to determine a critical mobility that marks the onset of this spiraling state sharply. In contrast, we demonstrate that the conventional finite size stability analysis with respect to spatial size is of limited use for identifying the onset of the spiraling regime.

  17. Estimates of effective population size and inbreeding in South African indigenous chicken populations: implications for the conservation of unique genetic resources.

    PubMed

    Mtileni, Bohani; Dzama, Kennedy; Nephawe, Khathutshelo; Rhode, Clint

    2016-06-01

    Conservation of locally adapted indigenous livestock breeds has become an important objective in sustainable animal breeding, as these breeds represent a unique genetic resource. Therefore, the Agricultural Research Council of South Africa initiated a conservation programme for four South African indigenous chicken breeds. The evaluation and monitoring of the genetic constitution of these conservation flocks is important for proper management of the conservation programme. Using molecular genetic analyses, the effective population sizes and relatedness of these conservation flocks were compared to village (field) chicken populations from which they were derived. Genetic diversity within and between these populations are further discussed within the context of population size. The conservation flocks for the respective breeds had relatively small effective population sizes (point estimate range 38.6-78.6) in comparison to the field populations (point estimate range 118.9-580.0). Furthermore, evidence supports a transient heterozygous excess, generally associated with the occurrence of a recent population bottleneck. Genetic diversity, as measured by the number of alleles, heterozygosity and information index, was also significantly reduced in the conservation flocks. The average relatedness amongst the conservation flocks was high, whilst it remained low for the field populations. There was also significant evidence for population differentiation between field and conservation populations. F st estimates for conservation flocks were moderate to high with a maximum reached between VD_C and VD_F (0.285). However, F st estimates for field population were excessively low between the NN_C and EC_F (0.007) and between EC_F and OV_F (0.009). The significant population differentiation of the conservation flocks from their geographically correlated field populations of origin is further supported by the analysis of molecular variance (AMOVA), with 10.51 % of genetic

  18. Stock enhancement or sea ranching? Insights from monitoring the genetic diversity, relatedness and effective population size in a seeded great scallop population (Pecten maximus).

    PubMed

    Morvezen, R; Boudry, P; Laroche, J; Charrier, G

    2016-09-01

    The mass release of hatchery-propagated stocks raises numerous questions concerning its efficiency in terms of local recruitment and effect on the genetic diversity of wild populations. A seeding program, consisting of mass release of hatchery-produced juveniles in the local naturally occurring population of great scallops (Pecten maximus L.), was initiated in the early 1980s in the Bay of Brest (France). The present study aims at evaluating whether this seeding program leads to actual population enhancement, with detectable effects on genetic diversity and effective population size, or consists of sea ranching with limited genetic consequences on the wild stock. To address this question, microsatellite-based genetic monitoring of three hatchery-born and naturally recruited populations was conducted over a 5-year period. Results showed a limited reduction in allelic richness but a strong alteration of allelic frequencies in hatchery populations, while genetic diversity appeared very stable over time in the wild populations. A temporal increase in relatedness was observed in both cultured stock and wild populations. Effective population size (Ne) estimates were low and variable in the wild population. Moreover, the application of the Ryman-Laikre model suggested a high contribution of hatchery-born scallops to the reproductive output of the wild population. Overall, the data suggest that the main objective of the seeding program, which is stock enhancement, is fulfilled. Moreover, gene flow from surrounding populations and/or the reproductive input of undetected sub-populations within the bay may buffer the Ryman-Laikre effect and ensure the retention of the local genetic variability.

  19. Equilibrium Strategy and Population-Size Effects in Lowest Unique Bid Auctions

    NASA Astrophysics Data System (ADS)

    Pigolotti, Simone; Bernhardsson, Sebastian; Juul, Jeppe; Galster, Gorm; Vivo, Pierpaolo

    2012-02-01

    In lowest unique bid auctions, N players bid for an item. The winner is whoever places the lowest bid, provided that it is also unique. We use a grand canonical approach to derive an analytical expression for the equilibrium distribution of strategies. We then study the properties of the solution as a function of the mean number of players, and compare them with a large data set of internet auctions. The theory agrees with the data with striking accuracy for small population-size N, while for larger N a qualitatively different distribution is observed. We interpret this result as the emergence of two different regimes, one in which adaptation is feasible and one in which it is not. Our results question the actual possibility of a large population to adapt and find the optimal strategy when participating in a collective game.

  20. On Being the Right Size: The Impact of Population Size and Stochastic Effects on the Evolution of Drug Resistance in Hospitals and the Community

    PubMed Central

    Bonhoeffer, Sebastian

    2011-01-01

    The evolution of drug resistant bacteria is a severe public health problem, both in hospitals and in the community. Currently, some countries aim at concentrating highly specialized services in large hospitals in order to improve patient outcomes. Emergent resistant strains often originate in health care facilities, but it is unknown to what extent hospital size affects resistance evolution and the resulting spillover of hospital-associated pathogens to the community. We used two published datasets from the US and Ireland to investigate the effects of hospital size and controlled for several confounders such as antimicrobial usage, sampling frequency, mortality, disinfection and length of stay. The proportion of patients acquiring both sensitive and resistant infections in a hospital strongly correlated with hospital size. Moreover, we observe the same pattern for both the percentage of resistant infections and the increase of hospital-acquired infections over time. One interpretation of this pattern is that chance effects in small hospitals impede the spread of drug-resistance. To investigate to what extent the size distribution of hospitals can directly affect the prevalence of antibiotic resistance, we use a stochastic epidemiological model describing the spread of drug resistance in a hospital setting as well as the interaction between one or several hospitals and the community. We show that the level of drug resistance typically increases with population size: In small hospitals chance effects cause large fluctuations in pathogen population size or even extinctions, both of which impede the acquisition and spread of drug resistance. Finally, we show that indirect transmission via environmental reservoirs can reduce the effect of hospital size because the slow turnover in the environment can prevent extinction of resistant strains. This implies that reducing environmental transmission is especially important in small hospitals, because such a reduction not only

  1. Effect of population structure and size on aggregation behavior of Cimex lectularius (Hemiptera: Cimicidae).

    PubMed

    Pfiester, Margie; Koehler, Philip G; Pereira, Roberto M

    2009-09-01

    The bed bug, Cimex lectularius L. (Hemiptera: Cimicidae), occurs in aggregations until the conditions are no longer beneficial, leading to dispersal. Active and passive bed bug dispersal causes migrations from main aggregations either within a room, from room to room within a building, or from building to building. Because bed bug movement is an important factor in the spread of infestations, we wanted to determine how population structure and size affect bed bug aggregations. Engorged bed bugs were placed in glass petri dish arenas at varying densities, sex ratios, and population compositions. Nymphs had a high tendency to aggregate, varying between 94 and 98%, and therefore were not the likely dispersal stage of the bed bug. At densities of 10 and 40 adults at a 1:1 sex ratio, there were significantly more lone females than lone males. When the population composition was varied, the percentage of lone females was significantly higher than that of males and nymphs at population compositions of 40 and 80% adults. When the sex ratio of adults was varied, there were significantly more lone females than males in arenas with 20, 50, and 80% males. Females, being found away from aggregations significantly more often than any other life stage, are potentially the dispersal stage of the bed bug. Active female dispersal away from main aggregations can potentially lead to treatment failures and should be taken into account when using control methods.

  2. Sociocultural Behavior, Sex-Biased Admixture, and Effective Population Sizes in Central African Pygmies and Non-Pygmies

    PubMed Central

    Verdu, Paul; Becker, Noémie S.A.; Froment, Alain; Georges, Myriam; Grugni, Viola; Quintana-Murci, Lluis; Hombert, Jean-Marie; Van der Veen, Lolke; Le Bomin, Sylvie; Bahuchet, Serge; Heyer, Evelyne; Austerlitz, Frédéric

    2013-01-01

    Sociocultural phenomena, such as exogamy or phylopatry, can largely determine human sex-specific demography. In Central Africa, diverging patterns of sex-specific genetic variation have been observed between mobile hunter–gatherer Pygmies and sedentary agricultural non-Pygmies. However, their sex-specific demography remains largely unknown. Using population genetics and approximate Bayesian computation approaches, we inferred male and female effective population sizes, sex-specific migration, and admixture rates in 23 Central African Pygmy and non-Pygmy populations, genotyped for autosomal, X-linked, Y-linked, and mitochondrial markers. We found much larger effective population sizes and migration rates among non-Pygmy populations than among Pygmies, in agreement with the recent expansions and migrations of non-Pygmies and, conversely, the isolation and stationary demography of Pygmy groups. We found larger effective sizes and migration rates for males than for females for Pygmies, and vice versa for non-Pygmies. Thus, although most Pygmy populations have patrilocal customs, their sex-specific genetic patterns resemble those of matrilocal populations. In fact, our results are consistent with a lower prevalence of polygyny and patrilocality in Pygmies compared with non-Pygmies and a potential female transmission of reproductive success in Pygmies. Finally, Pygmy populations showed variable admixture levels with the non-Pygmies, with often much larger introgression from male than from female lineages. Social discrimination against Pygmies triggering complex movements of spouses in intermarriages can explain these male-biased admixture patterns in a patrilocal context. We show how gender-related sociocultural phenomena can determine highly variable sex-specific demography among populations, and how population genetic approaches contrasting chromosomal types allow inferring detailed human sex-specific demographic history. PMID:23300254

  3. Genetic estimates of contemporary effective population size in an endangered butterfly indicate a possible role for genetic compensation.

    PubMed

    Saarinen, Emily V; Austin, James D; Daniels, Jaret C

    2010-01-01

    The effective population size (N e ) is a critical evolutionary and conservation parameter that can indicate the adaptive potential of populations. Robust estimates of N e of endangered taxa have been previously hampered by estimators that are sensitive to sample size. We estimated N e on two remaining populations of the endangered Miami blue butterfly, a formerly widespread taxon in Florida. Our goal was to determine the consistency of various temporal and point estimators on inferring N e and to determine the utility of this information for understanding the role of genetic stochasticity. We found that recently developed 'unbiased estimators' generally performed better than some older methods in that the former had more realistic N e estimates and were more consistent with what is known about adult population size. Overall, N e /N ratios based on census point counts were high. We suggest that this pattern may reflect genetic compensation caused by reduced reproductive variance due to breeding population size not being limited by resources. Assuming N e and N are not heavily biased, it appears that the lack of gene flow between distant populations may be a greater genetic threat in the short term than the loss of heterozygosity due to inbreeding.

  4. Genetic estimates of contemporary effective population size in an endangered butterfly indicate a possible role for genetic compensation

    PubMed Central

    Saarinen, Emily V; Austin, James D; Daniels, Jaret C

    2010-01-01

    The effective population size (Ne) is a critical evolutionary and conservation parameter that can indicate the adaptive potential of populations. Robust estimates of Ne of endangered taxa have been previously hampered by estimators that are sensitive to sample size. We estimated Ne on two remaining populations of the endangered Miami blue butterfly, a formerly widespread taxon in Florida. Our goal was to determine the consistency of various temporal and point estimators on inferring Ne and to determine the utility of this information for understanding the role of genetic stochasticity. We found that recently developed ‘unbiased estimators’ generally performed better than some older methods in that the former had more realistic Ne estimates and were more consistent with what is known about adult population size. Overall, Ne/N ratios based on census point counts were high. We suggest that this pattern may reflect genetic compensation caused by reduced reproductive variance due to breeding population size not being limited by resources. Assuming Ne and N are not heavily biased, it appears that the lack of gene flow between distant populations may be a greater genetic threat in the short term than the loss of heterozygosity due to inbreeding. PMID:25567901

  5. Assessing effective population size, coancestry and inbreeding effects on litter size using the pedigree and SNP data in closed lines of the Iberian pig breed.

    PubMed

    Silió, L; Barragán, C; Fernández, A I; García-Casco, J; Rodríguez, M C

    2016-04-01

    The complete pedigree of two closed Iberian pig lines (Gamito and Torbiscal), with 798 and 4077 reproducers, has been used to measure the evolution of coancestry (f) and inbreeding (F) for autosomal and X-linked genes along 16 and 28 respective equivalent discrete generations. At the last generation, the mean values of each line were f = 0.41 and 0.22, F = 0.35 and 0.18, fX  = 0.46 and 0.22 and FX  = 0.47 and 0.19, respectively. Other calculated parameters were the effective number of founders (final values, 6.8 and 35.2) and non-founders (1.5 and 2.4), founder genome equivalents (1.2 and 2.3) and effective population size (16.0 and 57.7). Measures of Torbiscal effective size based on rates of coancestry (66.1), inbreeding (65.0) and linkage disequilibrium (71.0) were estimated from whole-genome SNP genotyping data. Values of new and old inbreeding and their respective rates by generation were computed to detect purging effects of natural selection. The analysis of 6854 Torbiscal litters showed significant negative impacts of new and fast inbreeding on litter size, as expected from the purging hypothesis: -0.20 born piglets per litter by a 10% of new inbreeding, and -0.03 and -0.02 piglets by 1% of total and new inbreeding rates, respectively. The analysis performed on 1274 litters of the Gamito line failed to show purging effects. The only significant results were reductions in -0.91 and -0.17 piglets by a 10% of old and X-linked genes inbreeding, respectively. These results may be useful for some practical issues in conservation programs of farm or captive wild animals. © 2015 Blackwell Verlag GmbH.

  6. Examining the Role of Effective Population Size on Mitochondrial and Multilocus Divergence Time Discordance in a Songbird

    PubMed Central

    Smith, Brian Tilston; Klicka, John

    2013-01-01

    Estimates of speciation times are subject to a number of potential errors. One source of bias is that effective population size (Ne) has been shown to influence substitution rates. This issue is of particular interest for phylogeographic studies because population sizes can vary dramatically among genetically structured populations across species’ ranges. In this study, we used multilocus data to examine temporal phylogeographic patterns in a widespread North American songbird, the Northern Cardinal (Cardinalis cardinalis). Species tree estimation indicated that the phylogeographic structure of C. cardinalis was comprised of four well-supported mainland lineages with large population sizes (large Ne) and two island lineages comprised of much smaller populations (small Ne). We inferred speciation times from mtDNA and multilocus data and found there was discordance between events that represented island-mainland divergences, whereas both estimates were similar for divergences among mainland lineages. We performed coalescent simulations and found that the difference in speciation times could be attributed to stochasticity for a recently diverged island lineage. However, the magnitude of the change between speciation times estimated from mtDNA and multilocus data of an older island lineage was substantially greater than predicted by coalescent simulations. For this divergence, we found the discordance in time estimates was due to a substantial increase in the mtDNA substitution rate in the small island population. These findings indicate that in phylogeographic studies the relative tempo of evolution between mtDNA and nuclear DNA can become highly discordant in small populations. PMID:23457463

  7. Effect of rotational disruption on the size-frequency distribution of the Main Belt asteroid population

    NASA Astrophysics Data System (ADS)

    Jacobson, Seth A.; Marzari, Francesco; Rossi, Alessandro; Scheeres, Daniel J.; Davis, Donald R.

    2014-03-01

    The size distribution of small asteroids in the Main Belt is assumed to be determined by an equilibrium between the creation of new bodies out of the impact debris of larger asteroids and the destruction of small asteroids by collisions with smaller projectiles. However, for a diameter less than 6 km, we find that YORP-induced rotational disruption significantly contributes to the erosion even exceeding the effects of collisional fragmentation. Including this additional grinding mechanism in a collision evolution model for the asteroid belt, we generate size-frequency distributions from either an accretional or an `Asteroids were born big' initial size-frequency distribution that are consistent with observations reported in Gladman et al. Rotational disruption is a new mechanism that must be included in all future collisional evolution models of asteroids.

  8. Reduced microsatellite heterozygosity in island endemics supports the role of long-term effective population size in avian microsatellite diversity

    PubMed Central

    2011-01-01

    Because of the high mutation rate of microsatellites, polymorphism at microsatellite loci might be predicted to reflect the effective population size over a time span of about 10,000 years and thus to be associated with biogeographic factors impacting species on that time frame. This prediction was tested by comparing heterozygosity at microsatellite loci from 294 bird species, including 58 species endemic to oceanic islands. Controlling statistically for phylogenetic effects, mean heterozygosity was significantly reduced in oceanic island endemics compared to other species. There was also an effect of current endangerment, statistically independent of the effect of island endemicity. These results support the hypothesis that long-term effective population size can be an important causative factor behind differences among species with respect to microsatellite heterozygosity. PMID:21104002

  9. Genetic diversity of four Filipino negrito populations from Luzon: comparison of male and female effective population sizes and differential integration of immigrants into Aeta and Agta communities.

    PubMed

    Heyer, E; Georges, M; Pachner, M; Endicott, P

    2013-01-01

    Genetic data corresponding to four negrito populations (two Aeta and two Agta; n = 120) from the Luzon region of the Philippines have been analyzed. These data comprise mitochondrial DNA (mtDNA) hypervariable segment 1 haplotypes and haplogroups, Y-chromosome haplogroups and short tandem repeats (STRs), autosomal STRs, and X-chromosome STRs. The genetic diversity and structure of the populations were investigated at a local, regional, and interregional level. We found a high level of autosomal differentiation, combined with no significant reduction in diversity, consistent with long-term settlement of the Luzon region by the ancestors of the Agta and Aeta followed by reduced gene flow between these two ethnolinguistic groups. Collectively, the Aeta have a much higher ratio of female:male effective population size than do the Agta, a finding that supports phylogenetic analysis of their mtDNA and Y-chromosome haplogroups, which suggests different genetic sex-biased contributions from putative Austronesian source populations. We propose that factors of social organization that led to the reduction in Agta female effective population size may also be linked to the limited incorporation of female lineages associated with the settlement of the Philippines by Austronesian speakers; conversely, the reduction in Aeta male effective population size, relative to females, could be indicative of a limited incorporation of male lineages associated with this demographic process. Copyright © 2013 Wayne State University Press, Detroit, Michigan 48201-1309.

  10. Effects of positive interactions, size symmetry of competition and abiotic stress on self-thinning in simulated plant populations

    PubMed Central

    Chu, Cheng-Jin; Weiner, Jacob; Maestre, Fernando T.; Wang, You-Shi; Morris, Charles; Xiao, Sa; Yuan, Jian-Li; Du, Guo-Zhen; Wang, Gang

    2010-01-01

    Background and Aims Competition drives self-thinning (density-dependent mortality) in crowded plant populations. Facilitative interactions have been shown to affect many processes in plant populations and communities, but their effects on self-thinning trajectories have not been investigated. Methods Using an individual-based ‘zone-of-influence’ model, we studied the potential effects of the size symmetry of competition, abiotic stress and facilitation on self-thinning trajectories in plant monocultures. In the model, abiotic stress reduced the growth of all individuals and facilitation ameliorated the effects of stress on interacting individuals. Key Results Abiotic stress made the log biomass – log density relationship during self-thinning steeper, but this effect was reduced by positive interactions among individuals. Size-asymmetric competition also influenced the self-thinning slope. Conclusions Although competition drives self-thinning, its course can be affected by abiotic stress, facilitation and competitive symmetry. PMID:20643802

  11. The interacting effects of diversity and propagule pressure on early colonization and population size.

    PubMed

    Hedge, Luke H; Leung, Brian; O'Connor, Wayne A; Johnston, Emma L

    2014-01-01

    We are now beginning to understand the role of intraspecific diversity on fundamental ecological phenomena. There exists a paucity of knowledge, however, regarding how intraspecific, or genetic diversity, may covary with other important factors such as propagule pressure. A combination of theoretical modelling and experimentation was used to explore the way propagule pressure and genetic richness may interact. We compare colonization rates of the Australian bivalve Saccostrea glomerata (Gould 1885). We cross propagule size and genetic richness in a factorial design in order to examine the generalities of our theoretical model. Modelling showed that diversity and propagule pressure should generally interact synergistically when positive feedbacks occur (e.g. aggregation). The strength of genotype effects depended on propagule size, or the numerical abundance of arriving individuals. When propagule size was very small (<4 individuals), however, greater genetic richness unexpectedly reduced colonization. The probability of S. glomerata colonization was 76% in genetically rich, larger propagules, almost 39 percentage points higher than in genetically poor propagules of similar size. This pattern was not observed in less dense, smaller propagules. We predict that density-dependent interactions between larvae in the water column may explain this pattern.

  12. Alternative reproductive tactics increase effective population size and decrease inbreeding in wild Atlantic salmon

    PubMed Central

    Perrier, Charles; Normandeau, Éric; Dionne, Mélanie; Richard, Antoine; Bernatchez, Louis

    2014-01-01

    While nonanadromous males (stream-resident and/or mature male parr) contribute to reproduction in anadromous salmonids, little is known about their impacts on key population genetic parameters. Here, we evaluated the contribution of Atlantic salmon mature male parr to the effective number of breeders (Nb) using both demographic (variance in reproductive success) and genetic (linkage disequilibrium) methods, the number of alleles, and the relatedness among breeders. We used a recently published pedigree reconstruction of a wild anadromous Atlantic salmon population in which 2548 fry born in 2010 were assigned parentage to 144 anadromous female and 101 anadromous females that returned to the river to spawn in 2009 and to 462 mature male parr. Demographic and genetic methods revealed that mature male parr increased population Nb by 1.79 and 1.85 times, respectively. Moreover, mature male parr boosted the number of alleles found among progenies. Finally, mature male parr were in average less related to anadromous females than were anadromous males, likely because of asynchronous sexual maturation between mature male parr and anadromous fish of a given cohort. By increasing Nb and allelic richness, and by decreasing inbreeding, the reproductive contribution of mature male parr has important evolutionary and conservation implications for declining Atlantic salmon populations. PMID:25553070

  13. Quantification of adaptive evolution of genes expressed in avian brain and the population size effect on the efficacy of selection.

    PubMed

    Axelsson, Erik; Ellegren, Hans

    2009-05-01

    Whether protein evolution is mainly due to fixation of beneficial alleles by positive selection or to random genetic drift has remained a contentious issue over the years. Here, we use two genomewide polymorphism data sets collected from chicken populations, together with divergence data from >5,000 chicken-zebra finch gene orthologs expressed in brain, to assess the amount of adaptive evolution in protein-coding genes of birds. First, we show that estimates of the fixation index (FI, the ratio of fixed nonsynonymous-to-synonymous changes over the ratio of the corresponding polymorphisms) are highly dependent on the character of the underlying data sets. Second, by using polymorphism data from high-frequency alleles, to avoid the confounding effect of slightly deleterious mutations segregating at low frequency, we estimate that about 20% of amino acid changes have been brought to fixation through positive selection during avian evolution. This estimate is intermediate to that obtained in humans (lower) and flies as well as bacteria (higher), and is consistent with population genetics theory that stipulates a positive relationship between the efficiency of selection and the effective population size. Further, by comparing the FIs for common and all alleles, we estimate that approximately 20% of nonsynonymous variation segregating in chicken populations represent slightly deleterious mutations, which is less than in Drosophila. Overall, these results highlight the link between the effective population size and positive as well as negative selection.

  14. Effects of Potyvirus Effective Population Size in Inoculated Leaves on Viral Accumulation and the Onset of Symptoms

    PubMed Central

    Daròs, José-Antonio; Elena, Santiago F.

    2012-01-01

    Effective population size (Ne) is a key parameter for understanding evolutionary processes, but it is generally not considered in epidemiological studies or in studying infections of individual hosts. Whether Ne has an effect on the onset of symptoms and viral accumulation in Tobacco etch virus (TEV) infection of Nicotiana tabacum plants is considered here. Using mixtures of TEV variants carrying fluorescent markers, the dose dependence of Ne was confirmed, and the inoculation procedure was found to be the main source of variation in these experiments. Whereas the onset of symptoms was independent of Ne, there was less and more variable accumulation at 6 days postinoculation for small Ne values (Ne < 5). The observed variation in accumulation was not heritable, however, suggesting that this variation was not due to the fixation of deleterious mutations in the small founder populations. On the other hand, virus-induced fluorescence and accumulation in the inoculated leaf were strongly Ne dependent. Systemic accumulation was independent of Ne, although removal of the inoculated leaf led to a small reduction in systemic accumulation for small Ne values. For whole plants, Ne-dependent effects on accumulation were no longer observed at 9 days postinoculation. Therefore, the effects of Ne on accumulation are due mainly to limited expansion in the inoculated leaf and are transient. In this system, Ne-dependent effects will be strongest at low doses and early in infection. We conclude that Ne can have implications for epidemiology and infection at the individual host level, beyond determining the rate of mixed-genotype infection. PMID:22740417

  15. Effects of potyvirus effective population size in inoculated leaves on viral accumulation and the onset of symptoms.

    PubMed

    Zwart, Mark P; Daròs, José-Antonio; Elena, Santiago F

    2012-09-01

    Effective population size (N(e)) is a key parameter for understanding evolutionary processes, but it is generally not considered in epidemiological studies or in studying infections of individual hosts. Whether N(e) has an effect on the onset of symptoms and viral accumulation in Tobacco etch virus (TEV) infection of Nicotiana tabacum plants is considered here. Using mixtures of TEV variants carrying fluorescent markers, the dose dependence of N(e) was confirmed, and the inoculation procedure was found to be the main source of variation in these experiments. Whereas the onset of symptoms was independent of N(e), there was less and more variable accumulation at 6 days postinoculation for small N(e) values (N(e) < 5). The observed variation in accumulation was not heritable, however, suggesting that this variation was not due to the fixation of deleterious mutations in the small founder populations. On the other hand, virus-induced fluorescence and accumulation in the inoculated leaf were strongly N(e) dependent. Systemic accumulation was independent of N(e), although removal of the inoculated leaf led to a small reduction in systemic accumulation for small N(e) values. For whole plants, N(e)-dependent effects on accumulation were no longer observed at 9 days postinoculation. Therefore, the effects of N(e) on accumulation are due mainly to limited expansion in the inoculated leaf and are transient. In this system, N(e)-dependent effects will be strongest at low doses and early in infection. We conclude that N(e) can have implications for epidemiology and infection at the individual host level, beyond determining the rate of mixed-genotype infection.

  16. The effects of heavy metal mine drainage on population size structure, reproduction, and condition of western mosquitofish, Gambusia affinis.

    PubMed

    Franssen, Courtney M

    2009-07-01

    Anthropogenic degradation of aquatic environments worldwide results in disturbed habitats, altered communities, and stressed populations. Surface waters located in an abandoned lead-zinc mining district in northeastern Oklahoma are no exception. This study examines the reproductive and somatic responses of a pollution-tolerant fish, the western mosquitofish, Gambusia affinis (Teleostei: Poeciliidae), living in mine outflow waters contaminated by heavy metals. Populations were sampled from four streams, which were classified into three habitat types. Populations from Tar Creek and an Unnamed Tributary of Tar Creek receive direct input of mine drainage, while populations living in reference creeks are not known to have mining influence. The influence of mine drainage directly or indirectly (via altered competitor and predator regimes or changes in food availability) affects G. affinis at both the population and the individual level. Metal-contaminated sites had reduced proportions of males and reproductively active females and altered male population size structures. Individual-level effects were apparent, as all G. affinis from Tar Creek invested less in liver weights, and mature males and reproductively active females from Tar Creek invested less in gonad weights. Furthermore, males from impacted sites were significantly lighter than those from reference creeks. Gravid females from Tar Creek had smaller clutch sizes, but average embryo weight did not differ among streams.

  17. Innovativeness, population size and cumulative cultural evolution.

    PubMed

    Kobayashi, Yutaka; Aoki, Kenichi

    2012-08-01

    Henrich [Henrich, J., 2004. Demography and cultural evolution: how adaptive cultural processes can produce maladaptive losses-the Tasmanian case. Am. Antiquity 69, 197-214] proposed a model designed to show that larger population size facilitates cumulative cultural evolution toward higher skill levels. In this model, each newborn attempts to imitate the most highly skilled individual of the parental generation by directly-biased social learning, but the skill level he/she acquires deviates probabilistically from that of the exemplar (cultural parent). The probability that the skill level of the imitator exceeds that of the exemplar can be regarded as the innovation rate. After reformulating Henrich's model rigorously, we introduce an overlapping-generations analog based on the Moran model and derive an approximate formula for the expected change per generation of the highest skill level in the population. For large population size, our overlapping-generations model predicts a much larger effect of population size than Henrich's discrete-generations model. We then investigate by way of Monte Carlo simulations the case where each newborn chooses as his/her exemplar the most highly skilled individual from among a limited number of acquaintances. When the number of acquaintances is small relative to the population size, we find that a change in the innovation rate contributes more than a proportional change in population size to the cumulative cultural evolution of skill level.

  18. Multiple estimates of effective population size for monitoring a long-lived vertebrate: an application to Yellowstone grizzly bears.

    PubMed

    Kamath, Pauline L; Haroldson, Mark A; Luikart, Gordon; Paetkau, David; Whitman, Craig; van Manen, Frank T

    2015-11-01

    Effective population size (N(e)) is a key parameter for monitoring the genetic health of threatened populations because it reflects a population's evolutionary potential and risk of extinction due to genetic stochasticity. However, its application to wildlife monitoring has been limited because it is difficult to measure in natural populations. The isolated and well-studied population of grizzly bears (Ursus arctos) in the Greater Yellowstone Ecosystem provides a rare opportunity to examine the usefulness of different N(e) estimators for monitoring. We genotyped 729 Yellowstone grizzly bears using 20 microsatellites and applied three single-sample estimators to examine contemporary trends in generation interval (GI), effective number of breeders (N(b)) and N(e) during 1982-2007. We also used multisample methods to estimate variance (N(eV)) and inbreeding N(e) (N(eI)). Single-sample estimates revealed positive trajectories, with over a fourfold increase in N(e) (≈100 to 450) and near doubling of the GI (≈8 to 14) from the 1980s to 2000s. N(eV) (240-319) and N(eI) (256) were comparable with the harmonic mean single-sample N(e) (213) over the time period. Reanalysing historical data, we found N(eV) increased from ≈80 in the 1910s-1960s to ≈280 in the contemporary population. The estimated ratio of effective to total census size (N(e) /N(c)) was stable and high (0.42-0.66) compared to previous brown bear studies. These results support independent demographic evidence for Yellowstone grizzly bear population growth since the 1980s. They further demonstrate how genetic monitoring of N(e) can complement demographic-based monitoring of N(c) and vital rates, providing a valuable tool for wildlife managers.

  19. Multiple estimates of effective population size for monitoring a long-lived vertebrate: An application to Yellowstone grizzly bears

    USGS Publications Warehouse

    Kamath, Pauline L.; Haroldson, Mark A.; Luikart, Gordon; Paetkau, David; Whitman, Craig L.; van Manen, Frank T.

    2015-01-01

    Effective population size (Ne) is a key parameter for monitoring the genetic health of threatened populations because it reflects a population's evolutionary potential and risk of extinction due to genetic stochasticity. However, its application to wildlife monitoring has been limited because it is difficult to measure in natural populations. The isolated and well-studied population of grizzly bears (Ursus arctos) in the Greater Yellowstone Ecosystem provides a rare opportunity to examine the usefulness of different Ne estimators for monitoring. We genotyped 729 Yellowstone grizzly bears using 20 microsatellites and applied three single-sample estimators to examine contemporary trends in generation interval (GI), effective number of breeders (Nb) and Ne during 1982–2007. We also used multisample methods to estimate variance (NeV) and inbreeding Ne (NeI). Single-sample estimates revealed positive trajectories, with over a fourfold increase in Ne (≈100 to 450) and near doubling of the GI (≈8 to 14) from the 1980s to 2000s. NeV (240–319) and NeI (256) were comparable with the harmonic mean single-sample Ne (213) over the time period. Reanalysing historical data, we found NeV increased from ≈80 in the 1910s–1960s to ≈280 in the contemporary population. The estimated ratio of effective to total census size (Ne/Nc) was stable and high (0.42–0.66) compared to previous brown bear studies. These results support independent demographic evidence for Yellowstone grizzly bear population growth since the 1980s. They further demonstrate how genetic monitoring of Ne can complement demographic-based monitoring of Nc and vital rates, providing a valuable tool for wildlife managers.

  20. Effective population size dynamics reveal impacts of historic climatic events and recent anthropogenic pressure in African elephants.

    PubMed

    Okello, J B A; Wittemyer, G; Rasmussen, H B; Arctander, P; Nyakaana, S; Douglas-Hamilton, I; Siegismund, H R

    2008-09-01

    Two hundred years of elephant hunting for ivory, peaking in 1970-1980s, caused local extirpations and massive population declines across Africa. The resulting genetic impacts on surviving populations have not been studied, despite the importance of understanding the evolutionary repercussions of such human-mediated events on this keystone species. Using Bayesian coalescent-based genetic methods to evaluate time-specific changes in effective population size, we analysed genetic variation in 20 highly polymorphic microsatellite loci from 400 elephants inhabiting the greater Samburu-Laikipia region of northern Kenya. This area experienced a decline of between 80% and 90% in the last few decades when ivory harvesting was rampant. The most significant change in effective population size, however, occurred approximately 2500 years ago during a mid-Holocene period of climatic drying in tropical Africa. Contrary to expectations, detailed analyses of four contemporary age-based cohorts showed that the peak poaching epidemic in the 1970s caused detectable temporary genetic impacts, with genetic diversity rebounding as juveniles surviving the poaching era became reproductively mature. This study demonstrates the importance of climatic history in shaping the distribution and genetic history of a keystone species and highlights the utility of coalescent-based demographic approaches in unravelling ancestral demographic events despite a lack of ancient samples. Unique insights into the genetic signature of mid-Holocene climatic change in Africa and effects of recent poaching pressure on elephants are discussed.

  1. Temporal genetic variation of mitochondrial DNA and the female effective population size of red drum (Sciaenops ocellatus) in the northern Gulf of Mexico.

    PubMed

    1999-07-01

    We studied genetic drift of mitochondrial DNA (mtDNA) haplotype frequencies in a natural population of red drum (Sciaenops ocellatus) from the northern Gulf of Mexico (Gulf). The amount of genetic drift observed across temporally adjacent year classes (1986-89) was used to estimate variance effective (female) population size (Nef). Nef was estimated to be 14 308 and the ratio of female effective size to adult female census size was approximately 0.004, which is among the lowest value reported for vertebrate animals. Low effective size relative to census size among red drum in the northern Gulf may result from yearly fluctuations in the number of breeding females, high variance in female reproductive success, or both. Despite low genetic effective size relative to census size, the genetic effective population size of red drum in the northern Gulf appears sufficiently large to preclude potentially deleterious effects of inbreeding.

  2. Interspecific hybridization contributes to high genetic diversity and apparent effective population size in an endemic population of mottled ducks (Anas fulvigula maculosa)

    USGS Publications Warehouse

    Peters, Jeffrey L.; Sonsthagen, Sarah A.; Lavretsky, Philip; Rezsutek, Michael; Johnson, William P.; McCracken, Kevin G.

    2014-01-01

    Under drift-mutation equilibrium, genetic diversity is expected to be correlated with effective population size (Ne). Changes in population size and gene flow are two important processes that can cause populations to deviate from this expected relationship. In this study, we used DNA sequences from six independent loci to examine the influence of these processes on standing genetic diversity in endemic mottled ducks (Anas fulvigula) and geographically widespread mallards (A. platyrhynchos), two species known to hybridize. Mottled ducks have an estimated census size that is about two orders-of-magnitude smaller than that of mallards, yet these two species have similar levels of genetic diversity, especially at nuclear DNA. Coalescent analyses suggest that a population expansion in the mallard at least partly explains this discrepancy, but the mottled duck harbors higher genetic diversity and apparent N e than expected for its census size even after accounting for a population decline. Incorporating gene flow into the model, however, reduced the estimated Ne of mottled ducks to 33 % of the equilibrium Ne and yielded an estimated Ne consistent with census size. We also examined the utility of these loci to distinguish among mallards, mottled ducks, and their hybrids. Most putatively pure individuals were correctly assigned to species, but the power for detecting hybrids was low. Although hybridization with mallards potentially poses a conservation threat to mottled ducks by creating a risk of extinction by hybridization, introgression of mallard alleles has helped maintain high genetic diversity in mottled ducks and might be important for the adaptability and survival of this species.

  3. The botanist effect revisited: plant species richness, county area, and human population size in the United States.

    PubMed

    Pautasso, Marco; McKinney, Michael L

    2007-10-01

    The "botanist effect" is thought to be the reason for higher plant species richness in areas where botanists are disproportionately present as an artefactual consequence of a more thorough sampling. We examined whether this was the case for U.S. counties. We collated the number of species of vascular plants, human population size, and the area of U.S. counties. Controlling for spatial autocorrelation and county area, plant species richness increased with human population size and density in counties with and without universities and/or botanical gardens, with no significant differences in the relation between the two subsets. This is consistent with previous findings and further evidence of a broad-scale positive correlation between species richness and human population presence, which has important consequences for the experience of nature by inhabitants of densely populated regions. Combined with the many reports of a negative correlation between the two variables at a local scale, the positive relation between plant species richness in U.S. counties and human population presence stresses the need for the conservation of seminatural areas in urbanized ecosystems and for the containment of urban and suburban sprawl.

  4. Accurate Estimation of Effective Population Size in the Korean Dairy Cattle Based on Linkage Disequilibrium Corrected by Genomic Relationship Matrix

    PubMed Central

    Shin, Dong-Hyun; Cho, Kwang-Hyun; Park, Kyoung-Do; Lee, Hyun-Jeong; Kim, Heebal

    2013-01-01

    Linkage disequilibrium between markers or genetic variants underlying interesting traits affects many genomic methodologies. In many genomic methodologies, the effective population size (Ne) is important to assess the genetic diversity of animal populations. In this study, dairy cattle were genotyped using the Illumina BovineHD Genotyping BeadChips for over 777,000 SNPs located across all autosomes, mitochondria and sex chromosomes, and 70,000 autosomal SNPs were selected randomly for the final analysis. We characterized more accurate linkage disequilibrium in a sample of 96 dairy cattle producing milk in Korea. Estimated linkage disequilibrium was relatively high between closely linked markers (>0.6 at 10 kb) and decreased with increasing distance. Using formulae that related the expected linkage disequilibrium to Ne, and assuming a constant actual population size, Ne was estimated to be approximately 122 in this population. Historical Ne, calculated assuming linear population growth, was suggestive of a rapid increase Ne over the past 10 generations, and increased slowly thereafter. Additionally, we corrected the genomic relationship structure per chromosome in calculating r2 and estimated Ne. The observed Ne based on r2 corrected by genomics relationship structure can be rationalized using current knowledge of the history of the dairy cattle breeds producing milk in Korea. PMID:25049757

  5. Accurate estimation of effective population size in the korean dairy cattle based on linkage disequilibrium corrected by genomic relationship matrix.

    PubMed

    Shin, Dong-Hyun; Cho, Kwang-Hyun; Park, Kyoung-Do; Lee, Hyun-Jeong; Kim, Heebal

    2013-12-01

    Linkage disequilibrium between markers or genetic variants underlying interesting traits affects many genomic methodologies. In many genomic methodologies, the effective population size (Ne) is important to assess the genetic diversity of animal populations. In this study, dairy cattle were genotyped using the Illumina BovineHD Genotyping BeadChips for over 777,000 SNPs located across all autosomes, mitochondria and sex chromosomes, and 70,000 autosomal SNPs were selected randomly for the final analysis. We characterized more accurate linkage disequilibrium in a sample of 96 dairy cattle producing milk in Korea. Estimated linkage disequilibrium was relatively high between closely linked markers (>0.6 at 10 kb) and decreased with increasing distance. Using formulae that related the expected linkage disequilibrium to Ne, and assuming a constant actual population size, Ne was estimated to be approximately 122 in this population. Historical Ne, calculated assuming linear population growth, was suggestive of a rapid increase Ne over the past 10 generations, and increased slowly thereafter. Additionally, we corrected the genomic relationship structure per chromosome in calculating r(2) and estimated Ne. The observed Ne based on r(2) corrected by genomics relationship structure can be rationalized using current knowledge of the history of the dairy cattle breeds producing milk in Korea.

  6. Population Structure, Genetic Diversity, Effective Population Size, Demographic History and Regional Connectivity Patterns of the Endangered Dusky Grouper, Epinephelus marginatus (Teleostei: Serranidae), within Malta's Fisheries Management Zone.

    PubMed

    Buchholz-Sørensen, Molly; Vella, Adriana

    2016-01-01

    The objective of this study is to describe the genetic population structure and demographic history of the endangered marine fish, Epinephelus marginatus, within Malta's Fisheries Management Zone for the purpose of localised conservation planning. Epinephelus marginatus is a long-lived, sedentary, reef-associated protogynous hermaphrodite with high commercial and recreational value that is at risk of extinction throughout its global distribution. Based on global trends, population substructuring and gaps in local knowledge this has led to an increased interest in evaluation of local stock. Assessment of Maltese demography was based on historical and contemporary catch landings data whilst genetic population structure and regional connectivity patterns were evaluated by examining 175 individuals collected within the central Mediterranean region between 2002 and 2009 using 14 nuclear microsatellite loci. Demographic stock assessment of Maltese E. marginatus' revealed a 99% decline in catch landings between 1947 and 2009 within the Fisheries Management Zone. A contemporary modest mean size was observed, 3 ± 3 kg, where approximately 17% of the population was juvenile, 68% female/sex-changing and 15% were male with a male-to-female sex ratio of 1:5. Genetic analysis describes the overall population of E. marginatus' within the Fisheries Management Zone as decreasing in size (ƟH = 2.2), which has gone through a significant size reduction in the past (M = 0.41) and consequently shows signs of moderate inbreeding (FIS = 0.10, p < 0.001) with an estimated effective population size of 130 individuals. Results of spatially explicit Bayesian genetic cluster analysis detected two geographically distinct subpopulations within Malta's Fisheries Management Zone and that they are connected to a larger network of E. marginatus' within the Sicily Channel. Results suggest conservation management should be designed to reflect E. marginatus' within Malta's Fisheries Management Zone

  7. The role of population size, pleiotropy and fitness effects of mutations in the evolution of overlapping gene functions.

    PubMed

    Wagner, A

    2000-03-01

    Sheltered from deleterious mutations, genes with overlapping or partially redundant functions may be important sources of novel gene functions. While most partially redundant genes originated in gene duplications, it is much less clear why genes with overlapping functions have been retained, in some cases for hundreds of millions of years. A case in point is the many partially redundant genes in vertebrates, the result of ancient gene duplications in primitive chordates. Their persistence and ubiquity become surprising when it is considered that duplicate and original genes often diversify very rapidly, especially if the action of natural selection is involved. Are overlapping gene functions perhaps maintained because of their protective role against otherwise deleterious mutations? There are two principal objections against this hypothesis, which are the main subject of this article. First, because overlapping gene functions are maintained in populations by a slow process of "second order" selection, population sizes need to be very high for this process to be effective. It is shown that even in small populations, pleiotropic mutations that affect more than one of a gene's functions simultaneously can slow the mutational decay of functional overlap after a gene duplication by orders of magnitude. Furthermore, brief and transient increases in population size may be sufficient to maintain functional overlap. The second objection regards the fact that most naturally occurring mutations may have much weaker fitness effects than the rather drastic "knock-out" mutations that lead to detection of partially redundant functions. Given weak fitness effects of most mutations, is selection for the buffering effect of functional overlap strong enough to compensate for the diversifying force exerted by mutations? It is shown that the extent of functional overlap maintained in a population is not only independent of the mutation rate, but also independent of the average fitness

  8. The role of population size, pleiotropy and fitness effects of mutations in the evolution of overlapping gene functions.

    PubMed Central

    Wagner, A

    2000-01-01

    Sheltered from deleterious mutations, genes with overlapping or partially redundant functions may be important sources of novel gene functions. While most partially redundant genes originated in gene duplications, it is much less clear why genes with overlapping functions have been retained, in some cases for hundreds of millions of years. A case in point is the many partially redundant genes in vertebrates, the result of ancient gene duplications in primitive chordates. Their persistence and ubiquity become surprising when it is considered that duplicate and original genes often diversify very rapidly, especially if the action of natural selection is involved. Are overlapping gene functions perhaps maintained because of their protective role against otherwise deleterious mutations? There are two principal objections against this hypothesis, which are the main subject of this article. First, because overlapping gene functions are maintained in populations by a slow process of "second order" selection, population sizes need to be very high for this process to be effective. It is shown that even in small populations, pleiotropic mutations that affect more than one of a gene's functions simultaneously can slow the mutational decay of functional overlap after a gene duplication by orders of magnitude. Furthermore, brief and transient increases in population size may be sufficient to maintain functional overlap. The second objection regards the fact that most naturally occurring mutations may have much weaker fitness effects than the rather drastic "knock-out" mutations that lead to detection of partially redundant functions. Given weak fitness effects of most mutations, is selection for the buffering effect of functional overlap strong enough to compensate for the diversifying force exerted by mutations? It is shown that the extent of functional overlap maintained in a population is not only independent of the mutation rate, but also independent of the average fitness

  9. The Effects of Population Size Histories on Estimates of Selection Coefficients from Time-Series Genetic Data

    PubMed Central

    Jewett, Ethan M.; Steinrücken, Matthias; Song, Yun S.

    2016-01-01

    Many approaches have been developed for inferring selection coefficients from time series data while accounting for genetic drift. These approaches have been motivated by the intuition that properly accounting for the population size history can significantly improve estimates of selective strengths. However, the improvement in inference accuracy that can be attained by modeling drift has not been characterized. Here, by comparing maximum likelihood estimates of selection coefficients that account for the true population size history with estimates that ignore drift by assuming allele frequencies evolve deterministically in a population of infinite size, we address the following questions: how much can modeling the population size history improve estimates of selection coefficients? How much can mis-inferred population sizes hurt inferences of selection coefficients? We conduct our analysis under the discrete Wright–Fisher model by deriving the exact probability of an allele frequency trajectory in a population of time-varying size and we replicate our results under the diffusion model. For both models, we find that ignoring drift leads to estimates of selection coefficients that are nearly as accurate as estimates that account for the true population history, even when population sizes are small and drift is high. This result is of interest because inference methods that ignore drift are widely used in evolutionary studies and can be many orders of magnitude faster than methods that account for population sizes. PMID:27550904

  10. Concurrent habitat and life history influences on effective/census population size ratios in stream-dwelling trout

    PubMed Central

    Belmar-Lucero, Sebastian; Wood, Jacquelyn L A; Scott, Sherylyne; Harbicht, Andrew B; Hutchings, Jeffrey A; Fraser, Dylan J

    2012-01-01

    Lower effective sizes (Ne) than census sizes (N) are routinely documented in natural populations, but knowledge of how multiple factors interact to lower Ne/N ratios is often limited. We show how combined habitat and life-history influences drive a 2.4- to 6.1-fold difference in Ne/N ratios between two pristine brook trout (Salvelinus fontinalis) populations occupying streams separated by only 750 m. Local habitat features, particularly drainage area and stream depth, govern trout biomass produced in each stream. They also generate higher trout densities in the shallower stream by favoring smaller body size and earlier age-at-maturity. The combination of higher densities and reduced breeding site availability in the shallower stream likely leads to more competition among breeding trout, which results in greater variance in individual reproductive success and a greater reduction in Ne relative to N. A similar disparity between juvenile or adult densities and breeding habitat availability is reported for other species and hence may also result in divergent Ne/N ratios elsewhere. These divergent Ne/N ratios between adjacent populations are also an instructive reminder for species conservation programs that genetic and demographic parameters may differ dramatically within species. PMID:22822435

  11. Concurrent habitat and life history influences on effective/census population size ratios in stream-dwelling trout.

    PubMed

    Belmar-Lucero, Sebastian; Wood, Jacquelyn L A; Scott, Sherylyne; Harbicht, Andrew B; Hutchings, Jeffrey A; Fraser, Dylan J

    2012-03-01

    Lower effective sizes (N(e)) than census sizes (N) are routinely documented in natural populations, but knowledge of how multiple factors interact to lower N(e)/N ratios is often limited. We show how combined habitat and life-history influences drive a 2.4- to 6.1-fold difference in N(e)/N ratios between two pristine brook trout (Salvelinus fontinalis) populations occupying streams separated by only 750 m. Local habitat features, particularly drainage area and stream depth, govern trout biomass produced in each stream. They also generate higher trout densities in the shallower stream by favoring smaller body size and earlier age-at-maturity. The combination of higher densities and reduced breeding site availability in the shallower stream likely leads to more competition among breeding trout, which results in greater variance in individual reproductive success and a greater reduction in N(e) relative to N. A similar disparity between juvenile or adult densities and breeding habitat availability is reported for other species and hence may also result in divergent N(e)/N ratios elsewhere. These divergent N(e)/N ratios between adjacent populations are also an instructive reminder for species conservation programs that genetic and demographic parameters may differ dramatically within species.

  12. Interpreting the WHOQOL-Bref: Preliminary Population Norms and Effect Sizes

    ERIC Educational Resources Information Center

    Hawthorne, Graeme; Herrman, Helen; Murphy, Barbara

    2006-01-01

    Since publication use of the WHOQOL-Bref has rapidly risen. However, as yet no population norms have been published as a reference point against which researchers can interpret their findings. This study provides preliminary population norms for this purpose. Randomly sampled community residents from two studies were pooled and used to examine the…

  13. Model-Based Predictions of the Effects of Harvest Mortality on Population Size and Trend of Yellow-Billed Loons

    USGS Publications Warehouse

    Schmutz, Joel A.

    2009-01-01

    Yellow-billed loons (Gavia adamsii) breed in low densities in northern tundra habitats in Alaska, Canada, and Russia. They migrate to coastal marine habitats at mid to high latitudes where they spend their winters. Harvest may occur throughout the annual cycle, but of particular concern are recent reports of harvest from the Bering Strait region, which lies between Alaska and Russia and is an area used by yellow-billed loons during migration. Annual harvest for this region was reported to be 317, 45, and 1,077 during 2004, 2005, and 2007, respectively. I developed a population model to assess the effect of this reported harvest on population size and trend of yellow-billed loons. Because of the uncertainty regarding actual harvest and definition of the breeding population(s) affected by this harvest, I considered 25 different scenarios. Predicted trends across these 25 scenarios ranged from stability to rapid decline (24 percent per year) with halving of the population in 3 years. Through an assessment of literature and unpublished satellite tracking data, I suggest that the most likely of these 25 scenarios is one where the migrant population subjected to harvest in the Bering Strait includes individuals from breeding populations in Alaska (Arctic coastal plain and the Kotzebue region) and eastern Russia, and for which the magnitude of harvest varies among years and emulates the annual variation of reported harvest during 2004-07 (317, 45, and 1,077 yellow-billed loons). This scenario, which assumes no movement of Canadian breeders through the Bering Strait, predicts a 4.6 percent rate of annual population decline, which would halve the populations in 15 years. Although these model outputs reflect the best available information, confidence in these predictions and applicable scenarios would be greatly enhanced by more information on harvest, rates of survival and reproduction, and migratory pathways.

  14. Genetic variation, relatedness, and effective population size of polar bears (Ursus maritimus) in the southern Beaufort Sea, Alaska

    USGS Publications Warehouse

    Cronin, M.A.; Amstrup, Steven C.; Talbot, S.L.; Sage, G.K.; Amstrup, K.S.

    2009-01-01

    Polar bears (Ursus maritimus) are unique among bears in that they are adapted to the Arctic sea ice environment. Genetic data are useful for understanding their evolution and can contribute to management. We assessed parentage and relatedness of polar bears in the southern Beaufort Sea, Alaska, with genetic data and field observations of age, sex, and mother-offspring and sibling relationships. Genotypes at 14 microsatellite DNA loci for 226 bears indicate that genetic variation is comparable to other populations of polar bears with mean number of alleles per locus of 7.9 and observed and expected heterozygosity of 0.71. The genetic data verified 60 field-identified mother-offspring pairs and identified 10 additional mother-cub pairs and 48 father-offspring pairs. The entire sample of related and unrelated bears had a mean pairwise relatedness index (rxy) of approximately zero, parent-offspring and siblings had rxy of approximately 0.5, and 5.2% of the samples had rxy values within the range expected for parent-offspring. Effective population size (Ne = 277) and the ratio of Ne to total population size (Ne/N = 0.182) were estimated from the numbers of reproducing males and females. Ne estimates with genetic methods gave variable results. Our results verify and expand field data on reproduction by females and provide new data on reproduction by males and estimates of relatedness and Ne in a polar bear population. ?? The American Genetic Association. 2009. All rights reserved.

  15. Effects of plant availability on population size and dynamics of an insect community: diamondback moth and two of its parasitoids.

    PubMed

    Soufbaf, M; Fathipour, Y; Karimzadeh, J; Zalucki, M P

    2014-08-01

    To understand the effect of plant availability/structure on the population size and dynamics of insects, a specialist herbivore in the presence of two of its parasitoids was studied in four replicated time-series experiments with high and low plant availabilities; under the latter condition, the herbivore suffered from some periods of resource limitation (starvation) and little plant-related structural refuges. Population dynamics of the parasitoid Cotesia vestalis was governed mainly by the delayed density-dependent process under both plant setups. The parasitoid, Diadegma semiclausum, under different plant availabilities and different coexistence situations (either +competitor or -competitor) showed dynamics patterns that were governed mainly by the delayed density process (significant lags at weeks 2-4). Both the competing parasitoids did not experience beneficial or costly interferences from each other in terms of their own population size when the plant resource was limited. Variation in the Plutella xylostella population under limited plant availability is higher than that under the other plant setup. For both parasitoids, under limited plant setup, the extinction risk was lower when parasitoids were engaged in competition, while under the unlimited plant setup, the mentioned risk was higher when parasitoids competed. In this situation, parasitoids suffered from two forces, competition and higher escaped hosts.

  16. Population size and selection intensity effects on short-term response for a selection index in Tribolium.

    PubMed

    Campo, J L; Turrado, H

    1997-01-12

    The effects of population size and selection intensity on the short-term response to selection were investigated in an experiment with Tribolium, using a two-trait empirical selection index for pupal and adult weights. Twenty lines were selected following a factorial design of five population sizes (1, 2, 4, 8, and 16 pairs of parents) and four selection intensities (20, 25, 33, and 50%), with three replicates. For each replicate, an unselected control with 16 pairs of parents was produced. There were four generations of selection per line. Selection response was significant in all lines with the 20% selection intensity and/or the 16-pair population size. Selection intensity and population size were significant effects and there was significant interaction between them. Higher selection intensities produced more overall significant response to selection (20% > (25% = 33%) > 50%); this significance was also found for the 16-pair population size. There was an overall significant difference among population sizes, with the larger population sizes giving more response than the smaller sizes (16-pair = 8-pair = 4-pair) > (2-pair = 1-pair); this significance was also found for the 20% selection intensity. There was a good agreement between observed and expected responses, except for the 50% selection intensity and/or 1-pair population size; expected values in generation 1 overestimated observed values. The realized heritability was similar in all lines. With equal and high numbers of individuals scored, it was better to choose a high selection intensity than a large population size. The results show that the effect of population size cannot be ignored, even in short-term selection response; the main influence of population size is through selection differential. RESUMEN: Los efectos del tamaño de población y la intensidad de selección sobre la respuesta a corto plazo para un índice de selección en Tribolium Los efectos del tamaño de población y la intensidad de

  17. Effective Population Size and Signatures of Selection Using Bovine 50K SNP Chips in Korean Native Cattle (Hanwoo)

    PubMed Central

    Li, Yi; Kim, Jong-Joo

    2015-01-01

    Inferring the effective population size and the pattern of selection signatures is of interest both from an evolutionary perspective and to improve models for mapping of quantitative trait genes. We used DNA samples of 61 sires and 486 progeny of the Hanwoo, genotyped by the Illumina Bovine SNP50 BeadChip, to analyze the genetic structure. Our study showed a persistent decline in effective population size throughout the period considered, but suggested a marked decline at one distinctive time point (100th generation) and two sharp decline intervals (50th–25th generation and 25th–10th generation). This pattern can be explained by Hanwoo formation and the modern breeding program. Our results revealed 95 regions exhibiting the footprint of recent positive selection at a threshold level of 0.01. We found an overlap of the 11 core regions presenting top P-values and those that had previously been identified as harboring quantitative trait loci from other breeds. The information generated from this study can be used to better understand the mechanism of selection in Hanwoo breeding, and provide important implications for the design and application of association studies in the Hanwoo population. PMID:26244003

  18. Can floral display size compensate for Allee effects caused by low population abundance and density in Synthyris bullii (Plantaginaceae), a rare species?

    PubMed

    Chi, Katherine; Molano-Flores, Brenda

    2014-03-01

    Conservation seeks to address the issues of small population size, and the reproductive limitations confronting these populations. Sparse, small plant populations often suffer Allee effects such as pollinator limitation. However, some studies show that plants in sparse populations experience reduced resource competition. As a result, these plants may produce larger floral displays, which are also predicted to attract pollinators. The negative impacts from reduced floral quantity may thus be offset by improved floral quality. In a 2-yr field study, population abundance and density were quantified for 24 populations of Synthyris bullii (Plantaginaceae), a rare prairie endemic. In each population, data were collected on inflorescence size, fruit/seed set, and seed germination. Inflorescence size had a positive relationship with population inflorescence abundance and density. Fruit set and germination responded positively to floral quality (i.e., flower density). In comparison, seed set showed a positive relationship with only floral quantity (i.e., population abundance). Contrary to our predictions, inflorescence size and population size were not inversely related. While attractive floral displays in sparse populations potentially compensate in terms of fruit set, population abundance nevertheless plays an important role in seed set. Because floral quality and quantity differ in their ability to explain reproductive outcomes, studies should examine reproduction at several stages, otherwise the impacts of population size may be overlooked. Allee effects manifesting at a critical stage of reproduction, such as seed production, may act as a bottleneck impeding successful recruitment.

  19. Genomic Prediction in Pea: Effect of Marker Density and Training Population Size and Composition on Prediction Accuracy

    PubMed Central

    Tayeh, Nadim; Klein, Anthony; Le Paslier, Marie-Christine; Jacquin, Françoise; Houtin, Hervé; Rond, Céline; Chabert-Martinello, Marianne; Magnin-Robert, Jean-Bernard; Marget, Pascal; Aubert, Grégoire; Burstin, Judith

    2015-01-01

    Pea is an important food and feed crop and a valuable component of low-input farming systems. Improving resistance to biotic and abiotic stresses is a major breeding target to enhance yield potential and regularity. Genomic selection (GS) has lately emerged as a promising technique to increase the accuracy and gain of marker-based selection. It uses genome-wide molecular marker data to predict the breeding values of candidate lines to selection. A collection of 339 genetic resource accessions (CRB339) was subjected to high-density genotyping using the GenoPea 13.2K SNP Array. Genomic prediction accuracy was evaluated for thousand seed weight (TSW), the number of seeds per plant (NSeed), and the date of flowering (BegFlo). Mean cross-environment prediction accuracies reached 0.83 for TSW, 0.68 for NSeed, and 0.65 for BegFlo. For each trait, the statistical method, the marker density, and/or the training population size and composition used for prediction were varied to investigate their effects on prediction accuracy: the effect was large for the size and composition of the training population but limited for the statistical method and marker density. Maximizing the relatedness between individuals in the training and test sets, through the CDmean-based method, significantly improved prediction accuracies. A cross-population cross-validation experiment was further conducted using the CRB339 collection as a training population set and nine recombinant inbred lines populations as test set. Prediction quality was high with mean Q2 of 0.44 for TSW and 0.59 for BegFlo. Results are discussed in the light of current efforts to develop GS strategies in pea. PMID:26635819

  20. Territorial defense, territory size, and population regulation.

    PubMed

    López-Sepulcre, Andrés; Kokko, Hanna

    2005-09-01

    The carrying capacity of an environment is determined partly by how individuals compete over the available resources. To territorial animals, space is an important resource, leading to conflict over its use. We build a model where the carrying capacity for an organism in a given environment results from the evolution of territorial defense effort and the consequent space use. The same evolutionary process can yield two completely different modes of population regulation. Density dependence arises through expanding and shrinking territories if fecundity is low, breeding success increases gradually with territory size, and/or defense is cheap. By contrast, when fecundity is high, breeding success sharply saturates with territory size, and/or defense is costly, we predict fixed territory sizes and regulation by floaters. These "surplus" individuals form a buffer against population fluctuations. Yet floaters can also harm breeder performance, and by comparing population growth of a territorial population to a nonterritorial (and individually suboptimal) alternative, we can quantify the harmful effect of evolutionary conflict on population performance. Territoriality has often been found to increase population stability, but this may come at a cost of reduced equilibrium densities.

  1. Likelihood-based estimation of the effective population size using temporal changes in allele frequencies: a genealogical approach.

    PubMed Central

    Berthier, Pierre; Beaumont, Mark A; Cornuet, Jean-Marie; Luikart, Gordon

    2002-01-01

    A new genetic estimator of the effective population size (N(e)) is introduced. This likelihood-based (LB) estimator uses two temporally spaced genetic samples of individuals from a population. We compared its performance to that of the classical F-statistic-based N(e) estimator (N(eFk)) by using data from simulated populations with known N(e) and real populations. The new likelihood-based estimator (N(eLB)) showed narrower credible intervals and greater accuracy than (N(eFk)) when genetic drift was strong, but performed only slightly better when genetic drift was relatively weak. When drift was strong (e.g., N(e) = 20 for five generations), as few as approximately 10 loci (heterozygosity of 0.6; samples of 30 individuals) are sufficient to consistently achieve credible intervals with an upper limit <50 using the LB method. In contrast, approximately 20 loci are required for the same precision when using the classical F-statistic approach. The N(eLB) estimator is much improved over the classical method when there are many rare alleles. It will be especially useful in conservation biology because it less often overestimates N(e) than does N(eLB) and thus is less likely to erroneously suggest that a population is large and has a low extinction risk. PMID:11861575

  2. Estimation of inbreeding and effective population size of full-blood Wagyu cattle registered with the American Wagyu Cattle Association.

    PubMed

    Scraggs, E; Zanella, R; Wojtowicz, A; Taylor, J F; Gaskins, C T; Reeves, J J; de Avila, J M; Neibergs, H L

    2014-02-01

    The objective of this research was to examine the population structure of full-blood (100%) Wagyu cattle registered in the United States with the American Wagyu Association, with the aim of estimating and comparing the levels of inbreeding from both pedigree and genotypic data. A total of 4132 full-blood Wagyu cattle pedigrees were assessed and used to compute the inbreeding coefficients (FIT and FST ) and the effective population size (Ne ) from pedigree data for the period 1994 to 2011. In addition to pedigree analysis, 47 full-blood Wagyu cattle representing eight prominent sire lines in the American Wagyu cattle population were genotyped using the Illumina BovineSNP50 BeadChip. Genotypic data were then used to estimate genomic inbreeding coefficients (FROH ) by calculating runs of homozygosity. The mean inbreeding coefficient based on the pedigree data was estimated at 4.80%. The effective population size averaged 17 between the years 1994 and 2011 with an increase of 42.9 in 2000 and a drop of 1.8 in 2011. Examination of the runs of homozygosity revealed that the 47 Wagyu cattle from the eight prominent sire lines had a mean genomic inbreeding coefficient (FROH ) estimated at 9.08% compared to a mean inbreeding coefficient based on pedigree data of 4.8%. These data suggest that the mean genotype inbreeding coefficient of full-blood Wagyu cattle exceeds the inbreeding coefficient identified by pedigree. Inbreeding has increased slowly at a rate of 0.03% per year over the past 17 years. Wagyu breeders should continue to utilize many sires from divergent lines and consider outcrossing to other breeds to enhance genetic diversity and minimize the adverse effects of inbreeding in Wagyu.

  3. Cytoplasmically Inherited Reproductive Incompatibility in Tribolium Flour Beetles: The Rate of Spread and Effect on Population Size

    PubMed Central

    Stevens, L.; Wade, M. J.

    1990-01-01

    This paper reports on the effects of a cytoplasmically inherited reproductive incompatibility in different genetic strains of the flour beetle, Tribolium confusum. We measured the rate of spread and the effect of host population size using different initial frequencies of infection with a cytoplasmic factor that mediates reproductive incompatibility. There were two experiments, in one the infected and uninfected lines were from the same genetic strain, b-Yugoslavia. In the other, the infected line was from the ``high cannibalism'' bIV strain and the uninfected line from the ``low cannibalism'' bI strain. We estimate that the fitness ratio of infected to uninfected in b-Yugoslavia is 0.63 and the observed rate of spread for this strain corresponds to a model of cytoplasmic inheritance that takes into account the productivity differences between the infected and cured lines. In the bI-bIV experiment, because the uninfected and infected lines are from different genetic strains, we cannot partition the effects of the cytoplasmic factor from other factors. The rate of spread in the bI-bIV experiment is faster in males and slower in females than predicted from a model of cytoplasmic inheritance. In both experiments, productivity varies with initial infection frequency; however, the relationship is not explained by a simple model that predicts lower population size at intermediate infection frequencies. PMID:2307358

  4. Estimates of linkage disequilibrium and effective population sizes in Chinese Merino (Xinjiang type) sheep by genome-wide SNPs.

    PubMed

    Liu, Shudong; He, Sangang; Chen, Lei; Li, Wenrong; Di, Jiang; Liu, Mingjun

    2017-01-01

    Knowledge of linkage disequilibrium (LD) is important for effective genome-wide association studies and accurate genomic prediction. Chinese Merino (Xinjiang type) is well-known fine wool sheep breed. However, the extent of LD across the genome remains unexplored. In this study, we calculated autosomal LD based on genome-wide SNPs of 635 Chinese Merino (Xinjiang type) sheep by Illumina Ovine SNP50 BeadChip. A moderate level of LD (r(2) ≥ 0.25) across the whole genome was observed at short distances of 0-10 kb. Further, the ancestral effective population size (Ne ) was analyzed by extent of LD and found that Ne increased with the increase of generations and declined rapidly within the most recent 50 generations, which is consistent with the history of Chinese Merino sheep breeding, initiated in 1971. We also noted that even when the effective population size was estimated across different single chromosomes, Ne only ranged from 140.36 to 183.33 at five generations in the past, exhibiting a rapid decrease compared with that at ten generations in the past. These results indicated that the genetic diversity in Chinese Merino sheep recently decreased and proper protective measures should be taken to maintain the diversity. Our datasets provided essential genetic information to track molecular variations which potentially contribute to phenotypic variation in Chinese Merino sheep.

  5. Effect of conservation efforts and ecological variables on waterbird population sizes in wetlands of the Yangtze River

    PubMed Central

    Zhang, Yong; Jia, Qiang; Prins, Herbert H. T.; Cao, Lei; de Boer, Willem Frederik

    2015-01-01

    Forage quality and availability, climatic factors, and a wetland’s conservation status are expected to affect the densities of wetland birds. However, the conservation effectiveness is often poorly studied. Here, using twelve years’ census data collected from 78 wetlands in the Yangtze River floodplain, we aimed to understand the effect of these variables on five Anatidae species, and evaluate the effectiveness of the conservation measures by comparing population trends of these species among wetlands that differ in conservations status. We showed that the slope angle of a wetland and the variation thereof best explain the differences in densities of four species. We also found that the population abundances of the Anatidae species generally declined in wetlands along the Yangtze River floodplain over time, with a steeper decline in wetlands with a lower protection status, indicating that current conservation policies might deliver benefits for wintering Anatidae species in China, as population sizes of the species were buffered to some extent against decline in numbers in wetlands with a higher level protection status. We recommend several protection measures to stop the decline of these Anatidae species in wetlands along the Yangtze River floodplain, which are of great importance for the East Asian-Australasian Flyway. PMID:26601785

  6. Effect of conservation efforts and ecological variables on waterbird population sizes in wetlands of the Yangtze River

    NASA Astrophysics Data System (ADS)

    Zhang, Yong; Jia, Qiang; Prins, Herbert H. T.; Cao, Lei; de Boer, Willem Frederik

    2015-11-01

    Forage quality and availability, climatic factors, and a wetland’s conservation status are expected to affect the densities of wetland birds. However, the conservation effectiveness is often poorly studied. Here, using twelve years’ census data collected from 78 wetlands in the Yangtze River floodplain, we aimed to understand the effect of these variables on five Anatidae species, and evaluate the effectiveness of the conservation measures by comparing population trends of these species among wetlands that differ in conservations status. We showed that the slope angle of a wetland and the variation thereof best explain the differences in densities of four species. We also found that the population abundances of the Anatidae species generally declined in wetlands along the Yangtze River floodplain over time, with a steeper decline in wetlands with a lower protection status, indicating that current conservation policies might deliver benefits for wintering Anatidae species in China, as population sizes of the species were buffered to some extent against decline in numbers in wetlands with a higher level protection status. We recommend several protection measures to stop the decline of these Anatidae species in wetlands along the Yangtze River floodplain, which are of great importance for the East Asian-Australasian Flyway.

  7. Effect of conservation efforts and ecological variables on waterbird population sizes in wetlands of the Yangtze River.

    PubMed

    Zhang, Yong; Jia, Qiang; Prins, Herbert H T; Cao, Lei; de Boer, Willem Frederik

    2015-11-25

    Forage quality and availability, climatic factors, and a wetland's conservation status are expected to affect the densities of wetland birds. However, the conservation effectiveness is often poorly studied. Here, using twelve years' census data collected from 78 wetlands in the Yangtze River floodplain, we aimed to understand the effect of these variables on five Anatidae species, and evaluate the effectiveness of the conservation measures by comparing population trends of these species among wetlands that differ in conservations status. We showed that the slope angle of a wetland and the variation thereof best explain the differences in densities of four species. We also found that the population abundances of the Anatidae species generally declined in wetlands along the Yangtze River floodplain over time, with a steeper decline in wetlands with a lower protection status, indicating that current conservation policies might deliver benefits for wintering Anatidae species in China, as population sizes of the species were buffered to some extent against decline in numbers in wetlands with a higher level protection status. We recommend several protection measures to stop the decline of these Anatidae species in wetlands along the Yangtze River floodplain, which are of great importance for the East Asian-Australasian Flyway.

  8. Davidson Trauma Scale (DTS): normative scores in the general population and effect sizes in placebo-controlled SSRI trials.

    PubMed

    Davidson, Jonathan R T; Tharwani, Haresh M; Connor, Kathryn M

    2002-01-01

    The Davidson Trauma Scale (DTS) was developed as a self-rating for use in diagnosing and measuring symptom severity and treatment outcome in post-traumatic stress disorder (PTSD); 630 subjects were identified by random digit dialing and evaluated for a history of trauma. Prevalence rates of PTSD and subthreshold PTSD with impairment were 2.2 and 4.1%, respectively. In this general population sample, 438 subjects endorsed at least one trauma, and four groups were generated: A) threshold PTSD (n = 13), B) subthreshold PTSD with impairment (n = 26), C) subthreshold PTSD without impairment (n = 78), and D) no PTSD (n = 321). Mean (SD) DTS score in the entire population was 11.0 +/- 18.1. Differences were found in four of the five pairwise between-group contrasts. In a second sample of 447 clinical trial participants from three SSRI vs. placebo studies, we assessed treatment effect size according to different measures. In all three clinical trials, effect size with the DTS was equal to, or better than, those found for the Impact of Event Scale (IES), Clinician Administered PTSD Scale (CAPS), and Structured Interview for PTSD (SIP). These results further affirm the utility of the DTS as a self-rating measure of PTSD symptom severity and in evaluating treatment response.

  9. Effects of premolar extractions on Bolton overall ratios and tooth-size discrepancies in a north Indian population

    PubMed Central

    Kumar, Piush; Singh, Vishal; Kumar, Pragya; Sharma, Payal; Sharma, Rakesh

    2013-01-01

    Aim: The purpose of this study was to evaluate the Bolton overall ratio in a north Indian population reporting for orthodontic treatment and to determine the effect of extractions on the Bolton ratios. Another aim of the study was to check the effects of different extraction patterns on the final Bolton ratio. Materials and Methods: One hundred and twenty pre-treatment dental casts (60 males and 60 females) of orthodontic patients were selected randomly. Mesio-distal dimensions of the mandibular and maxillary teeth were measured before treatment, and subjected to Bolton analysis. Hypothetical tooth extraction by the following combinations: All the first premolars, all the second premolars, upper first and lower second premolars and upper second and lower first premolars were performed for each patient. The measurement results were again subjected to Bolton analysis to see whether any tooth-size discrepancy had been created. Results and Conclusion: The tooth material ratio of the studied north Indian population shows a mild maxillary tooth material excess. Extraction of premolars in any combination causes the maxillary tooth material to further increase. There is no significant sex difference in the tooth material ratios with or without extractions. In patients requiring extraction; all first premolar extraction or maxillary first and mandibular second premolar extraction should be preferred. For deciding a treatment plan involving extraction of teeth, we need to consider that the maxillary tooth mass may increase after extraction. Furthermore, the normal or the clinically significant tooth size discrepancies may change following extraction of teeth. PMID:24987639

  10. Effects of habitat fragmentation, population size and demographic history on genetic diversity: the Cross River gorilla in a comparative context.

    PubMed

    Bergl, Richard A; Bradley, Brenda J; Nsubuga, Anthony; Vigilant, Linda

    2008-09-01

    In small and fragmented populations, genetic diversity may be reduced owing to increased levels of drift and inbreeding. This reduced diversity is often associated with decreased fitness and a higher threat of extinction. However, it is difficult to determine when a population has low diversity except in a comparative context. We assessed genetic variability in the critically endangered Cross River gorilla (Gorilla gorilla diehli), a small and fragmented population, using 11 autosomal microsatellite loci. We show that levels of diversity in the Cross River population are not evenly distributed across the three genetically identified subpopulations, and that one centrally located subpopulation has higher levels of variability than the others. All measures of genetic variability in the Cross River population were comparable to those of the similarly small mountain gorilla (G. beringei beringei) populations (Bwindi and Virunga). However, for some measures both the Cross River and mountain gorilla populations show lower levels of diversity than a sample from a large, continuous western gorilla population (Mondika, G. gorilla gorilla). Finally, we tested for the genetic signature of a bottleneck in each of the four populations. Only Cross River showed strong evidence of a reduction in population size, suggesting that the reduction in size of this population was more recent or abrupt than in the two mountain gorilla populations. These results emphasize the need for maintaining connectivity in fragmented populations and highlight the importance of allowing small populations to expand.

  11. Genetic Structure and Effective Population Sizes in European Red Deer (Cervus elaphus) at a Continental Scale: Insights from Microsatellite DNA.

    PubMed

    Zachos, Frank E; Frantz, Alain C; Kuehn, Ralph; Bertouille, Sabine; Colyn, Marc; Niedziałkowska, Magdalena; Pérez-González, Javier; Skog, Anna; Sprĕm, Nikica; Flamand, Marie-Christine

    2016-07-01

    We analyzed more than 600 red deer (Cervus elaphus) from large parts of its European distribution range at 13 microsatellite loci, presenting the first continent-wide study of this species using nuclear markers. Populations were clearly differentiated (overall F ST = 0.166, Jost's D est = 0.385), and the BAPS clustering algorithm yielded mainly geographically limited and adjacent genetic units. When forced into only 3 genetic clusters our data set produced a very similar geographic pattern as previously found in mtDNA phylogeographic studies: a western group from Iberia to central and parts of Eastern Europe, an eastern group from the Balkans to Eastern Europe, and a third group including the threatened relict populations from Sardinia and Mesola in Italy. This result was also confirmed by a multivariate approach to analyzing our data set, a discriminant analysis of principal components. Calculations of genetic diversity and effective population sizes (linkage disequilibrium approach) yielded the lowest results for Italian (Sardinia, Mesola; N e between 2 and 8) and Scandinavian red deer, in line with known bottlenecks in these populations. Our study is the first to present comparative nuclear genetic data in red deer across Europe and may serve as a baseline for future analyses of genetic diversity and structuring in this widespread ungulate.

  12. Universal size effects for populations in group-outcome decision-making problems

    NASA Astrophysics Data System (ADS)

    Borghesi, Christian; Hernández, Laura; Louf, Rémi; Caparros, Fabrice

    2013-12-01

    Elections constitute a paradigm of decision-making problems that have puzzled experts of different disciplines for decades. We study two decision-making problems, where groups make decisions that impact only themselves as a group. In both studied cases, participation in local elections and the number of democratic representatives at different scales (from local to national), we observe a universal scaling with the constituency size. These results may be interpreted as constituencies having a hierarchical structure, where each group of N agents, at each level of the hierarchy, is divided in about Nδ subgroups with δ≈1/3. Following this interpretation, we propose a phenomenological model of vote participation where abstention is related to the perceived link of an agent to the rest of the constituency and which reproduces quantitatively the observed data.

  13. Genetic variation, relatedness, and effective population size of polar bears (Ursus maritimus) in the southern Beaufort Sea, Alaska.

    PubMed

    Cronin, Matthew A; Amstrup, Steven C; Talbot, Sandra L; Sage, George K; Amstrup, Kristin S

    2009-01-01

    Polar bears (Ursus maritimus) are unique among bears in that they are adapted to the Arctic sea ice environment. Genetic data are useful for understanding their evolution and can contribute to management. We assessed parentage and relatedness of polar bears in the southern Beaufort Sea, Alaska, with genetic data and field observations of age, sex, and mother-offspring and sibling relationships. Genotypes at 14 microsatellite DNA loci for 226 bears indicate that genetic variation is comparable to other populations of polar bears with mean number of alleles per locus of 7.9 and observed and expected heterozygosity of 0.71. The genetic data verified 60 field-identified mother-offspring pairs and identified 10 additional mother-cub pairs and 48 father-offspring pairs. The entire sample of related and unrelated bears had a mean pairwise relatedness index (r(xy)) of approximately zero, parent-offspring and siblings had r(xy) of approximately 0.5, and 5.2% of the samples had r(xy) values within the range expected for parent-offspring. Effective population size (N(e) = 277) and the ratio of N(e) to total population size (N(e)/N = 0.182) were estimated from the numbers of reproducing males and females. N(e) estimates with genetic methods gave variable results. Our results verify and expand field data on reproduction by females and provide new data on reproduction by males and estimates of relatedness and N(e) in a polar bear population.

  14. Effects of consumption-oriented versus trophy-oriented fisheries on Muskellunge population size structure in northern Wisconsin

    USGS Publications Warehouse

    Faust, Matthew D.; Hansen, Michael J.

    2016-01-01

    To determine whether a consumption-oriented fishery was compatible with a trophy-oriented fishery for Muskellunge Esox masquinongy, we modeled effects of a spearing fishery and recreational angling fishery on population size structure (i.e., numbers of fish ≥ 102, 114, and 127 cm) in northern Wisconsin. An individual-based simulation model was used to quantify the effect of harvest mortality at currently observed levels of recreational angling and tribal spearing fishery exploitation, along with simulated increases in exploitation, for three typical growth potentials (i.e., low, moderate, and high) of Muskellunge in northern Wisconsin across a variety of minimum length limits (i.e., 71, 102, 114, and 127 cm). Populations with moderate to high growth potential and minimum length limits ≥ 114 cm were predicted to have lower declines in numbers of trophy Muskellunge when subjected to angling-only and mixed fisheries at observed and increased levels of exploitation, which suggested that fisheries with disparate motivations may be able to coexist under certain conditions such as restrictive length limits and low levels of exploitation. However, for most Muskellunge populations in northern Wisconsin regulated by a 102-cm minimum length limit, both angling and spearing fisheries may reduce numbers of trophy Muskellunge as larger declines were predicted across all growth potentials. Our results may be useful if Muskellunge management options in northern Wisconsin are re-examined in the future.

  15. Being abundant is not enough: a decrease in effective population size over eight generations in a Norwegian population of the seaweed, Fucus serratus.

    PubMed

    Coyer, James A; Hoarau, Galice; Sjøtun, Kjersti; Olsen, Jeanine L

    2008-12-23

    The brown alga Fucus serratus is a key foundation species on rocky intertidal shores of northern Europe. We sampled the same population off the coast of southern Norway in 2000 and 2008, and using 26 microsatellite loci, we estimated the changes in genetic diversity and effective population size (Ne). The unexpectedly low Ne (73-386) and Ne/N ratio (10-3-10-4), in combination with a significant decrease (14%) in allelic richness over the 8-year period, suggests an increased local extinction risk. If small Ne proves to be a common feature of F. serratus, then being abundant may not be enough for the species to weather future environmental changes.

  16. Temporal trends in genetic data and effective population size support efficacy of management practices in critically endangered dusky gopher frogs (Lithobates sevosus).

    PubMed

    Hinkson, Kristin M; Richter, Stephen C

    2016-05-01

    Monitoring temporal changes in population genetic diversity and effective population size can provide vital information on future viability. The dusky gopher frog, Lithobates sevosus, is a critically endangered species found only in coastal Mississippi, with low genetic variability as a consequence of isolation and population size reduction. Conservation management practices have been implemented, but their efficacy has not been addressed. We genotyped individuals collected 1997-2014 to determine temporal trends in population genetic variation, structure, and effective size. Observed and expected heterozygosity and allelic richness revealed temporally stable, but low, levels of genetic variation. Positive levels of inbreeding were found in each year. There was weak genetic structure among years, which can be attributed to increased effects of genetic drift and inbreeding in small populations. L. sevosus exhibited an increase in effective population size, and currently has an estimated effective size of 33.0-58.6 individuals, which is approximately half the census size. This large ratio could possibly be explained by genetic compensation. We found that management practices have been effective at maintaining and improving effective size and genetic diversity, but that additional strategies need to be implemented to enhance viability of the species.

  17. Myotis rufoniger genome sequence and analyses: M. rufoniger's genomic feature and the decreasing effective population size of Myotis bats.

    PubMed

    Bhak, Youngjune; Jeon, Yeonsu; Jeon, Sungwon; Chung, Oksung; Jho, Sungwoong; Jun, JeHoon; Kim, Hak-Min; Cho, Yongsoo; Yoon, Changhan; Lee, Seungwoo; Kang, Jung-Hoon; Lim, Jong-Deock; An, Junghwa; Cho, Yun Sung; Ryu, Doug-Young; Bhak, Jong

    2017-01-01

    Myotis rufoniger is a vesper bat in the genus Myotis. Here we report the whole genome sequence and analyses of the M. rufoniger. We generated 124 Gb of short-read DNA sequences with an estimated genome size of 1.88 Gb at a sequencing depth of 66× fold. The sequences were aligned to M. brandtii bat reference genome at a mapping rate of 96.50% covering 95.71% coding sequence region at 10× coverage. The divergence time of Myotis bat family is estimated to be 11.5 million years, and the divergence time between M. rufoniger and its closest species M. davidii is estimated to be 10.4 million years. We found 1,239 function-altering M. rufoniger specific amino acid sequences from 929 genes compared to other Myotis bat and mammalian genomes. The functional enrichment test of the 929 genes detected amino acid changes in melanin associated DCT, SLC45A2, TYRP1, and OCA2 genes possibly responsible for the M. rufoniger's red fur color and a general coloration in Myotis. N6AMT1 gene, associated with arsenic resistance, showed a high degree of function alteration in M. rufoniger. We further confirmed that the M. rufoniger also has bat-specific sequences within FSHB, GHR, IGF1R, TP53, MDM2, SLC45A2, RGS7BP, RHO, OPN1SW, and CNGB3 genes that have already been published to be related to bat's reproduction, lifespan, flight, low vision, and echolocation. Additionally, our demographic history analysis found that the effective population size of Myotis clade has been consistently decreasing since ~30k years ago. M. rufoniger's effective population size was the lowest in Myotis bats, confirming its relatively low genetic diversity.

  18. Fat or fiction? Effects of body size, eating pathology, and sex upon the body schema of an undergraduate population.

    PubMed

    Wignall, Sophie J; Thomas, Nicole A; Nicholls, Michael E R

    2017-10-06

    Although there is a growing consensus that women with anorexia nervosa have a distorted body schema, the origins of this disturbance remain uncertain. The present investigation examined the effects of body size, eating pathology, and sex upon the body schema of an at-risk, undergraduate population. In Study 1, 98 participants mentally simulated their passage through apertures. When aperture width was manipulated, narrow and broad women over- and under-estimated their spatial requirements for passage, respectively. This relationship was exacerbated by dietary restraint. When aperture height was manipulated, short and tall men over- and under-estimated their spatial requirements for passage, respectively. Study 2 (N=32) replicated the association between women's veridical and internally-represented widths, although no significant effects of eating pathology were observed. Our findings suggest that body schema enlargement is not necessarily pathological, and may be driven by normal perceptual biases and internalised sociocultural body ideals. Copyright © 2017 Elsevier Ltd. All rights reserved.

  19. Effects of premolar extractions on Bolton overall ratios and tooth-size discrepancies in a Japanese orthodontic population.

    PubMed

    Endo, Toshiya; Ishida, Katuyuki; Shundo, Isao; Sakaeda, Kosuke; Shimooka, Shohachi

    2010-04-01

    The purpose of this study was to investigate the effects of premolar extractions on the Bolton overall ratios and overall tooth-size discrepancies in a Japanese orthodontic population. Mesiodistal tooth widths were measured on 198 pretreatment dental casts of subjects with Class I, Class II, and Class III malocclusions. The overall ratios and tooth-size discrepancies were determined before and after hypothetical premolar extractions. Before and after extractions, the subjects were divided into small, normal, and large overall ratio groups categorized by the Bolton standard deviation definition, and into small, normal, and large correction groups by the actual amount of change calculated for tooth-size correction in millimeters. Extractions were performed in the following combinations: (1) all first premolars, (2) all second premolars, (3) maxillary first and mandibular second premolars, and (4) maxillary second and mandibular first premolars. For statistical evaluations, analysis of variance, Kruskal-Wallis, Friedman, Scheffé, Bonferroni, and Tukey tests were performed. The overall ratios decreased in every malocclusion group after extraction of any combination of premolars. The decreases were significantly notable in combinations 2 and 4. Some subjects in the normal overall ratio and maxillary and mandibular correction groups moved into the clinically significant tooth-size discrepancy group after premolar extraction, and the reverse was also true. In formulating a treatment plan involving premolar extractions, orthodontists should consider that the overall ratios might decrease, and normal and clinically significant tooth-size discrepancies could change mutually after extractions. Copyright (c) 2010 American Association of Orthodontists. Published by Mosby, Inc. All rights reserved.

  20. The 1p13.3 LDL (C)-Associated Locus Shows Large Effect Sizes in Young Populations

    PubMed Central

    Devaney, Joseph M.; Thompson, Paul D.; Visich, Paul S.; Saltarelli, William A.; Gordon, Paul M.; Orkunoglu-Suer, E. Funda; Gordish-Dressman, Heather; Harmon, Brennan T.; Bradbury, Margaret K.; Panchapakesan, Karuna; Khianey, Rahul; Hubal, Monica J.; Clarkson, Priscilla M.; Pescatello, Linda S.; Zoeller, Robert F.; Moyna, Niall M.; Angelopoulos, Theodore J.; Kraus, William E.; Hoffman, Eric P.

    2013-01-01

    Genome-wide association studies (GWAS) have identified polymorphic loci associated with coronary artery disease (CAD) risk factors (i. e. serum lipids) in adult populations (42–69 yrs). We hypothesized that younger populations would show a greater relative genetic component due to fewer confounding variables. We examined the influence of 20 GWAS loci associated with serum lipids and insulin metabolism, in a university student cohort (n=548; mean age= 24 yrs), and replicated statistically associated results in a second study cohort of primary school students (n=810, mean age= 11.5 yrs). 19 loci showed no relationship with studied risk factors in young adults. However, the ancestral allele of the rs646776 (SORT1) locus was strongly associated with increased low density lipoprotein cholesterol {LDL (C)} in young adults (TT: 97.6 ± 1.0 mg/dL {n=345}, vs. CT/CC: 87.3 ± 1.0 mg/dL {n=203}; p = 3 × 10−6) and children (TT: 94.0 ± 1.3 mg/dL {n=551}, vs. CT/CC: 84.7 ± 1.4 mg/dL {n=259}; p = 4 × 10−6). This locus is responsible for 3.6% of population variance in young adults and 2.5% of population variance in children. The effect size of the SORT1 locus is considerably higher in young populations (2.5%–4.1%) compared to older subjects (1%). PMID:21297524

  1. A method for detecting recent changes in contemporary effective population size from linkage disequilibrium at linked and unlinked loci.

    PubMed

    Hollenbeck, C M; Portnoy, D S; Gold, J R

    2016-10-01

    Estimation of contemporary effective population size (Ne) from linkage disequilibrium (LD) between unlinked pairs of genetic markers has become an important tool in the field of population and conservation genetics. If data pertaining to physical linkage or genomic position are available for genetic markers, estimates of recombination rate between loci can be combined with LD data to estimate contemporary Ne at various times in the past. We extend the well-known, LD-based method of estimating contemporary Ne to include linkage information and show via simulation that even relatively small, recent changes in Ne can be detected reliably with a modest number of single-nucleotide polymorphism (SNP) loci. We explore several issues important to interpretation of the results and quantify the bias in estimates of contemporary Ne associated with the assumption that all loci in a large SNP data set are unlinked. The approach is applied to an empirical data set of SNP genotypes from a population of a marine fish where a recent, temporary decline in Ne is known to have occurred.

  2. Spatial homogeneity and temporal heterogeneity of red drum (Sciaenops ocellatus) microsatellites: effective population sizes and management implications.

    PubMed

    Chapman, Robert W; Ball, A O; Mash, Lisa R

    2002-12-01

    The red drum (Sciaenops ocellatus) is one of a number of species that occupy estuarine waters as juveniles and migrate to open ocean waters as adults. This species has experienced dramatic declines in population numbers over the past 2 decades, which has prompted increasing fishery restriction. In addition, hatchery augmentation has been initiated by several states to increase the abundance of juveniles in local areas. In South Carolina hatchery-reared fish have made significant (20%) contributions to the juvenile population on very local scales. As hatchery-reared fish are typically produced by a small number of individuals, the genetic consequences of augmentation programs are of concern. In this article we assess genetic variation at 5 microsatellite loci in S. ocellatus. The data indicate little geographic differentiation among samples collected along the Atlantic Coast of the United States, but substantial differences among year classes taken from South Carolina. The gene frequency differences among year classes were used to estimate the effective population size (Nc) of S. ocellatus in South Carolina and suggested that Ne was less than 300 from 1990 to 1993 and increased to about 1000 in 1994 and 1995. Whether this increase reflects the effectiveness of management regulations or simply a random fluctuation in S. ocellatus populations is not clear. The data suggest that a limited number of individuals produce the bulk of a given year class and support the sweepstakes hypothesis. Given the small Ne and estimates of the contribution of hatchery-reared fish to the wild stock, it is suggested that programs have the potential to increase, rather than decrease; Ne in the wild.

  3. Efficient and Unbiased Estimation of Population Size

    PubMed Central

    Cruz, Marcos; Gómez, Domingo; Cruz-Orive, Luis M.

    2015-01-01

    Population sizing from still aerial pictures is of wide applicability in ecological and social sciences. The problem is long standing because current automatic detection and counting algorithms are known to fail in most cases, and exhaustive manual counting is tedious, slow, difficult to verify and unfeasible for large populations. An alternative is to multiply population density with some reference area but, unfortunately, sampling details, handling of edge effects, etc., are seldom described. For the first time we address the problem using principles of geometric sampling. These principles are old and solid, but largely unknown outside the areas of three dimensional microscopy and stereology. Here we adapt them to estimate the size of any population of individuals lying on an essentially planar area, e.g. people, animals, trees on a savanna, etc. The proposed design is unbiased irrespective of population size, pattern, perspective artifacts, etc. The implementation is very simple—it is based on the random superimposition of coarse quadrat grids. Also, an objective error assessment is often lacking. For the latter purpose the quadrat counts are often assumed to be independent. We demonstrate that this approach can perform very poorly, and we propose (and check via Monte Carlo resampling) a new theoretical error prediction formula. As far as efficiency, counting about 50 (100) individuals in 20 quadrats, can yield relative standard errors of about 8% (5%) in typical cases. This fact effectively breaks the barrier hitherto imposed by the current lack of automatic face detection algorithms, because semiautomatic sampling and manual counting becomes an attractive option. PMID:26535587

  4. Life-history traits and effective population size in species with overlapping generations revisited: the importance of adult mortality.

    PubMed

    Waples, R S

    2016-10-01

    The relationship between life-history traits and the key eco-evolutionary parameters effective population size (Ne) and Ne/N is revisited for iteroparous species with overlapping generations, with a focus on the annual rate of adult mortality (d). Analytical methods based on populations with arbitrarily long adult lifespans are used to evaluate the influence of d on Ne, Ne/N and the factors that determine these parameters: adult abundance (N), generation length (T), age at maturity (α), the ratio of variance to mean reproductive success in one season by individuals of the same age (φ) and lifetime variance in reproductive success of individuals in a cohort (Vk•). Although the resulting estimators of N, T and Vk• are upwardly biased for species with short adult lifespans, the estimate of Ne/N is largely unbiased because biases in T are compensated for by biases in Vk• and N. For the first time, the contrasting effects of T and Vk• on Ne and Ne/N are jointly considered with respect to d and φ. A simple function of d and α based on the assumption of constant vital rates is shown to be a robust predictor (R(2)=0.78) of Ne/N in an empirical data set of life tables for 63 animal and plant species with diverse life histories. Results presented here should provide important context for interpreting the surge of genetically based estimates of Ne that has been fueled by the genomics revolution.

  5. On Effect Size

    ERIC Educational Resources Information Center

    Kelley, Ken; Preacher, Kristopher J.

    2012-01-01

    The call for researchers to report and interpret effect sizes and their corresponding confidence intervals has never been stronger. However, there is confusion in the literature on the definition of effect size, and consequently the term is used inconsistently. We propose a definition for effect size, discuss 3 facets of effect size (dimension,…

  6. On Effect Size

    ERIC Educational Resources Information Center

    Kelley, Ken; Preacher, Kristopher J.

    2012-01-01

    The call for researchers to report and interpret effect sizes and their corresponding confidence intervals has never been stronger. However, there is confusion in the literature on the definition of effect size, and consequently the term is used inconsistently. We propose a definition for effect size, discuss 3 facets of effect size (dimension,…

  7. Adaptive Parent Population Sizing in Evolution Strategies.

    PubMed

    LaPorte, G Jake; Branke, Juergen; Chen, Chun-Hung

    2015-01-01

    Adaptive population sizing aims at improving the overall progress of an evolution strategy. At each generation, it determines the parental population size that promises the largest fitness gain, based on the information collected during the evolutionary process. In this paper, we develop an adaptive variant of a (μ/μ, λ) evolution strategy. Based on considerations on the sphere, we derive two approaches for adaptive population sizing. We then test these approaches empirically on the sphere model using a normalized mutation strength and cumulative mutation strength adaption. Finally, we compare the methodology on more general functions with a fixed population, covariance matrix adaption evolution strategy (CMA-ES). The results confirm that our adaptive population sizing methods yield better results than even the best fixed population size.

  8. Relationship between effective population size, inbreeding and adult fitness-related traits in a steelhead (Oncorhynchus mykiss) population released in the wild.

    PubMed

    Naish, K A; Seamons, T R; Dauer, M B; Hauser, L; Quinn, T P

    2013-03-01

    Inbreeding is of concern in supportive breeding programmes in Pacific salmonids, Oncorhynchus spp, where the number of breeding adults is limited by rearing space or poor survival to adulthood, and large numbers are released to supplement wild stocks and fisheries. We reconstructed the pedigree of 6602 migratory hatchery steelhead (Oncorhynchus mykiss) over four generations, to determine the incidence and fitness consequences of inbreeding in a northwest USA programme. The hatchery maintained an effective population size, Ñ(e) = 107.9 from F(0) to F(2), despite an increasing census size (N), which resulted in a decreasing N(e)/N ratio (0.35 in F(0) to 0.08 in F(2)). The reduced ratio was attributed to a small broodstock size, nonrandom transfers and high variance in reproductive success (particularly in males). We observed accumulation of inbreeding from the founder generation (in F(4), percentage individuals with inbreeding coefficients Δf > 0 = 15.7%). Generalized linear mixed models showed that body length and weight decreased significantly with increasing Δf, and inbred fish returned later to spawn in a model that included father identity. However, there was no significant correlation between Δf and age at return, female fecundity or gonad weight. Similarly, there was no relationship between Δf and reproductive success of F(2) and F(3) individuals, which might be explained by the fact that reproductive success is partially controlled by hatchery mating protocols. This study is one of the first to show that small changes in inbreeding coefficient can affect some fitness-related traits in a monitored population propagated and released to the wild.

  9. Estimating total population size for Songbirds

    Treesearch

    Jonathan Bart

    2005-01-01

    A conviction has developed during the past few years within the avian conservation community that estimates of total population size are needed for many species, especially ones that warrant conservation action. For example, the recently completed monitoring plans for North American shorebirds and landbirds establish estimating population size as a major objective....

  10. Does the invasive Lupinus polyphyllus increase pollinator visitation to a native herb through effects on pollinator population sizes?

    PubMed

    Jakobsson, Anna; Padrón, Benigno

    2014-01-01

    Invasive plants may compete with native species for abiotic factors as light, space and nutrients, and have also been shown to affect native pollination interactions. Studies have mainly focused on how invasive plants affect pollinator behaviour, i.e. attraction of pollinators to or away from native flowers. However, when an invasive plant provides resources utilized by native pollinators this could increase pollinator population sizes and thereby pollination success in natives. Effects mediated through changes in pollinator population sizes have been largely ignored in previous studies, and the dominance of negative interactions suggested by meta-analyses may therefore be biased. We investigated the impact of the invasive Lupinus polyphyllus on pollination in the native Lotus corniculatus using a study design comparing invaded and uninvaded sites before and after the flowering period of the invasive. We monitored wild bee abundance in transects, and visit rate and seed production of potted Lotus plants. Bumblebee abundance increased 3.9 times in invaded sites during the study period, whereas it was unaltered in uninvaded sites. Total visit rate per Lotus plant increased 2.1 times in invaded sites and decreased 4.4 times in uninvaded sites. No corresponding change in seed production of Lotus was found. The increase in visit rate to Lotus was driven by an increase in solitary bee visitation, whereas mainly bumblebees were observed to visit the invasive Lupinus. The mechanism by which the invasive increases pollinator visit rates to Lotus could be increased availability of other flower resources for solitary bees when bumblebees forage on Lupinus.

  11. Estimating contemporary effective population size in non-model species using linkage disequilibrium across thousands of loci.

    PubMed

    Waples, R K; Larson, W A; Waples, R S

    2016-10-01

    Contemporary effective population size (Ne) can be estimated using linkage disequilibrium (LD) observed across pairs of loci presumed to be selectively neutral and unlinked. This method has been commonly applied to data sets containing 10-100 loci to inform conservation and study population demography. Performance of these Ne estimates could be improved by incorporating data from thousands of loci. However, these thousands of loci exist on a limited number of chromosomes, ensuring that some fraction will be physically linked. Linked loci have elevated LD due to limited recombination, which if not accounted for can cause Ne estimates to be downwardly biased. Here, we present results from coalescent and forward simulations designed to evaluate the bias of LD-based Ne estimates ([Ncirc ]e). Contrary to common perceptions, increasing the number of loci does not increase the magnitude of linkage. Although we show it is possible to identify some pairs of loci that produce unusually large r(2) values, simply removing large r(2) values is not a reliable way to eliminate bias. Fortunately, the magnitude of bias in [Ncirc ]e is strongly and negatively correlated with the process of recombination, including the number of chromosomes and their length, and this relationship provides a general way to adjust for bias. Additionally, we show that with thousands of loci, precision of [Ncirc ]e is much lower than expected based on the assumption that each pair of loci provides completely independent information.

  12. Monitoring Dolphins in an Urban Marine System: Total and Effective Population Size Estimates of Indo-Pacific Bottlenose Dolphins in Moreton Bay, Australia

    PubMed Central

    Ansmann, Ina C.; Lanyon, Janet M.; Seddon, Jennifer M.; Parra, Guido J.

    2013-01-01

    Moreton Bay, Queensland, Australia is an area of high biodiversity and conservation value and home to two sympatric sub-populations of Indo-Pacific bottlenose dolphins (Tursiops aduncus). These dolphins live in close proximity to major urban developments. Successful management requires information regarding their abundance. Here, we estimate total and effective population sizes of bottlenose dolphins in Moreton Bay using photo-identification and genetic data collected during boat-based surveys in 2008–2010. Abundance (N) was estimated using open population mark-recapture models based on sighting histories of distinctive individuals. Effective population size (Ne) was estimated using the linkage disequilibrium method based on nuclear genetic data at 20 microsatellite markers in skin samples, and corrected for bias caused by overlapping generations (Nec). A total of 174 sightings of dolphin groups were recorded and 365 different individuals identified. Over the whole of Moreton Bay, a population size N of 554±22.2 (SE) (95% CI: 510–598) was estimated. The southern bay sub-population was small at an estimated N = 193±6.4 (SE) (95% CI: 181–207), while the North sub-population was more numerous, with 446±56 (SE) (95% CI: 336–556) individuals. The small estimated effective population size of the southern sub-population (Nec = 56, 95% CI: 33–128) raises conservation concerns. A power analysis suggested that to reliably detect small (5%) declines in size of this population would require substantial survey effort (>4 years of annual mark-recapture surveys) at the precision levels achieved here. To ensure that ecological as well as genetic diversity within this population of bottlenose dolphins is preserved, we consider that North and South sub-populations should be treated as separate management units. Systematic surveys over smaller areas holding locally-adapted sub-populations are suggested as an alternative method for increasing ability to detect

  13. A Classroom Investigation of the Effect of Population Size and Income on Success in the London 2012 Olympics

    ERIC Educational Resources Information Center

    Carter, Nancy; Felton, Nathan; Schwertman, Neil

    2014-01-01

    Engaging students in active learning can enhance their understanding and appreciation of a subject such as statistics. Classroom activities and projects help to engage students and further promote the learning process. In this paper, an activity investigating the influence of population size and wealth on the medal counts from the 2012 London…

  14. A Classroom Investigation of the Effect of Population Size and Income on Success in the London 2012 Olympics

    ERIC Educational Resources Information Center

    Carter, Nancy; Felton, Nathan; Schwertman, Neil

    2014-01-01

    Engaging students in active learning can enhance their understanding and appreciation of a subject such as statistics. Classroom activities and projects help to engage students and further promote the learning process. In this paper, an activity investigating the influence of population size and wealth on the medal counts from the 2012 London…

  15. The Effect of Small-Size Habitat Disturbances on Population Density and Time to Extinction of the Prairie Vole

    SciTech Connect

    Kostova, T; Carlsen, T

    2004-12-13

    We present a study, based on simulations with SERDYCA, a spatially-explicit individual-based model of rodent dynamics, on the relation between population persistence and the presence of numerous isolated disturbances in the habitat. We are specifically interested in the effect of disturbances that do not fragment the environment on population persistence. Our results suggest that the presence of disturbances in the absence of fragmentation can actually increase the average time to extinction of the modeled population. The presence of disturbances decreases population density but can increase the chance for mating in monogamous species and consequently, the ratio of juveniles in the population. It thus provides a better chance for the population to restore itself after a severe period with critically low population density. We call this the ''disturbance-forced localization effect''.

  16. Population size and the rate of evolution.

    PubMed

    Lanfear, Robert; Kokko, Hanna; Eyre-Walker, Adam

    2014-01-01

    Does evolution proceed faster in larger or smaller populations? The relationship between effective population size (Ne) and the rate of evolution has consequences for our ability to understand and interpret genomic variation, and is central to many aspects of evolution and ecology. Many factors affect the relationship between Ne and the rate of evolution, and recent theoretical and empirical studies have shown some surprising and sometimes counterintuitive results. Some mechanisms tend to make the relationship positive, others negative, and they can act simultaneously. The relationship also depends on whether one is interested in the rate of neutral, adaptive, or deleterious evolution. Here, we synthesize theoretical and empirical approaches to understanding the relationship and highlight areas that remain poorly understood. Copyright © 2013. Published by Elsevier Ltd.

  17. The effect of Wolbachia-induced cytoplasmic incompatibility on host population size in natural and manipulated systems.

    PubMed Central

    Dobson, Stephen L; Fox, Charles W; Jiggins, Francis M

    2002-01-01

    Obligate, intracellular bacteria of the genus Wolbachia often behave as reproductive parasites by manipulating host reproduction to enhance their vertical transmission. One of these reproductive manipulations, cytoplasmic incompatibility, causes a reduction in egg-hatch rate in crosses between individuals with differing infections. Applied strategies based upon cytoplasmic incompatibility have been proposed for both the suppression and replacement of host populations. As Wolbachia infections occur within a broad range of invertebrates, these strategies are potentially applicable to a variety of medically and economically important insects. Here, we examine the interaction between Wolbachia infection frequency and host population size. We use a model to describe natural invasions of Wolbachia infections, artificial releases of infected hosts and releases of sterile males, as part of a traditional sterile insect technique programme. Model simulations demonstrate the importance of understanding the reproductive rate and intraspecific competition type of the targeted population, showing that releases of sterile or incompatible individuals may cause an undesired increase in the adult number. In addition, the model suggests a novel applied strategy that employs Wolbachia infections to suppress host populations. Releases of Wolbachia-infected hosts can be used to sustain artificially an unstable coexistence of multiple incompatible infections within a host population, allowing the host population size to be reduced, maintained at low levels, or eliminated. PMID:11886634

  18. Effects of earlier sea ice breakup on survival and population size of polar bears in western Hudson Bay

    USGS Publications Warehouse

    Regehr, E.V.; Lunn, N.J.; Amstrup, Steven C.; Stirling, I.

    2007-01-01

    Some of the most pronounced ecological responses to climatic warming are expected to occur in polar marine regions, where temperature increases have been the greatest and sea ice provides a sensitive mechanism by which climatic conditions affect sympagic (i.e., with ice) species. Population-level effects of climatic change, however, remain difficult to quantify. We used a flexible extension of Cormack-Jolly-Seber capture-recapture models to estimate population size and survival for polar bears (Ursus maritimus), one of the most ice-dependent of Arctic marine mammals. We analyzed data for polar bears captured from 1984 to 2004 along the western coast of Hudson Bay and in the community of Churchill, Manitoba, Canada. The Western Hudson Bay polar bear population declined from 1,194 (95% CI = 1,020-1,368) in 1987 to 935 (95% CI = 794-1,076) in 2004. Total apparent survival of prime-adult polar bears (5-19 yr) was stable for females (0.93; 95% CI = 0.91-0.94) and males (0.90; 95% CI = 0.88-0.91). Survival of juvenile, subadult, and senescent-adult polar bears was correlated with spring sea ice breakup date, which was variable among years and occurred approximately 3 weeks earlier in 2004 than in 1984. We propose that this correlation provides evidence for a causal association between earlier sea ice breakup (due to climatic warming) and decreased polar bear survival. It may also explain why Churchill, like other communities along the western coast of Hudson Bay, has experienced an increase in human-polar bear interactions in recent years. Earlier sea ice breakup may have resulted in a larger number of nutritionally stressed polar bears, which are encroaching on human habitations in search of supplemental food. Because western Hudson Bay is near the southern limit of the species' range, our findings may foreshadow the demographic responses and management challenges that more northerly polar bear populations will experience if climatic warming in the Arctic continues as

  19. Contrasting effects of large density changes on relative testes size in fluctuating populations of sympatric vole species

    PubMed Central

    Klemme, Ines; Soulsbury, Carl D.; Henttonen, Heikki

    2014-01-01

    Across species, there is usually a positive relationship between sperm competition level and male reproductive effort on ejaculates, typically measured using relative testes size (RTS). Within populations, demographic and ecological processes may drastically alter the level of sperm competition and thus, potentially affect the evolution of testes size. Here, we use longitudinal records (across 38 years) from wild sympatric Fennoscandian populations of five species of voles to investigate whether RTS responds to natural fluctuations in population density, i.e. variation in sperm competition risk. We show that for some species RTS increases with density. However, our results also show that this relationship can be reversed in populations with large-scale between-year differences in density. Multiple mechanisms are suggested to explain the negative RTS–density relationship, including testes size response to density-dependent species interactions, an evolutionary response to sperm competition levels that is lagged when density fluctuations are over a certain threshold, or differing investment in pre- and post-copulatory competition at different densities. The results emphasize that our understanding of sperm competition in fluctuating environments is still very limited. PMID:25122229

  20. Effective population size, genetic variation, and their relevance for conservation: the bighorn sheep in Tiburon Island and comparisons with managed artiodactyls.

    PubMed

    Gasca-Pineda, Jaime; Cassaigne, Ivonne; Alonso, Rogelio A; Eguiarte, Luis E

    2013-01-01

    The amount of genetic diversity in a finite biological population mostly depends on the interactions among evolutionary forces and the effective population size (N(e)) as well as the time since population establishment. Because the N(e) estimation helps to explore population demographic history, and allows one to predict the behavior of genetic diversity through time, N(e) is a key parameter for the genetic management of small and isolated populations. Here, we explored an N(e)-based approach using a bighorn sheep population on Tiburon Island, Mexico (TI) as a model. We estimated the current (N(crnt)) and ancestral stable (N(stbl)) inbreeding effective population sizes as well as summary statistics to assess genetic diversity and the demographic scenarios that could explain such diversity. Then, we evaluated the feasibility of using TI as a source population for reintroduction programs. We also included data from other bighorn sheep and artiodactyl populations in the analysis to compare their inbreeding effective size estimates. The TI population showed high levels of genetic diversity with respect to other managed populations. However, our analysis suggested that TI has been under a genetic bottleneck, indicating that using individuals from this population as the only source for reintroduction could lead to a severe genetic diversity reduction. Analyses of the published data did not show a strict correlation between H(E) and N(crnt) estimates. Moreover, we detected that ancient anthropogenic and climatic pressures affected all studied populations. We conclude that the estimation of N(crnt) and N(stbl) are informative genetic diversity estimators and should be used in addition to summary statistics for conservation and population management planning.

  1. Effective Population Size, Genetic Variation, and Their Relevance for Conservation: The Bighorn Sheep in Tiburon Island and Comparisons with Managed Artiodactyls

    PubMed Central

    Gasca-Pineda, Jaime; Cassaigne, Ivonne; Alonso, Rogelio A.; Eguiarte, Luis E.

    2013-01-01

    The amount of genetic diversity in a finite biological population mostly depends on the interactions among evolutionary forces and the effective population size (Ne) as well as the time since population establishment. Because the Ne estimation helps to explore population demographic history, and allows one to predict the behavior of genetic diversity through time, Ne is a key parameter for the genetic management of small and isolated populations. Here, we explored an Ne-based approach using a bighorn sheep population on Tiburon Island, Mexico (TI) as a model. We estimated the current (Ncrnt) and ancestral stable (Nstbl) inbreeding effective population sizes as well as summary statistics to assess genetic diversity and the demographic scenarios that could explain such diversity. Then, we evaluated the feasibility of using TI as a source population for reintroduction programs. We also included data from other bighorn sheep and artiodactyl populations in the analysis to compare their inbreeding effective size estimates. The TI population showed high levels of genetic diversity with respect to other managed populations. However, our analysis suggested that TI has been under a genetic bottleneck, indicating that using individuals from this population as the only source for reintroduction could lead to a severe genetic diversity reduction. Analyses of the published data did not show a strict correlation between HE and Ncrnt estimates. Moreover, we detected that ancient anthropogenic and climatic pressures affected all studied populations. We conclude that the estimation of Ncrnt and Nstbl are informative genetic diversity estimators and should be used in addition to summary statistics for conservation and population management planning. PMID:24147115

  2. Determining the Population Size of Pond Phytoplankton.

    ERIC Educational Resources Information Center

    Hummer, Paul J.

    1980-01-01

    Discusses methods for determining the population size of pond phytoplankton, including water sampling techniques, laboratory analysis of samples, and additional studies worthy of investigation in class or as individual projects. (CS)

  3. One is enough: in vivo effective population size is dose-dependent for a plant RNA virus.

    PubMed

    Zwart, Mark P; Daròs, José-Antonio; Elena, Santiago F

    2011-07-01

    Effective population size (N(e)) determines the strength of genetic drift and the frequency of co-infection by multiple genotypes, making it a key factor in viral evolution. Experimental estimates of N(e) for different plant viruses have, however, rendered diverging results. The independent action hypothesis (IAH) states that each virion has a probability of infection, and that virions act independent of one another during the infection process. A corollary of IAH is that N(e) must be dose dependent. A test of IAH for a plant virus has not been reported yet. Here we perform a test of an IAH infection model using a plant RNA virus, Tobacco etch virus (TEV) variants carrying GFP or mCherry fluorescent markers, in Nicotiana tabacum and Capsicum annuum plants. The number of primary infection foci increased linearly with dose, and was similar to a Poisson distribution. At high doses, primary infection foci containing both genotypes were found at a low frequency (<2%). The probability that a genotype that infected the inoculated leaf would systemically infect that plant was near 1, although in a few rare cases genotypes could be trapped in the inoculated leaf by being physically surrounded by the other genotype. The frequency of mixed-genotype infection could be predicted from the mean number of primary infection foci using the independent-action model. Independent action appears to hold for TEV, and N(e) is therefore dose-dependent for this plant RNA virus. The mean number of virions causing systemic infection can be very small, and approaches 1 at low doses. Dose-dependency in TEV suggests that comparison of N(e) estimates for different viruses are not very meaningful unless dose effects are taken into consideration.

  4. Global phylogeography of the dolphinfish (Coryphaena hippurus): the influence of large effective population size and recent dispersal on the divergence of a marine pelagic cosmopolitan species.

    PubMed

    Díaz-Jaimes, P; Uribe-Alcocer, M; Rocha-Olivares, A; García-de-León, F J; Nortmoon, P; Durand, J D

    2010-12-01

    Pelagic fish that are distributed circumtropically are characterised by a low population structure level as a result of a high capacity for dispersion and large population sizes. Nevertheless, historical and contemporary processes, including past demographic and/or range expansions, secondary contact, dispersal, gene flow, and the achievement of large effective population sizes, may play a part in the detection of divergence signals, especially in the case of tropical pelagic species, whose distribution range depends strongly on the sea surface temperature. The connectivity and historical demography of Atlantic, Indian, Pacific and Mediterranean populations of dolphinfish (Coryphaena hippurus) was studied using partial sequences of the mitochondrial DNA NADH dehydrogenase subunit 1 (ND1). AMOVA analyses revealed significant inter-oceanic divergence with three phylogroups located in the Indo-Pacific, Eastern Atlantic, and Mediterranean Sea, the last one being the most divergent. However, it was not possible to clearly observe any genetic differentiation between the Indo-Pacific and Atlantic populations, as has been reported for most tropical pelagic species of tuna and billfishes. This supports the assumption of recent dispersal among basins facilitated by the actual continuous distribution of dolphinfish populations. Moreover, the lack of a divergence signal for populations separated by the Panamanian Isthmus reveals that genetic drift does not exert a strong influence on tropical pelagic species with large effective population sizes.

  5. Pollen limitation and Allee effect related to population size and sex ratio in the endangered Ottelia acuminata (Hydrocharitaceae): implications for conservation and reintroduction.

    PubMed

    Xia, J; Lu, J; Wang, Z X; Hao, B B; Wang, H B; Liu, G H

    2013-03-01

    Small populations may suffer more severe pollen limitation and result in Allee effects. Sex ratio may also affect pollination and reproduction success in dioecious species, which is always overlooked when performing conservation and reintroduction tasks. In this study, we investigated whether and how population size and sex ratio affected pollen limitation and reproduction in the endangered Ottelia acuminata, a dioecious submerged species. We established experimental plots with increasing population size and male sex ratio. We observed insect visitation, estimated pollen limitation by hand-pollinations and counted fruit set and seed production per fruit. Fruit set and seed production decreased significantly in small populations due to pollinator scarcity and thus suffered more severe pollen limitation. Although frequently visited, female-biased larger populations also suffered severe pollen limitation due to few effective visits and insufficient pollen availability. Rising male ratio enhanced pollination service and hence reproduction. Unexpectedly, pollinator preferences did not cause reduced reproduction in male-biased populations because of high pollen availability. However, reproductive outputs showed more variability in severe male-biased populations. Our results revealed two component Allee effects in fruit set and seed production, mediated by pollen limitation in O. acuminata. Moreover, reproduction decreased significantly in larger female-biased populations, increasing the risk of an Allee effect. © 2012 German Botanical Society and The Royal Botanical Society of the Netherlands.

  6. Can a Sex-Biased Human Demography Account for the Reduced Effective Population Size of Chromosome X in Non-Africans?

    PubMed Central

    Keinan, Alon; Reich, David

    2010-01-01

    Sex-biased demographic events can result in asymmetries in female and male effective population size that can lead to different patterns of genetic variation on chromosome X than are expected based on the patterns on the autosomes. Previous studies point to a period around the time of the dispersal of anatomically modern humans out of Africa when chromosome X experienced a significant reduction in effective population size relative to the autosomes. Here, we explore whether a sex-biased demographic history could explain these observations. We use coalescent simulations to show that a model of primarily male migration during the out-of-Africa dispersal can produce the striking patterns that are observed when comparing patterns of genetic variation on the autosomes and chromosome X. The model involves a history in which after the founder population of non-Africans lost much of its genetic diversity, subsequent mostly male gene flow from an African source brought new diversity into the population. We also explore two additional models, one of sex-biased generation time and one of a substructured population during the dispersal out of Africa with primarily female migration among demes. These latter models cannot account for the magnitude of the observed reduction in chromosome X effective population size, although it is plausible that they played a more minor role in producing the striking chromosome X/autosome patterns. PMID:20453016

  7. Estimating population size by genotyping faeces.

    PubMed

    Kohn, M H; York, E C; Kamradt, D A; Haught, G; Sauvajot, R M; Wayne, R K

    1999-04-07

    Population size is a fundamental biological parameter that is difficult to estimate. By genotyping coyote (Canis latrans) faeces systematically collected in the Santa Monica Mountains near Los Angeles, California, we exemplify a general, non-invasive method to census large mammals. Four steps are involved in the estimation. First, presumed coyote faeces are collected along paths or roadways where coyotes, like most carnivores, often defaecate and mark territorial boundaries. Second, DNA is extracted from the faeces and species identity and sex is determined by mitochondrial DNA and Y-chromosome typing. Third, hypervariable microsatellite loci are typed from the faeces. Lastly, rarefaction analysis is used to estimate population size from faecal genotypes. This method readily provides a point count estimate of population size and sex ratio. Additionally, we show that home range use paternity and kinship can be inferred from the distribution and relatedness patterns of faecal genotypes.

  8. Estimating avian population size using Bowden's estimator

    USGS Publications Warehouse

    Diefenbach, D.R.

    2009-01-01

    Avian researchers often uniquely mark birds, and multiple estimators could be used to estimate population size using individually identified birds. However, most estimators of population size require that all sightings of marked birds be uniquely identified, and many assume homogeneous detection probabilities. Bowden's estimator can incorporate sightings of marked birds that are not uniquely identified and relax assumptions required of other estimators. I used computer simulation to evaluate the performance of Bowden's estimator for situations likely to be encountered in bird studies. When the assumptions of the estimator were met, abundance and variance estimates and confidence-interval coverage were accurate. However, precision was poor for small population sizes (N < 50) unless a large percentage of the population was marked (>75%) and multiple (≥8) sighting surveys were conducted. If additional birds are marked after sighting surveys begin, it is important to initially mark a large proportion of the population (pm ≥ 0.5 if N ≤ 100 or pm > 0.1 if N ≥ 250) and minimize sightings in which birds are not uniquely identified; otherwise, most population estimates will be overestimated by >10%. Bowden's estimator can be useful for avian studies because birds can be resighted multiple times during a single survey, not all sightings of marked birds have to uniquely identify individuals, detection probabilities among birds can vary, and the complete study area does not have to be surveyed. I provide computer code for use with pilot data to design mark-resight surveys to meet desired precision for abundance estimates.

  9. Microsatellite loci over a thirty-three year period for a malaria parasite (Plasmodium mexicanum): bottleneck in effective population size and effect on allele frequencies.

    PubMed

    Schall, J J; St Denis, K M

    2013-01-01

    Changes in population allele frequencies may be driven by several forces, including selection and drift, and are revealed only by sampling over many generations. Such studies, however, are rare for protist parasites. Microsatellite allele frequencies for 4 loci were followed in a population of Plasmodium mexicanum, a malaria parasite of lizards in California USA at 1 site from 1978 to 2010. Rapid turnover of the lizards indicates the parasite was studied for a minimum of 33 transmission cycles and possibly twice that number. Sample sizes ranged from 841 to 956 scored parasite clones per locus. DNA was extracted from frozen dried blood and blood removed from stained blood smears from the earliest years, and a verification study demonstrated DNA from the blood smears provided valid genetic data. Parasite prevalence and effective population size (Ne) dropped after 2000, remaining lower for the next decade. For 2 loci, allele frequencies appeared stable for the first 2 decades of the study, but changed more rapidly after the decline in prevalence. Allele frequencies changed more gradually for the other 2 loci. Genetic drift could account for changes in allele frequencies, especially after the drop in prevalence and Ne, but the force of selection could also have driven the observed patterns.

  10. Effective population size of steelhead trout: influence of variance in reproductive success, hatchery programs, and genetic compensation between life-history forms.

    PubMed

    Araki, Hitoshi; Waples, Robin S; Ardren, William R; Cooper, Becky; Blouin, Michael S

    2007-03-01

    The effective population size is influenced by many biological factors in natural populations. To evaluate their relative importance, we estimated the effective number of breeders per year (Nb) and effective population size per generation (Ne) in anadromous steelhead trout (Oncorhynchus mykiss) in the Hood River, Oregon (USA). Using demographic data and genetic parentage analysis on an almost complete sample of all adults that returned to the river over 15 years (>15,000 individuals), we estimated Nb for 13 run years and Ne for three entire generations. The results are as follows: (i) the ratio of Ne to the estimated census population size (N) was 0.17-0.40, with large variance in reproductive success among individuals being the primary cause of the reduction in Ne/N; (ii) fish from a traditional hatchery program (Htrad: nonlocal, multiple generations in a hatchery) had negative effects on Nb, not only by reducing mean reproductive success but also by increasing variance in reproductive success among breeding parents, whereas no sign of such effects was found in fish from supplementation hatchery programs (Hsupp: local, single generation in a hatchery); and (iii) Nb was relatively stable among run years, despite the widely fluctuating annual run sizes of anadromous adults. We found high levels of reproductive contribution of nonanadromous parents to anadromous offspring when anadromous run size is small, suggesting a genetic compensation between life-history forms (anadromous and nonanadromous). This is the first study showing that reproductive interaction between different life-history forms can buffer the genetic impact of fluctuating census size on Ne.

  11. Interannual variation in effective number of breeders and estimation of effective population size in long-lived iteroparous lake sturgeon (Acipenser fulvescens).

    PubMed

    Duong, Thuy Yen; Scribner, Kim T; Forsythe, Patrick S; Crossman, James A; Baker, Edward A

    2013-03-01

    Quantifying interannual variation in effective adult breeding number (N(b)) and relationships between N(b), effective population size (N(e)), adult census size (N) and population demographic characteristics are important to predict genetic changes in populations of conservation concern. Such relationships are rarely available for long-lived iteroparous species like lake sturgeon (Acipenser fulvescens). We estimated annual N(b) and generational N(e) using genotypes from 12 microsatellite loci for lake sturgeon adults (n = 796) captured during ten spawning seasons and offspring (n = 3925) collected during larval dispersal in a closed population over 8 years. Inbreeding and variance N(b) estimated using mean and variance in individual reproductive success derived from genetically identified parentage and using linkage disequilibrium (LD) were similar within and among years (interannual range of N(b) across estimators: 41-205). Variance in reproductive success and unequal sex ratios reduced N(b) relative to N on average 36.8% and 16.3%, respectively. Interannual variation in N(b)/N ratios (0.27-0.86) resulted from stable N and low standardized variance in reproductive success due to high proportions of adults breeding and the species' polygamous mating system, despite a 40-fold difference in annual larval production across years (437-16 417). Results indicated environmental conditions and features of the species' reproductive ecology interact to affect demographic parameters and N(b)/N. Estimates of N(e) based on three single-sample estimators, including LD, approximate Bayesian computation and sibship assignment, were similar to annual estimates of N(b). Findings have important implications concerning applications of genetic monitoring in conservation planning for lake sturgeon and other species with similar life histories and mating systems. © 2013 Blackwell Publishing Ltd.

  12. The effect of life-history variation on the population size structure of a rocky intertidal snail ( Littorina sitkana)

    NASA Astrophysics Data System (ADS)

    Rochette, Rémy; Dunmall, Karen; Dill, Lawrence M.

    2003-03-01

    On wave-sheltered shores of the northeastern Pacific, the population size structure of Littorina sitkana varies with intertidal height, as larger snails are mostly found only in the upper intertidal. This pattern has been attributed to high predation rates by crabs (and perhaps fish) on large snails inhabiting low-intertidal areas; i.e., large snails are presumed to be rare there simply because predators kill them. In this study we investigate the hypothesis that predation contributes to the shore-level size gradient displayed by L. sitkana by selecting for (or inducing) earlier sexual maturation and reduced somatic growth in low-shore snails relative to high-shore individuals. In the first part of our study, we carried out laboratory dissections, field experiments (mark-release-recapture and caging), and field surveys on a wave-protected shore in Bamfield Inlet, Barkley Sound (British Columbia, Canada). The principal results were: (1) adult survivorship was greater at higher, than at lower, intertidal level, (2) snails displayed a preference for their shore level of origin, (3) immature adults from the high intertidal displayed greater rates of somatic growth relative to immature adults from the low intertidal, and (4) low-shore snails matured at a smaller size than high-shore individuals. In the second part of the study, a large-scale survey showed intra-specific variation in size at sexual maturity (point 4 above) to be relatively consistent over time (winter of 1999 and 2001 for snails from our main study site) and space (13 different sites in winter 2001), although the magnitude of these differences varied greatly from shore to shore. Our results indicate that L. sitkana individuals inhabiting upper and lower parts of their intertidal range allocate resources differently to somatic and gonadal growth, an intra-specific difference that is best interpreted as a response to spatial and size-dependent variation in predation pressure. Taken together, results of

  13. The effect of soil type and plant age on the population size of rhizospheric methanotrophs and their activities in tropical rice soils.

    PubMed

    Vishwakarma, Pranjali; Dubey, Suresh Kumar

    2007-08-01

    A laboratory incubation experiment was conducted in tropical rain-fed (red soil) and irrigated (black soil) rice agroecosystem during the crop growing season to determine the effect of the type of soil, cultivation practices and the age of plant on MOB (methane oxidizing bacteria) population size and their activities. The average value of MOB population size was 11.7 +/- 4.5 x 10(5) cells g(-1) soil, with a range of 3.1 +/- 0.4 to 21.2 +/- 1.0 x 10(5) cells g(-1) soil for red soil, which was lower in comparison to black soil where population size varied between 84.2 +/- 3.8 and 289.4 +/- 7.0 x 10(5) cells g(-1) soil with an average of 182.8 +/- 53.5 x 10(5) cells g(-1) soil. The highest population size was recorded during the grain maturation stage which gradually declined during the grain filling, flowering and tillering stages of the rice plants. The HSD test indicated a significant variation in the MOB population size with the varying ages of the plant. CH4 oxidizing capacity was higher in black soil as compared to red soil. The highest CH4 oxidizing capacity was found at the grain-filling stage in both the soil types. The differences in soil types and cultivation practices, pattern of variation in MOB population size and methane oxidation were found similar in both the sites under the influence of plant age, even though the detected values differed significantly.

  14. Correlational effect size benchmarks.

    PubMed

    Bosco, Frank A; Aguinis, Herman; Singh, Kulraj; Field, James G; Pierce, Charles A

    2015-03-01

    Effect size information is essential for the scientific enterprise and plays an increasingly central role in the scientific process. We extracted 147,328 correlations and developed a hierarchical taxonomy of variables reported in Journal of Applied Psychology and Personnel Psychology from 1980 to 2010 to produce empirical effect size benchmarks at the omnibus level, for 20 common research domains, and for an even finer grained level of generality. Results indicate that the usual interpretation and classification of effect sizes as small, medium, and large bear almost no resemblance to findings in the field, because distributions of effect sizes exhibit tertile partitions at values approximately one-half to one-third those intuited by Cohen (1988). Our results offer information that can be used for research planning and design purposes, such as producing better informed non-nil hypotheses and estimating statistical power and planning sample size accordingly. We also offer information useful for understanding the relative importance of the effect sizes found in a particular study in relationship to others and which research domains have advanced more or less, given that larger effect sizes indicate a better understanding of a phenomenon. Also, our study offers information about research domains for which the investigation of moderating effects may be more fruitful and provide information that is likely to facilitate the implementation of Bayesian analysis. Finally, our study offers information that practitioners can use to evaluate the relative effectiveness of various types of interventions. PsycINFO Database Record (c) 2015 APA, all rights reserved.

  15. Hunting, pet trade, and forest size effects on population viability of a critically endangered Neotropical primate, Sapajus xanthosternos (Wied-Neuwied, 1826).

    PubMed

    da Silva, Fabiana Araújo; Canale, Gustavo Rodrigues; Kierulff, Maria Cecília M; Duarte, Gabriela Teixeira; Paglia, Adriano Pereira; Bernardo, Christine S S

    2016-09-01

    The yellow-breasted capuchin monkey (Sapajus xanthosternos) is one of the seven Brazilian primates that are currently threatened with extinction. Although the species is known to be threatened by habitat loss, hunting, and illegal pet trade, few data exist on how these threats influence its long-term population persistence. We conducted population viability analyses (PVAs) to estimate minimum viable populations of S. xanthosternos under 10 threat scenarios (i.e., varying hunting pressure and varying number of infants captured for the pet trade) for five forest fragments with different estimated carrying capacities (K). We also estimated the minimum forest fragment size required to sustain viable populations living under the same 10 threat scenarios, based on critical numbers of K obtained in sensitivity tests, below which the population would be unviable. Our PVAs suggests that hunting has a higher impact on population viability in comparison to threats from the pet trade. Annual losses of adult and young females from hunting had the most detrimental effect on population persistence under all forest fragment sizes. Such hunting pressure is not sustainable for populations living in areas ≤3,460 ha, since these areas may not support populations of ≥84 individuals. The seven largest of the 13 protected areas currently harboring capuchins should be effective at maintaining viable populations in the long term even under the greatest threat scenarios we modeled. Other large forest patches, mainly in the western part of the species distribution, are recommended as priority areas for protection to increase the chances of capuchins' survival for the long term. In addition, forest fragments of ≤782.8 ha cannot maintain viable populations, even when there are no threats from hunting or from captures for the pet trade. Increased law enforcement is necessary to prevent the hunting and capture of capuchins, especially within larger forest fragments. Am. J. Primatol. 78

  16. The effect of ethnicity and age on palatal size and shape: a study in a northern Chilean healthy population.

    PubMed

    Ferrario, V F; Sforza, C; Colombo, A; Tartaglia, G M; Carvajal, R; Palomino, H

    2000-01-01

    Race and ethnicity influence the form of the human craniofacial complex in varying ways. The aim of the present investigation was to quantify the effects of ethnicity (mestizos, Aymara, non-Aymara), age (adolescents and adults), and sex on the form (size and shape) of the hard palate in normal Native American individuals. From the dental casts of 51 individuals with a complete permanent dentition, the x, y, and z coordinates of several standardized palatal landmarks were obtained with a computerized 3-dimensional digitizer. Palatal landmarks were used to derive a mathematical equation for palatal shape in the frontal and sagittal planes. Palatal width and length, frontal and sagittal heights, sagittal slope, and deviation of the raphe from the midline were also calculated. In the Aymara subjects, there was no effect of sex on palatal size, but there was an effect on palatal shape independent of size, especially with respect to male growth. Indeed, female palates apparently did not change their shape between adolescence and adulthood, while male palates increased their posterior "height." Overall, the 3 ethnic groups appeared to possess similar palatal size, with small significant differences. In the adult individuals, ethnicity did not seem to influence palatal shape. In contrast, adolescent males showed differences: non-Aymara subjects had the "highest" palatal shape, Aymara the "lowest," and mestizos an intermediate position. In conclusion, ethnicity does not seem to be a factor of major variability of human hard palate morphology, at least in the present 3 northern Chilean groups, as already found for dental arch shape. Age probably has a larger effect, particularly in the posterior part of the palate, where the eruption of the second and third molars between adolescence and young adulthood may play a role. A further development of the present investigation may involve larger samples of individuals from different ethnic groups.

  17. Sexual selection has minimal impact on effective population sizes in species with high rates of random offspring mortality: An empirical demonstration using fitness distributions.

    PubMed

    Pischedda, Alison; Friberg, Urban; Stewart, Andrew D; Miller, Paige M; Rice, William R

    2015-10-01

    The effective population size (N(e)) is a fundamental parameter in population genetics that influences the rate of loss of genetic diversity. Sexual selection has the potential to reduce N(e) by causing the sex-specific distributions of individuals that successfully reproduce to diverge. To empirically estimate the effect of sexual selection on N(e), we obtained fitness distributions for males and females from an outbred, laboratory-adapted population of Drosophila melanogaster. We observed strong sexual selection in this population (the variance in male reproductive success was ∼14 times higher than that for females), but found that sexual selection had only a modest effect on N(e), which was 75% of the census size. This occurs because the substantial random offspring mortality in this population diminishes the effects of sexual selection on N(e), a result that necessarily applies to other high fecundity species. The inclusion of this random offspring mortality creates a scaling effect that reduces the variance/mean ratios for male and female reproductive success and causes them to converge. Our results demonstrate that measuring reproductive success without considering offspring mortality can underestimate Ne and overestimate the genetic consequences of sexual selection. Similarly, comparing genetic diversity among different genomic components may fail to detect strong sexual selection. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

  18. Sexual selection has minimal impact on effective population sizes in species with high rates of random offspring mortality: an empirical demonstration using fitness distributions

    PubMed Central

    Pischedda, Alison; Friberg, Urban; Stewart, Andrew D.; Miller, Paige M.; Rice, William R.

    2015-01-01

    The effective population size (Ne) is a fundamental parameter in population genetics that influences the rate of loss of genetic diversity. Sexual selection has the potential to reduce Ne by causing the sex-specific distributions of individuals that successfully reproduce to diverge. To empirically estimate the effect of sexual selection on Ne, we obtained fitness distributions for males and females from an outbred, laboratory-adapted population of Drosophila melanogaster. We observed strong sexual selection in this population (the variance in male reproductive success was ∼14 times higher than that for females), but found that sexual selection had only a modest effect on Ne, which was 75% of the census size. This occurs because the substantial random offspring mortality in this population diminishes the effects of sexual selection on Ne, a result that necessarily applies to other high fecundity species. The inclusion of this random offspring mortality creates a scaling effect that reduces the variance/mean ratios for male and female reproductive success and causes them to converge. Our results demonstrate that measuring reproductive success without considering offspring mortality can underestimate Ne and overestimate the genetic consequences of sexual selection. Similarly, comparing genetic diversity among different genomic components may fail to detect strong sexual selection. PMID:26374275

  19. Population size, pollination and phenotypic trait selection in Phyteuma spicatum

    NASA Astrophysics Data System (ADS)

    Weber, Anne; Kolb, Annette

    2013-02-01

    Plants in small populations may receive fewer visits, smaller pollen loads or pollen of poorer quality and suffer from reduced reproductive success compared to plants in larger populations. Consequently, pollen limitation of plants in small populations has been suggested to result in the evolution of reduced reliance on pollinators or the enhancement of traits that attract pollinators. The main aim of this study was to experimentally quantify the strength of pollinator-mediated selection on floral display size and flowering phenology in populations of varying size, using the self-incompatible, perennial herb Phyteuma spicatum as study species. We conducted supplementary hand pollinations in six populations (ranging in size between ca. 20-3000 flowering individuals) over two consecutive years and assessed selection gradients (i.e., trait-fitness relationships) in open- and hand-pollinated plants. Our results show that some populations are pollen limited in some years, but, contrary to our expectation, the degree of pollen limitation was not significantly related to population size. We found phenotypic selection for increased inflorescence size (in most populations and in both years), but we obtained no or no strong evidence that selection was pollinator-mediated or that the strength of selection was related to population size. This may have been the result of low statistical power, an inherent problem of studies examining effects of population size that require the inclusion of populations with only few individuals. In addition, given that selection appeared to be spatially and temporally variable, abiotic or biotic factors other than pollinators may have contributed to selection on inflorescence size.

  20. Complex genetic architecture of population differences in adult lifespan of a beetle: nonadditive inheritance, gender differences, body size and a large maternal effect.

    PubMed

    Fox, C W; Czesak, M E; Wallin, W G

    2004-09-01

    Evolutionary responses to selection can be complicated when there is substantial nonadditivity, which limits our ability to extrapolate from simple models of selection to population differentiation and speciation. Studies of Drosophila melanogaster indicate that lifespan and the rate of senescence are influenced by many genes that have environment- and sex-specific effects. These studies also demonstrate that interactions among alleles (dominance) and loci (epistasis) are common, with the degree of interaction differing between the sexes and among environments. However, little is known about the genetic architecture of lifespan or mortality rates for organisms other than D. melanogaster. We studied genetic architecture of differences in lifespan and shapes of mortality curves between two populations of the seed beetle, Callosobruchus maculatus (South India and Burkina Faso populations). These two populations differ in various traits (such as body size and adult lifespan) that have likely evolved via host-specific selection. We found that the genetic architecture of lifespan differences between populations differs substantially between males and females; there was a large maternal effect on male lifespan (but not on female lifespan), and substantial dominance of long-life alleles in females (but not males). The large maternal effect in males was genetically based (there was no significant cytoplasmic effect) likely due to population differences in maternal effects genes that influence lifespan of progeny. Rearing host did not affect the genetic architecture of lifespan, and there was no evidence that genes on the Y-chromosome influence the population differences in lifespan. Epistatic interactions among loci were detectable for the mortality rate of both males and females, but were detectable for lifespan only after controlling for body size variation among lines. The detection of epistasis, dominance, and sex-specific genetic effects on C. maculatus lifespan is

  1. Nutrient Availability and Atmospheric CO2 Partial Pressure Modulate the Effects of Nutrient Heterogeneity on the Size Structure of Populations in Grassland Species

    PubMed Central

    MAESTRE, FERNANDO T.; REYNOLDS, JAMES F.

    2006-01-01

    • Background and Aims Size-asymmetric competition occurs when larger plants have a disproportionate advantage in competition with smaller plants. It has been hypothesized that nutrient heterogeneity may promote it. Experiments testing this hypothesis are inconclusive, and in most cases have evaluated the effects of nutrient heterogeneity separately from other environmental factors. The aim of this study was to test, using populations of Lolium perenne, Plantago lanceolata and Holcus lanatus, two hypotheses: (a) nutrient heterogeneity promotes size-asymmetric competition; and (b) nutrient heterogeneity interacts with both atmospheric CO2 partial pressure (PCO2) and nutrient availability to determine the magnitude of this response. • Methods Microcosms consisting of monocultures of the three species were grown for 90 d in a factorial experiment with the following treatments: PCO2 (37·5 and 70 Pa) and nutrient availability (NA; 40 and 120  mg of N added as organic material) combined with different spatial distribution of the organic material (NH; homogeneous and heterogeneous). Differences in the size of individual plants within populations (size inequality) were quantified using the coefficient of variation of individual above-ground biomass and the combined biomass of the two largest individuals in each microcosm. Increases in size inequality were associated with size-asymmetric competition. • Key Results Size inequality increased when the nutrients were heterogeneously supplied in the three species. The effects of NH on this response were more pronounced under high nutrient supply in both Plantago and Holcus (significant NA × NH interactions) and under elevated PCO2 in Plantago (significant PCO2 × NA × NH interaction). No significant two- and three-way interactions were found for Lolium. • Conclusions Our first hypothesis was supported by our results, as nutrient heterogeneity promoted size-asymmetric competition in the three species evaluated

  2. Genetic differentiation and estimation of effective population size and migration rates in two sympatric ecotypes of the marine snail Littorina saxatilis.

    PubMed

    Fernández, J; Galindo, J; Fernández, B; Pérez-Figueroa, A; Caballero, A; Rolán-Alvarez, E

    2005-01-01

    On exposed rocky shores in Galicia (northwest Spain), a striking polymorphism exists between two ecotypes (RB and SU) of Littorina saxatilis that occupy different levels of the intertidal zone and exhibit an incomplete reproductive isolation. The setting has been suggested to represent ongoing sympatric speciation by ecological adaptation of the two ecotypes to their respective habitats. In this article we address whether or not the ecotypes have developed their own population structures in response to the rigors of their corresponding environments and life histories. We analyzed four to five allozymic loci from three surveys of the same sites, spanning a 14-year period. An experimental design including three localities with two transects per locality and three shore levels allowed studying temporal and spatial population structure and estimation of effective population sizes (N(e)), neighborhood sizes (N(n)), and migration rates (m). Genetic differentiation was significantly lower in RB populations (theta(ST) = 0.067) than in SU ones (theta(ST) = 0.124). Mean estimates of N(e), N(n), and m did not differ significantly between ecotypes, but local ecotype differences in migration between the two closest localities (larger migration rates in RB than in SU populations) could explain the pattern in population differentiation.

  3. Finite-Size Scaling of a First-Order Dynamical Phase Transition: Adaptive Population Dynamics and an Effective Model

    NASA Astrophysics Data System (ADS)

    Nemoto, Takahiro; Jack, Robert L.; Lecomte, Vivien

    2017-03-01

    We analyze large deviations of the time-averaged activity in the one-dimensional Fredrickson-Andersen model, both numerically and analytically. The model exhibits a dynamical phase transition, which appears as a singularity in the large deviation function. We analyze the finite-size scaling of this phase transition numerically, by generalizing an existing cloning algorithm to include a multicanonical feedback control: this significantly improves the computational efficiency. Motivated by these numerical results, we formulate an effective theory for the model in the vicinity of the phase transition, which accounts quantitatively for the observed behavior. We discuss potential applications of the numerical method and the effective theory in a range of more general contexts.

  4. Finite-Size Scaling of a First-Order Dynamical Phase Transition: Adaptive Population Dynamics and an Effective Model.

    PubMed

    Nemoto, Takahiro; Jack, Robert L; Lecomte, Vivien

    2017-03-17

    We analyze large deviations of the time-averaged activity in the one-dimensional Fredrickson-Andersen model, both numerically and analytically. The model exhibits a dynamical phase transition, which appears as a singularity in the large deviation function. We analyze the finite-size scaling of this phase transition numerically, by generalizing an existing cloning algorithm to include a multicanonical feedback control: this significantly improves the computational efficiency. Motivated by these numerical results, we formulate an effective theory for the model in the vicinity of the phase transition, which accounts quantitatively for the observed behavior. We discuss potential applications of the numerical method and the effective theory in a range of more general contexts.

  5. Bayesian inference of population size history from multiple loci.

    PubMed

    Heled, Joseph; Drummond, Alexei J

    2008-10-23

    Effective population size (Ne) is related to genetic variability and is a basic parameter in many models of population genetics. A number of methods for inferring current and past population sizes from genetic data have been developed since JFC Kingman introduced the n-coalescent in 1982. Here we present the Extended Bayesian Skyline Plot, a non-parametric Bayesian Markov chain Monte Carlo algorithm that extends a previous coalescent-based method in several ways, including the ability to analyze multiple loci. Through extensive simulations we show the accuracy and limitations of inferring population size as a function of the amount of data, including recovering information about evolutionary bottlenecks. We also analyzed two real data sets to demonstrate the behavior of the new method; a single gene Hepatitis C virus data set sampled from Egypt and a 10 locus Drosophila ananassae data set representing 16 different populations. The results demonstrate the essential role of multiple loci in recovering population size dynamics. Multi-locus data from a small number of individuals can precisely recover past bottlenecks in population size which can not be characterized by analysis of a single locus. We also demonstrate that sequence data quality is important because even moderate levels of sequencing errors result in a considerable decrease in estimation accuracy for realistic levels of population genetic variability.

  6. An LES study of pollen dispersal from isolated populations: Effects of source size and boundary-layer scaling

    NASA Astrophysics Data System (ADS)

    Chamecki, Marcelo; Meneveau, Charles; Parlange, Marc B.

    2008-11-01

    A framework to simulate pollen dispersal in the atmospheric boundary layer based on the large eddy simulation technique is developed. Pollen is represented by a continuum concentration field and is evolved following an advection-diffusion equation including a gravitational settling term. The approach is validated against classical data on point-source releases and our own field data for a natural ragweed field. The LES is further used as a tool to investigate the effect of source size on the patterns of pollen ground deposition, an issue of fundamental importance in the development of policies for genetically modified crops. The cross-wind integrated deposition is shown to scale with the pollen boundary-layer height at the trailing edge of the field and a simple practical expression based on the development of the pollen boundary layer is proposed to scale results from small test fields to realistic agricultural conditions.

  7. Gene flow, effective population size and selection at major histocompatibility complex genes: brown trout in the Hardanger Fjord, Norway.

    PubMed

    Hansen, Michael M; Skaala, Oystein; Jensen, Lasse Fast; Bekkevold, Dorte; Mensberg, Karen-Lise D

    2007-04-01

    Brown trout populations in the Hardanger Fjord, Norway, have declined drastically due to increased exposure to salmon lice from salmonid aquaculture. We studied contemporary samples from seven populations and historical samples (1972 and 1983) from the two largest populations, one of which has declined drastically whereas the other remains stable. We analysed 11 microsatellite loci, including one tightly linked to the UBA gene of the major histocompatibility class I complex (MHC) and another locus linked to the TAP2A gene, also associated with MHC. The results revealed asymmetric gene flow from the two largest populations to the other, smaller populations. This has important conservation implications, and we predict that possible future population recoveries will be mediated primarily by the remaining large population. Tests for selection suggested diversifying selection at UBA, whereas evidence was inconclusive for TAP2A. There was no evidence for temporally fluctuating selection. We assessed the distribution of adaptive divergence among populations. The results showed the most pronounced footprints of selection between the two largest populations subject to the least immigration. We suggest that asymmetric gene flow has an important influence on adaptive divergence and constrains local adaptive responses in the smaller populations. Even though UBA alleles may not affect salmon louse resistance, the results bear evidence of adaptive divergence among populations at immune system genes. This suggests that similar genetic differences could exist at salmon louse resistance loci, thus rendering it a realistic scenario that differential population declines could reflect differences in adaptive variation.

  8. Codon Usage Bias and Effective Population Sizes on the X Chromosome versus the Autosomes in Drosophila melanogaster

    PubMed Central

    Campos, Jose L.; Zeng, Kai; Parker, Darren J.; Charlesworth, Brian; Haddrill, Penelope R.

    2013-01-01

    Codon usage bias (CUB) in Drosophila is higher for X-linked genes than for autosomal genes. One possible explanation is that the higher effective recombination rate for genes on the X chromosome compared with the autosomes reduces their susceptibility to Hill–Robertson effects, and thus enhances the efficacy of selection on codon usage. The genome sequence of D. melanogaster was used to test this hypothesis. Contrary to expectation, it was found that, after correcting for the effective recombination rate, CUB remained higher on the X than on the autosomes. In contrast, an analysis of polymorphism data from a Rwandan population showed that mean nucleotide site diversity at 4-fold degenerate sites for genes on the X is approximately three-quarters of the autosomal value after correcting for the effective recombination rate, compared with approximate equality before correction. In addition, these data show that selection for preferred versus unpreferred synonymous variants is stronger on the X than the autosomes, which accounts for the higher CUB of genes on the X chromosome. This difference in the strength of selection does not appear to reflect the effects of dominance of mutations affecting codon usage, differences in gene expression levels between X and autosomes, or differences in mutational bias. Its cause therefore remains unexplained. The stronger selection on CUB on the X chromosome leads to a lower rate of synonymous site divergence compared with the autosomes; this will cause a stronger upward bias for X than A in estimates of the proportion of nonsynonymous mutations fixed by positive selection, for methods based on the McDonald–Kreitman test. PMID:23204387

  9. Rate of language evolution is affected by population size

    PubMed Central

    Bromham, Lindell; Hua, Xia; Fitzpatrick, Thomas G.; Greenhill, Simon J.

    2015-01-01

    The effect of population size on patterns and rates of language evolution is controversial. Do languages with larger speaker populations change faster due to a greater capacity for innovation, or do smaller populations change faster due to more efficient diffusion of innovations? Do smaller populations suffer greater loss of language elements through founder effects or drift, or do languages with more speakers lose features due to a process of simplification? Revealing the influence of population size on the tempo and mode of language evolution not only will clarify underlying mechanisms of language change but also has practical implications for the way that language data are used to reconstruct the history of human cultures. Here, we provide, to our knowledge, the first empirical, statistically robust test of the influence of population size on rates of language evolution, controlling for the evolutionary history of the populations and formally comparing the fit of different models of language evolution. We compare rates of gain and loss of cognate words for basic vocabulary in Polynesian languages, an ideal test case with a well-defined history. We demonstrate that larger populations have higher rates of gain of new words whereas smaller populations have higher rates of word loss. These results show that demographic factors can influence rates of language evolution and that rates of gain and loss are affected differently. These findings are strikingly consistent with general predictions of evolutionary models. PMID:25646448

  10. Rate of language evolution is affected by population size.

    PubMed

    Bromham, Lindell; Hua, Xia; Fitzpatrick, Thomas G; Greenhill, Simon J

    2015-02-17

    The effect of population size on patterns and rates of language evolution is controversial. Do languages with larger speaker populations change faster due to a greater capacity for innovation, or do smaller populations change faster due to more efficient diffusion of innovations? Do smaller populations suffer greater loss of language elements through founder effects or drift, or do languages with more speakers lose features due to a process of simplification? Revealing the influence of population size on the tempo and mode of language evolution not only will clarify underlying mechanisms of language change but also has practical implications for the way that language data are used to reconstruct the history of human cultures. Here, we provide, to our knowledge, the first empirical, statistically robust test of the influence of population size on rates of language evolution, controlling for the evolutionary history of the populations and formally comparing the fit of different models of language evolution. We compare rates of gain and loss of cognate words for basic vocabulary in Polynesian languages, an ideal test case with a well-defined history. We demonstrate that larger populations have higher rates of gain of new words whereas smaller populations have higher rates of word loss. These results show that demographic factors can influence rates of language evolution and that rates of gain and loss are affected differently. These findings are strikingly consistent with general predictions of evolutionary models.

  11. Population dynamic theory of size-dependent cannibalism.

    PubMed Central

    Claessen, David; de Roos, André M.; Persson, Lennart

    2004-01-01

    Cannibalism is characterized by four aspects: killing victims, gaining energy from victims, size-dependent interactions and intraspecific competition. In this review of mathematical models of cannibalistic populations, we relate the predicted population dynamic consequences of cannibalism to its four defining aspects. We distinguish five classes of effects of cannibalism: (i) regulation of population size; (ii) destabilization resulting in population cycles or chaos; (iii) stabilization by damping population cycles caused by other interactions; (iv) bistability such that, depending on the initial conditions, the population converges to one of two possible stable states; and (v) modification of the population size structure. The same effects of cannibalism may be caused by different combinations of aspects of cannibalism. By contrast, the same combination of aspects may lead to different effects. For particular cannibalistic species, the consequences of cannibalism will depend on the presence and details of the four defining aspects. Empirical evidence for the emerged theory of cannibalism is discussed briefly. The implications of the described dynamic effects of cannibalism are discussed in the context of community structure, making a comparison with the community effects of intraguild predation. PMID:15101690

  12. Large population sizes mitigate negative effects of variable weather conditions on fruit set in two spring woodland orchids

    PubMed Central

    Jacquemyn, Hans; Brys, Rein; Honnay, Olivier

    2009-01-01

    Global circulation models predict increased climatic variability, which could increase variability in demographic rates and affect long-term population viability. In animal-pollinated species, pollination services, and thus fruit and seed set, may be highly variable among years and sites, and depend on both local environmental conditions and climatic variables. Orchid species may be particularly vulnerable to disruption of their pollination services, as most species depend on pollinators for successful fruit set and because seed germination and seedling recruitment are to some extent dependent on the amount of fruits and seeds produced. Better insights into the factors determining fruit and seed set are therefore indispensable for a better understanding of population dynamics and viability of orchid populations under changing climatic conditions. However, very few studies have investigated spatio-temporal variation in fruit set in orchids. Here, we quantified fruit production in eight populations of the orchid Orchis purpurea that does not reward pollinators and 13 populations of the rewarding Neottia (Listera) ovata during five consecutive years (2002–2006). Fruit production in large populations showed much higher stability than that in small populations and was less affected by extreme weather conditions. Our results highlight the potential vulnerability of small orchid populations to an increasingly variable climate through highly unpredictable fruit-set patterns. PMID:19457885

  13. The effects of canopy openings and population size on the persistence of Southwest columbines at risk of extinction

    Treesearch

    Kelly G. Gallagher; Brook G. Milligan

    2001-01-01

    The habitat associated with riparian, understory, rare and endangered plant populations of the Southwest includes rocky places in high-altitude canyons, mostly along shady streams, pools, and dripping cliffs. The composition of these insular plant populations, which are separated by intervening desert, is influenced by several local environmental conditions. The...

  14. Empty Niches after Extinctions Increase Population Sizes of Modern Corals.

    PubMed

    Prada, Carlos; Hanna, Bishoy; Budd, Ann F; Woodley, Cheryl M; Schmutz, Jeremy; Grimwood, Jane; Iglesias-Prieto, Roberto; Pandolfi, John M; Levitan, Don; Johnson, Kenneth G; Knowlton, Nancy; Kitano, Hiroaki; DeGiorgio, Michael; Medina, Mónica

    2016-12-05

    Large environmental fluctuations often cause mass extinctions, extirpating species and transforming communities [1, 2]. While the effects on community structure are evident in the fossil record, demographic consequences for populations of individual species are harder to evaluate because fossils reveal relative, but not absolute, abundances. However, genomic analyses of living species that have survived a mass extinction event offer the potential for understanding the demographic effects of such environmental fluctuations on extant species. Here, we show how environmental variation since the Pliocene has shaped demographic changes in extant corals of the genus Orbicella, major extant reef builders in the Caribbean that today are endangered. We use genomic approaches to estimate previously unknown current and past population sizes over the last 3 million years. Populations of all three Orbicella declined around 2-1 million years ago, coincident with the extinction of at least 50% of Caribbean coral species. The estimated changes in population size are consistent across the three species despite their ecological differences. Subsequently, two shallow-water specialists expanded their population sizes at least 2-fold, over a time that overlaps with the disappearance of their sister competitor species O. nancyi (the organ-pipe Orbicella). Our study suggests that populations of Orbicella species are capable of rebounding from reductions in population size under suitable conditions and that the effective population size of modern corals provides rich standing genetic variation for corals to adapt to climate change. For conservation genetics, our study suggests the need to evaluate genetic variation under appropriate demographic models.

  15. The effective population sizes of the anthropoid ancestors of the human-chimpanzee lineage provide insights on the historical biogeography of the great apes.

    PubMed

    Schrago, Carlos G

    2014-01-01

    The recent development of methods that apply coalescent theory to phylogenetic problems has enabled the study of the population-level phenomena that drove the diversification of anthropoid primates. Effective population size, Ne, is one of the main parameters that constitute the theoretical underpinning of these new analytical approaches. For this reason, the ancestral N(e) of selected primate lineages has been thoroughly investigated. However, for some of these lineages, the estimates of ancestral N(e) reported in several studies present significant variation. This is the case for the common ancestor of humans and chimpanzees. Moreover, several ancestral anthropoid lineages have been ignored in the studies conducted so far. Because N(e) is fundamental to understand historic species demography, it is a crucial component of a complete description of the historical scenario of primate evolution. It also provides information that is helpful for differentiating between competing biogeographical hypotheses. In this study, the effective population sizes of the anthropoid ancestors of the human-chimp lineage are inferred using data sets of coding and noncoding sequences. A general pattern of a serial decline of population sizes is found between the ancestral lineage of Anthropoidea and that of Homo and Pan. When the theoretical distribution of gene trees was derived from the parametric estimates obtained, it closely corresponded to the empirical frequency of inferred gene trees along the genome. The most abrupt decrease of N(e) was found between the ancestors of all great apes and those of the African great apes alone. This suggests the occurrence of a genetic bottleneck during the evolution of Homininae, which corroborates the origin of African apes from a Eurasian ancestor.

  16. The effect of SNP discovery method and sample size on estimation of population genetic data for Chinese and Indian rhesus macaques (Macaca mulatta).

    PubMed

    Trask, Jessica A Satkoski; Malhi, Ripan S; Kanthaswamy, Sree; Johnson, Jesse; Garnica, Wendy T; Malladi, Venkat S; Smith, David Glenn

    2011-04-01

    This study was designed to address issues regarding sample size and marker location that have arisen from the discovery of SNPs in the genomes of poorly characterized primate species and the application of these markers to the study of primate population genetics. We predict the effect of discovery sample size on the probability of discovering both rare and common SNPs and then compare this prediction with the proportion of common and rare SNPs discovered when different numbers of individuals are sequenced. Second, we examine the effect of genomic region on estimates of common population genetic data, comparing markers from both coding and non-coding regions of the rhesus macaque genome and the population genetic data calculated from these markers, to measure the degree and direction of bias introduced by SNPs located in coding versus non-coding regions of the genome. We found that both discovery sample size and genomic region surveyed affect SNP marker attributes and population genetic estimates, even when these are calculated from an expanded data set containing more individuals than the original discovery data set. Although none of the SNP detection methods or genomic regions tested in this study was completely uninformative, these results show that each has a different kind of genetic variation that is suitable for different purposes, and each introduces specific types of bias. Given that each SNP marker has an individual evolutionary history, we calculated that the most complete and unbiased representation of the genetic diversity present in the individual can be obtained by incorporating at least 10 individuals into the discovery sample set, to ensure the discovery of both common and rare polymorphisms.

  17. IN-STREAM AND WATERSHED PREDICTORS OF GENETIC DIVERSITY, EFFECTIVE POPULATION SIZE AND IMMIGRATION ACROSS RIVER-STREAM NETWORKS

    EPA Science Inventory

    The influence of spatial processes on population dynamics within river-stream networks is poorly understood. Utilizing spatially explicit analyses of temporal genetic variance, we examined whether persistence of Central Stonerollers (Campostoma anomalum) reflects differences in h...

  18. IN-STREAM AND WATERSHED PREDICTORS OF GENETIC DIVERSITY, EFFECTIVE POPULATION SIZE AND IMMIGRATION ACROSS RIVER-STREAM NETWORKS

    EPA Science Inventory

    The influence of spatial processes on population dynamics within river-stream networks is poorly understood. Utilizing spatially explicit analyses of temporal genetic variance, we examined whether persistence of Central Stonerollers (Campostoma anomalum) reflects differences in h...

  19. Estimations of linkage disequilibrium, effective population size and ROH-based inbreeding coefficients in Spanish Churra sheep using imputed high-density SNP genotypes.

    PubMed

    Chitneedi, P K; Arranz, J J; Suarez-Vega, A; García-Gámez, E; Gutiérrez-Gil, B

    2017-08-01

    In this study, the availability of the Ovine HD SNP BeadChip (HD-chip) and the development of an imputation strategy provided an opportunity to further investigate the extent of linkage disequilibrium (LD) at short distances in the genome of the Spanish Churra dairy sheep breed. A population of 1686 animals, including 16 rams and their half-sib daughters, previously genotyped for the 50K-chip, was imputed to the HD-chip density based on a reference population of 335 individuals. After assessing the imputation accuracy for beagle v4.0 (0.922) and fimpute v2.2 (0.921) using a cross-validation approach, the imputed HD-chip genotypes obtained with beagle were used to update the estimates of LD and effective population size for the studied population. The imputed genotypes were also used to assess the degree of homozygosity by calculating runs of homozygosity and to obtain genomic-based inbreeding coefficients. The updated LD estimations provided evidence that the extent of LD in Churra sheep is even shorter than that reported based on the 50K-chip and is one of the shortest extents compared with other sheep breeds. Through different comparisons we have also assessed the impact of imputation on LD and effective population size estimates. The inbreeding coefficient, considering the total length of the run of homozygosity, showed an average estimate (0.0404) lower than the critical level. Overall, the improved accuracy of the updated LD estimates suggests that the HD-chip, combined with an imputation strategy, offers a powerful tool that will increase the opportunities to identify genuine marker-phenotype associations and to successfully implement genomic selection in Churra sheep. © 2017 Stichting International Foundation for Animal Genetics.

  20. Application of Real-Time PCR To Study Effects of Ammonium on Population Size of Ammonia-Oxidizing Bacteria in Soil

    PubMed Central

    Okano, Yutaka; Hristova, Krassimira R.; Leutenegger, Christian M.; Jackson, Louise E.; Denison, R. Ford; Gebreyesus, Binyam; Lebauer, David; Scow, Kate M.

    2004-01-01

    Ammonium oxidation by autotrophic ammonia-oxidizing bacteria (AOB) is a key process in agricultural and natural ecosystems and has a large global impact. In the past, the ecology and physiology of AOB were not well understood because these organisms are notoriously difficult to culture. Recent applications of molecular techniques have advanced our knowledge of AOB, but the necessity of using PCR-based techniques has made quantitative measurements difficult. A quantitative real-time PCR assay targeting part of the ammonia-monooxygenase gene (amoA) was developed to estimate AOB population size in soil. This assay has a detection limit of 1.3 × 105 cells/g of dry soil. The effect of the ammonium concentration on AOB population density was measured in soil microcosms by applying 0, 1.5, or 7.5 mM ammonium sulfate. AOB population size and ammonium and nitrate concentrations were monitored for 28 days after (NH4)2SO4 application. AOB populations in amended treatments increased from an initial density of approximately 4 × 106 cells/g of dry soil to peak values (day 7) of 35 × 106 and 66 × 106 cells/g of dry soil in the 1.5 and 7.5 mM treatments, respectively. The population size of total bacteria (quantified by real-time PCR with a universal bacterial probe) remained between 0.7 × 109 and 2.2 × 109 cells/g of soil, regardless of the ammonia concentration. A fertilization experiment was conducted in a tomato field plot to test whether the changes in AOB density observed in microcosms could also be detected in the field. AOB population size increased from 8.9 × 106 to 38.0 × 106 cells/g of soil by day 39. Generation times were 28 and 52 h in the 1.5 and 7.5 mM treatments, respectively, in the microcosm experiment and 373 h in the ammonium treatment in the field study. Estimated oxidation rates per cell ranged initially from 0.5 to 25.0 fmol of NH4+ h−1 cell−1 and decreased with time in both microcosms and the field. Growth yields were 5.6 × 106, 17.5 × 106

  1. Application of real-time PCR to study effects of ammonium on population size of ammonia-oxidizing bacteria in soil.

    PubMed

    Okano, Yutaka; Hristova, Krassimira R; Leutenegger, Christian M; Jackson, Louise E; Denison, R Ford; Gebreyesus, Binyam; Lebauer, David; Scow, Kate M

    2004-02-01

    Ammonium oxidation by autotrophic ammonia-oxidizing bacteria (AOB) is a key process in agricultural and natural ecosystems and has a large global impact. In the past, the ecology and physiology of AOB were not well understood because these organisms are notoriously difficult to culture. Recent applications of molecular techniques have advanced our knowledge of AOB, but the necessity of using PCR-based techniques has made quantitative measurements difficult. A quantitative real-time PCR assay targeting part of the ammonia-monooxygenase gene (amoA) was developed to estimate AOB population size in soil. This assay has a detection limit of 1.3 x 10(5) cells/g of dry soil. The effect of the ammonium concentration on AOB population density was measured in soil microcosms by applying 0, 1.5, or 7.5 mM ammonium sulfate. AOB population size and ammonium and nitrate concentrations were monitored for 28 days after (NH4)2SO4 application. AOB populations in amended treatments increased from an initial density of approximately 4 x 10(6) cells/g of dry soil to peak values (day 7) of 35 x 10(6) and 66 x 10(6) cells/g of dry soil in the 1.5 and 7.5 mM treatments, respectively. The population size of total bacteria (quantified by real-time PCR with a universal bacterial probe) remained between 0.7 x 10(9) and 2.2 x 10(9) cells/g of soil, regardless of the ammonia concentration. A fertilization experiment was conducted in a tomato field plot to test whether the changes in AOB density observed in microcosms could also be detected in the field. AOB population size increased from 8.9 x 10(6) to 38.0 x 10(6) cells/g of soil by day 39. Generation times were 28 and 52 h in the 1.5 and 7.5 mM treatments, respectively, in the microcosm experiment and 373 h in the ammonium treatment in the field study. Estimated oxidation rates per cell ranged initially from 0.5 to 25.0 fmol of NH4+ h(-1) cell(-1) and decreased with time in both microcosms and the field. Growth yields were 5.6 x 10(6), 17.5 x

  2. Population Structure, Genetic Diversity, Effective Population Size, Demographic History and Regional Connectivity Patterns of the Endangered Dusky Grouper, Epinephelus marginatus (Teleostei: Serranidae), within Malta’s Fisheries Management Zone

    PubMed Central

    Vella, Adriana

    2016-01-01

    The objective of this study is to describe the genetic population structure and demographic history of the endangered marine fish, Epinephelus marginatus, within Malta’s Fisheries Management Zone for the purpose of localised conservation planning. Epinephelus marginatus is a long-lived, sedentary, reef-associated protogynous hermaphrodite with high commercial and recreational value that is at risk of extinction throughout its global distribution. Based on global trends, population substructuring and gaps in local knowledge this has led to an increased interest in evaluation of local stock. Assessment of Maltese demography was based on historical and contemporary catch landings data whilst genetic population structure and regional connectivity patterns were evaluated by examining 175 individuals collected within the central Mediterranean region between 2002 and 2009 using 14 nuclear microsatellite loci. Demographic stock assessment of Maltese E. marginatus’ revealed a 99% decline in catch landings between 1947 and 2009 within the Fisheries Management Zone. A contemporary modest mean size was observed, 3 ± 3 kg, where approximately 17% of the population was juvenile, 68% female/sex-changing and 15% were male with a male-to-female sex ratio of 1:5. Genetic analysis describes the overall population of E. marginatus’ within the Fisheries Management Zone as decreasing in size (ƟH = 2.2), which has gone through a significant size reduction in the past (M = 0.41) and consequently shows signs of moderate inbreeding (FIS = 0.10, p < 0.001) with an estimated effective population size of 130 individuals. Results of spatially explicit Bayesian genetic cluster analysis detected two geographically distinct subpopulations within Malta’s Fisheries Management Zone and that they are connected to a larger network of E. marginatus’ within the Sicily Channel. Results suggest conservation management should be designed to reflect E. marginatus’ within Malta’s Fisheries

  3. Y-chromosome analysis confirms highly sex-biased dispersal and suggests a low male effective population size in bonobos (Pan paniscus).

    PubMed

    Eriksson, Jonas; Siedel, Heike; Lukas, Dieter; Kayser, Manfred; Erler, Axel; Hashimoto, Chie; Hohmann, Gottfried; Boesch, Christophe; Vigilant, Linda

    2006-04-01

    Dispersal is a rare event that is difficult to observe in slowly maturing, long-lived wild animal species such as the bonobo. In this study we used sex-linked (mitochondrial DNA sequence and Y-chromosome microsatellite) markers from the same set of individuals to estimate the magnitude of difference in effective dispersal between the sexes and to investigate the long-term demographic history of bonobos. We sampled 34 males from four distinct geographical areas across the bonobo distribution range. As predicted for a female-dispersing species, we found much higher levels of differentiation among local bonobo populations based upon Y-chromosomal than mtDNA genetic variation. Specifically, almost all of the Y-chromosomal variation distinguished populations, while nearly all of the mtDNA variation was shared between populations. Furthermore, genetic distance correlated with geographical distance for mtDNA but not for the Y chromosome. Female bonobos have a much higher migration rate and/or effective population size as compared to males, and the estimate for the mitochondrial TMRCA (time to most recent common ancestor) was approximately 10 times greater than the estimate for the Y chromosome (410,000 vs. 40,000-45,000). For humans the difference is merely a factor of two, suggesting a more stable demographic history in bonobos in comparison to humans.

  4. A high load of non-neutral amino-acid polymorphisms explains high protein diversity despite moderate effective population size in a marine bivalve with sweepstakes reproduction.

    PubMed

    Harrang, Estelle; Lapègue, Sylvie; Morga, Benjamin; Bierne, Nicolas

    2013-02-01

    Marine bivalves show among the greatest allozyme diversity ever reported in Eukaryotes, putting them historically at the heart of the neutralist-selectionist controversy on the maintenance of genetic variation. Although it is now acknowledged that this high diversity is most probably a simple consequence of a large population size, convincing support for this explanation would require a rigorous assessment of the silent nucleotide diversity in natural populations of marine bivalves, which has not yet been done. This study investigated DNA sequence polymorphism in a set of 37 nuclear loci in wild samples of the flat oyster Ostrea edulis. Silent diversity was found to be only moderate (0.7%), and there was no departure from demographic equilibrium under the Wright-Fisher model, suggesting that the effective population size might not be as large as might have been expected. In accordance with allozyme heterozygosity, nonsynonymous diversity was comparatively very high (0.3%), so that the nonsynonymous to silent diversity ratio reached a value rarely observed in any other organism. We estimated that one-quarter of amino acid-changing mutations behave as neutral in O. edulis, and as many as one-third are sufficiently weakly selected to segregate at low frequency in the polymorphism. Finally, we inferred that one oyster is expected to carry more than 4800 non-neutral alleles (or 4.2 cM(-1)). We conclude that a high load of segregating non-neutral amino-acid polymorphisms contributes to high protein diversity in O. edulis. The high fecundity of marine bivalves together with an unpredictable and highly variable success of reproduction and recruitment (sweepstakes reproduction) might produce a greater decoupling between Ne and N than in other organisms with lower fecundities, and we suggest this could explain why a higher segregating load could be maintained for a given silent mutation effective size.

  5. Critical mutation rate has an exponential dependence on population size in haploid and diploid populations.

    PubMed

    Aston, Elizabeth; Channon, Alastair; Day, Charles; Knight, Christopher G

    2013-01-01

    Understanding the effect of population size on the key parameters of evolution is particularly important for populations nearing extinction. There are evolutionary pressures to evolve sequences that are both fit and robust. At high mutation rates, individuals with greater mutational robustness can outcompete those with higher fitness. This is survival-of-the-flattest, and has been observed in digital organisms, theoretically, in simulated RNA evolution, and in RNA viruses. We introduce an algorithmic method capable of determining the relationship between population size, the critical mutation rate at which individuals with greater robustness to mutation are favoured over individuals with greater fitness, and the error threshold. Verification for this method is provided against analytical models for the error threshold. We show that the critical mutation rate for increasing haploid population sizes can be approximated by an exponential function, with much lower mutation rates tolerated by small populations. This is in contrast to previous studies which identified that critical mutation rate was independent of population size. The algorithm is extended to diploid populations in a system modelled on the biological process of meiosis. The results confirm that the relationship remains exponential, but show that both the critical mutation rate and error threshold are lower for diploids, rather than higher as might have been expected. Analyzing the transition from critical mutation rate to error threshold provides an improved definition of critical mutation rate. Natural populations with their numbers in decline can be expected to lose genetic material in line with the exponential model, accelerating and potentially irreversibly advancing their decline, and this could potentially affect extinction, recovery and population management strategy. The effect of population size is particularly strong in small populations with 100 individuals or less; the exponential model has

  6. Population size and time since island isolation determine genetic diversity loss in insular frog populations.

    PubMed

    Wang, Supen; Zhu, Wei; Gao, Xu; Li, Xianping; Yan, Shaofei; Liu, Xuan; Yang, Ji; Gao, Zengxiang; Li, Yiming

    2014-02-01

    Understanding the factors that contribute to loss of genetic diversity in fragmented populations is crucial for conservation measurements. Land-bridge archipelagoes offer ideal model systems for identifying the long-term effects of these factors on genetic variations in wild populations. In this study, we used nine microsatellite markers to quantify genetic diversity and differentiation of 810 pond frogs (Pelophylax nigromaculatus) from 24 islands of the Zhoushan Archipelago and three sites on nearby mainland China and estimated the effects of the island area, population size, time since island isolation, distance to the mainland and distance to the nearest larger island on reduced genetic diversity of insular populations. The mainland populations displayed higher genetic diversity than insular populations. Genetic differentiations and no obvious gene flow were detected among the frog populations on the islands. Hierarchical partitioning analysis showed that only time since island isolation (square-root-transformed) and population size (log-transformed) significantly contributed to insular genetic diversity. These results suggest that decreased genetic diversity and genetic differentiations among insular populations may have been caused by random genetic drift following isolation by rising sea levels during the Holocene. The results provide strong evidence for a relationship between retained genetic diversity and population size and time since island isolation for pond frogs on the islands, consistent with the prediction of the neutral theory for finite populations. Our study highlights the importance of the size and estimated isolation time of populations in understanding the mechanisms of genetic diversity loss and differentiation in fragmented wild populations. © 2013 John Wiley & Sons Ltd.

  7. Contemporary effective population and metapopulation size (Ne and meta-Ne): comparison among three salmonids inhabiting a fragmented system and differing in gene flow and its asymmetries

    PubMed Central

    Gomez-Uchida, Daniel; Palstra, Friso P; Knight, Thomas W; Ruzzante, Daniel E

    2013-01-01

    We estimated local and metapopulation effective sizes ( and meta-) for three coexisting salmonid species (Salmo salar, Salvelinus fontinalis, Salvelinus alpinus) inhabiting a freshwater system comprising seven interconnected lakes. First, we hypothesized that might be inversely related to within-species population divergence as reported in an earlier study (i.e., FST: S. salar> S. fontinalis> S. alpinus). Using the approximate Bayesian computation method implemented in ONeSAMP, we found significant differences in () between species, consistent with a hierarchy of adult population sizes (). Using another method based on a measure of linkage disequilibrium (LDNE: ), we found more finite values for S. salar than for the other two salmonids, in line with the results above that indicate that S. salar exhibits the lowest among the three species. Considering subpopulations as open to migration (i.e., removing putative immigrants) led to only marginal and non-significant changes in , suggesting that migration may be at equilibrium between genetically similar sources. Second, we hypothesized that meta- might be significantly smaller than the sum of local s (null model) if gene flow is asymmetric, varies among subpopulations, and is driven by common landscape features such as waterfalls. One ‘bottom-up’ or numerical approach that explicitly incorporates variable and asymmetric migration rates showed this very pattern, while a number of analytical models provided meta- estimates that were not significantly different from the null model or from each other. Our study of three species inhabiting a shared environment highlights the importance and utility of differentiating species-specific and landscape effects, not only on dispersal but also in the demography of wild populations as assessed through local s and meta-s and their relevance in ecology, evolution and conservation. PMID:23532448

  8. Recent divergences and size decreases of eastern gorilla populations

    PubMed Central

    Roy, Justin; Arandjelovic, Mimi; Bradley, Brenda J.; Guschanski, Katerina; Stephens, Colleen R.; Bucknell, Dan; Cirhuza, Henry; Kusamba, Chifundera; Kyungu, Jean Claude; Smith, Vince; Robbins, Martha M.; Vigilant, Linda

    2014-01-01

    Compared with other African apes, eastern gorillas (Gorilla beringei) have been little studied genetically. We used analysis of autosomal DNA genotypes obtained from non-invasively collected faecal samples to estimate the evolutionary histories of the two extant mountain gorilla populations and the closely related eastern lowland gorillas. Our results suggest that eastern lowland gorillas and mountain gorillas split beginning some 10 000 years ago, followed 5000 years ago by the split of the two mountain gorilla populations of Bwindi Impenetrable National Park and the Virungas Massif. All three populations have decreased in effective population size, with particularly substantial 10-fold decreases for the mountain gorillas. These dynamics probably reflect responses to habitat changes resulting from climate fluctuations over the past 20 000 years as well as increasing human influence in this densely populated region in the last several thousand years. PMID:25376805

  9. Recent divergences and size decreases of eastern gorilla populations.

    PubMed

    Roy, Justin; Arandjelovic, Mimi; Bradley, Brenda J; Guschanski, Katerina; Stephens, Colleen R; Bucknell, Dan; Cirhuza, Henry; Kusamba, Chifundera; Kyungu, Jean Claude; Smith, Vince; Robbins, Martha M; Vigilant, Linda

    2014-11-01

    Compared with other African apes, eastern gorillas (Gorilla beringei) have been little studied genetically. We used analysis of autosomal DNA genotypes obtained from non-invasively collected faecal samples to estimate the evolutionary histories of the two extant mountain gorilla populations and the closely related eastern lowland gorillas. Our results suggest that eastern lowland gorillas and mountain gorillas split beginning some 10 000 years ago, followed 5000 years ago by the split of the two mountain gorilla populations of Bwindi Impenetrable National Park and the Virungas Massif. All three populations have decreased in effective population size, with particularly substantial 10-fold decreases for the mountain gorillas. These dynamics probably reflect responses to habitat changes resulting from climate fluctuations over the past 20 000 years as well as increasing human influence in this densely populated region in the last several thousand years. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

  10. How Many Seals Were There? The Global Shelf Loss during the Last Glacial Maximum and Its Effect on the Size and Distribution of Grey Seal Populations

    PubMed Central

    Boehme, Lars; Thompson, Dave; Fedak, Mike; Bowen, Don; Hammill, Mike O.; Stenson, Garry B.

    2012-01-01

    Predicting how marine mammal populations respond to habitat changes will be essential for developing conservation management strategies in the 21st century. Responses to previous environmental change may be informative in the development of predictive models. Here we describe the likely effects of the last ice age on grey seal population size and distribution. We use satellite telemetry data to define grey seal foraging habitat in terms of the temperature and depth ranges exploited by the contemporary populations. We estimate the available extent of such habitat in the North Atlantic at present (between 1.42·106 km2 and 2.07·106 km2) and at the last glacial maximum (between 4.74·104 km2 and 2.11·105 km2); taking account of glacial and seasonal sea-ice coverage, estimated reductions of sea-level (123 m) and sea surface temperature hind-casts. Most of the extensive continental shelf waters (North Sea, Baltic Sea and Scotian Shelf), currently supporting >95% of grey seals, were unavailable during the last glacial maximum. A combination of lower sea-level and extensive ice-sheets, massively increased seasonal sea-ice coverage and southerly extent of cold water would have pushed grey seals into areas with no significant shelf waters. The habitat during the last glacial maximum might have been as small as 3% of today's extent and grey seal populations may have fallen to similarly low numbers. An alternative scenario involving a major change to a pelagic or bathy-pelagic foraging niche cannot be discounted. However, hooded seals currently dominate that niche and may have excluded grey seals from such habitat. If as seems likely, the grey seal population fell to very low levels it would have remained low for several thousand years before expanding into current habitats over the past 12,000 years or so. PMID:23300843

  11. How many seals were there? The global shelf loss during the last glacial maximum and its effect on the size and distribution of grey seal populations.

    PubMed

    Boehme, Lars; Thompson, Dave; Fedak, Mike; Bowen, Don; Hammill, Mike O; Stenson, Garry B

    2012-01-01

    Predicting how marine mammal populations respond to habitat changes will be essential for developing conservation management strategies in the 21st century. Responses to previous environmental change may be informative in the development of predictive models. Here we describe the likely effects of the last ice age on grey seal population size and distribution. We use satellite telemetry data to define grey seal foraging habitat in terms of the temperature and depth ranges exploited by the contemporary populations. We estimate the available extent of such habitat in the North Atlantic at present (between 1.42 · 10(6) km(2) and 2.07 · 10(6) km(2)) and at the last glacial maximum (between 4.74 · 10(4) km(2) and 2.11 · 10(5) km(2)); taking account of glacial and seasonal sea-ice coverage, estimated reductions of sea-level (123 m) and sea surface temperature hind-casts. Most of the extensive continental shelf waters (North Sea, Baltic Sea and Scotian Shelf), currently supporting >95% of grey seals, were unavailable during the last glacial maximum. A combination of lower sea-level and extensive ice-sheets, massively increased seasonal sea-ice coverage and southerly extent of cold water would have pushed grey seals into areas with no significant shelf waters. The habitat during the last glacial maximum might have been as small as 3% of today's extent and grey seal populations may have fallen to similarly low numbers. An alternative scenario involving a major change to a pelagic or bathy-pelagic foraging niche cannot be discounted. However, hooded seals currently dominate that niche and may have excluded grey seals from such habitat. If as seems likely, the grey seal population fell to very low levels it would have remained low for several thousand years before expanding into current habitats over the past 12,000 years or so.

  12. Estimating the size of hidden populations from register data

    PubMed Central

    2014-01-01

    Background Prevalence estimates of drug use, or of its consequences, are considered important in many contexts and may have substantial influence over public policy. However, it is rarely possible to simply count the relevant individuals, in particular when the defining characteristics might be illegal, as in the drug use case. Consequently methods are needed to estimate the size of such partly ‘hidden’ populations, and many such methods have been developed and used within epidemiology including studies of alcohol and drug use. Here we introduce a method appropriate for estimating the size of human populations given a single source of data, for example entries in a health-care registry. Methods The setup is the following: during a fixed time-period, e.g. a year, individuals belonging to the target population have a non-zero probability of being “registered”. Each individual might be registered multiple times and the time-points of the registrations are recorded. Assuming that the population is closed and that the probability of being registered at least once is constant, we derive a family of maximum likelihood (ML) estimators of total population size. We study the ML estimator using Monte Carlo simulations and delimit the range of cases where it is useful. In particular we investigate the effect of making the population heterogeneous with respect to probability of being registered. Results The new estimator is asymptotically unbiased and we show that high precision estimates can be obtained for samples covering as little as 25% of the total population size. However, if the total population size is small (say in the order of 500) a larger fraction needs to be sampled to achieve reliable estimates. Further we show that the estimator give reliable estimates even when individuals differ in the probability of being registered. We also compare the ML estimator to an estimator known as Chao’s estimator and show that the latter can have a substantial bias when

  13. Effect Sizes, Confidence Intervals, and Confidence Intervals for Effect Sizes

    ERIC Educational Resources Information Center

    Thompson, Bruce

    2007-01-01

    The present article provides a primer on (a) effect sizes, (b) confidence intervals, and (c) confidence intervals for effect sizes. Additionally, various admonitions for reformed statistical practice are presented. For example, a very important implication of the realization that there are dozens of effect size statistics is that "authors must…

  14. Plant genotypic diversity increases population size of a herbivorous insect

    PubMed Central

    Utsumi, Shunsuke; Ando, Yoshino; Craig, Timothy P.; Ohgushi, Takayuki

    2011-01-01

    It is critical to incorporate the process of population dynamics into community genetics studies to identify the mechanisms of the linkage between host plant genetics and associated communities. We studied the effects of plant genotypic diversity of tall goldenrod Solidago altissima on the population dynamics of the aphid Uroleucon nigrotuberculatum. We found genotypic variation in plant resistance to the aphid in our experiments. To determine the impact of plant genotypic diversity on aphid population dynamics, we compared aphid densities under conditions of three treatments: single-genotype plots, mixed-genotype plots and mixed-genotype-with-cages plots. In the latter treatment plants were individually caged to prevent natural enemy attack and aphid movement among plants. The synergistic effects of genotypes on population size were demonstrated by the greater aphid population size in the mixed-genotype treatment than expected from additive effects alone. Two non-exclusive hypotheses are proposed to explain this pattern. First, there is a source–sink relationship among plant genotypes: aphids move from plant genotypes where their reproduction is high to genotypes where their reproduction is low. Second, natural enemy mortality is reduced in mixed plots in a matrix of diverse plant genotypes. PMID:21378084

  15. Effects of parental number and duration of the breeding period on the effective population size and genetic diversity of a captive population of the endangered Tokyo bitterling Tanakia tanago (Teleostei: Cyprinidae).

    PubMed

    Kubota, Hitoshi; Watanabe, Katsutoshi

    2012-01-01

    The maintenance of genetic diversity is one of the chief concerns in the captive breeding of endangered species. Using microsatellite and mtDNA markers, we examined the effects of two key variables (parental number and duration of breeding period) on effective population size (N(e) ) and genetic diversity of offspring in an experimental breeding program for the endangered Tokyo bitterling, Tanakia tanago. Average heterozygosity and number of alleles of offspring estimated from microsatellite data increased with parental number in a breeding aquarium, and exhibited higher values for a long breeding period treatment (9 weeks) compared with a short breeding period (3 weeks). Haplotype diversity in mtDNA of offspring decreased with the reduction in parental number, and this tendency was greater for the short breeding period treatment. Genetic estimates of N(e) obtained with two single-sample estimation methods were consistently higher for the long breeding period treatment with the same number of parental fish. Average N(e) /N ratios were ranged from 0.5 to 1.4, and were high especially in the long breeding period with small and medium parental number treatments. Our results suggest that the spawning intervals of females and alternative mating behaviors of males influence the effective size and genetic diversity of offspring in bitterling. To maintain the genetic diversity of captive T. tanago, we recommend that captive breeding programs should be conducted for a sufficiently long period with an optimal level of parental density, as well as using an adequate number of parents. © 2011 Wiley Periodicals, Inc.

  16. Change-in-ratio methods for estimating population size

    USGS Publications Warehouse

    Udevitz, Mark S.; Pollock, Kenneth H.; McCullough, Dale R.; Barrett, Reginald H.

    2002-01-01

    Change-in-ratio (CIR) methods can provide an effective, low cost approach for estimating the size of wildlife populations. They rely on being able to observe changes in proportions of population subclasses that result from the removal of a known number of individuals from the population. These methods were first introduced in the 1940’s to estimate the size of populations with 2 subclasses under the assumption of equal subclass encounter probabilities. Over the next 40 years, closed population CIR models were developed to consider additional subclasses and use additional sampling periods. Models with assumptions about how encounter probabilities vary over time, rather than between subclasses, also received some attention. Recently, all of these CIR models have been shown to be special cases of a more general model. Under the general model, information from additional samples can be used to test assumptions about the encounter probabilities and to provide estimates of subclass sizes under relaxations of these assumptions. These developments have greatly extended the applicability of the methods. CIR methods are attractive because they do not require the marking of individuals, and subclass proportions often can be estimated with relatively simple sampling procedures. However, CIR methods require a carefully monitored removal of individuals from the population, and the estimates will be of poor quality unless the removals induce substantial changes in subclass proportions. In this paper, we review the state of the art for closed population estimation with CIR methods. Our emphasis is on the assumptions of CIR methods and on identifying situations where these methods are likely to be effective. We also identify some important areas for future CIR research.

  17. Discreteness effects in population dynamics

    NASA Astrophysics Data System (ADS)

    Guevara Hidalgo, Esteban; Lecomte, Vivien

    2016-05-01

    We analyse numerically the effects of small population size in the initial transient regime of a simple example population dynamics. These effects play an important role for the numerical determination of large deviation functions of additive observables for stochastic processes. A method commonly used in order to determine such functions is the so-called cloning algorithm which in its non-constant population version essentially reduces to the determination of the growth rate of a population, averaged over many realizations of the dynamics. However, the averaging of populations is highly dependent not only on the number of realizations of the population dynamics, and on the initial population size but also on the cut-off time (or population) considered to stop their numerical evolution. This may result in an over-influence of discreteness effects at initial times, caused by small population size. We overcome these effects by introducing a (realization-dependent) time delay in the evolution of populations, additional to the discarding of the initial transient regime of the population growth where these discreteness effects are strong. We show that the improvement in the estimation of the large deviation function comes precisely from these two main contributions.

  18. Molecular demographic history of the annual sunflowers Helianthus annuus and H. petiolaris--large effective population sizes and rates of long-term gene flow.

    PubMed

    Strasburg, Jared L; Rieseberg, Loren H

    2008-08-01

    Hybridization between distinct species may lead to introgression of genes across species boundaries, and this pattern can potentially persist for extended periods as long as selection at some loci or genomic regions prevents thorough mixing of gene pools. However, very few reliable estimates of long-term levels of effective migration are available between hybridizing species throughout their history. Accurate estimates of divergence dates and levels of gene flow require data from multiple unlinked loci as well as an analytical framework that can distinguish between lineage sorting and gene flow and incorporate the effects of demographic changes within each species. Here we use sequence data from 18 anonymous nuclear loci in two broadly sympatric sunflower species, Helianthus annuus and H. petiolaris, analyzed within an "isolation with migration" framework to make genome-wide estimates of the ages of these two species, long-term rates of gene flow between them, and effective population sizes and historical patterns of population growth. Our results indicate that H. annuus and H. petiolaris are approximately one million years old and have exchanged genes at a surprisingly high rate (long-term N(ef)m estimates of approximately 0.5 in each direction), with somewhat higher rates of introgression from H. annuus into H. petiolaris than vice versa. In addition, each species has undergone dramatic population expansion since divergence, and both species have among the highest levels of genetic diversity reported for flowering plants. Our results provide the most comprehensive estimate to date of long-term patterns of gene flow and historical demography in a nonmodel plant system, and they indicate that species integrity can be maintained even in the face of extensive gene flow over a prolonged period.

  19. MOLECULAR DEMOGRAPHIC HISTORY OF THE ANNUAL SUNFLOWERS HELIANTHUS ANNUUS AND H. PETIOLARIS—LARGE EFFECTIVE POPULATION SIZES AND RATES OF LONG-TERM GENE FLOW

    PubMed Central

    Strasburg, Jared L.; Rieseberg, Loren H.

    2008-01-01

    Hybridization between distinct species may lead to introgression of genes across species boundaries, and this pattern can potentially persist for extended periods as long as selection at some loci or genomic regions prevents thorough mixing of gene pools. However, very few reliable estimates of long-term levels of effective migration are available between hybridizing species throughout their history. Accurate estimates of divergence dates and levels of gene flow require data from multiple unlinked loci as well as an analytical framework that can distinguish between lineage sorting and gene flow and incorporate the effects of demographic changes within each species. Here we use sequence data from 18 anonymous nuclear loci in two broadly sympatric sunflower species, Helianthus annuus and H. petiolaris, analyzed within an “isolation with migration” framework to make genome-wide estimates of the ages of these two species, long-term rates of gene flow between them, and effective population sizes and historical patterns of population growth. Our results indicate that H. annuus and H. petiolaris are approximately one million years old and have exchanged genes at a surprisingly high rate (long-term Nef m estimates of approximately 0.5 in each direction), with somewhat higher rates of introgression from H. annuus into H. petiolaris than vice versa. In addition, each species has undergone dramatic population expansion since divergence, and both species have among the highest levels of genetic diversity reported for flowering plants. Our results provide the most comprehensive estimate to date of long-term patterns of gene flow and historical demography in a nonmodel plant system, and they indicate that species integrity can be maintained even in the face of extensive gene flow over a prolonged period. PMID:18462213

  20. A reanalysis of protein polymorphism in Drosophila melanogaster, D. simulans, D. sechellia and D. mauritiana: effects of population size and selection.

    PubMed

    Morton, Richard A; Choudhary, Madhu; Cariou, Marie-Louise; Singh, Rama S

    2004-03-01

    Comparison of synonymous and nonsynonymous variation/substitution within and between species at individual genes has become a widely used general approach to detect the effect of selection versus drift. The sibling species group comprised of two cosmopolitan (Drosophila melanogaster and Drosophila simulans) and two island (Drosophila mauritiana and Drosophila sechellia) species has become a model system for such studies. In the present study we reanalyzed the pattern of protein variation in these species, and the results were compared against the patterns of nucleotide variation obtained from the literature, mostly available for melanogaster and simulans. We have mainly focused on the contrasting patterns of variation between the cosmopolitan pair. The results can be summarized as follows: (1) As expected the island species D. mauritiana and D. sechellia showed much less variation than the cosmopolitan species D. melanogaster and D. simulans. (2) The chromosome 2 showed significantly less variation than chromosome 3 and X in all four species which may indicate effects of past selective sweeps. (3) In contrast to its overall low variation, D. mauritiana showed highest variation for X-linked loci which may indicate introgression from its sibling, D. simulans. (4) An average population of D. simulans was as heterozygous as that of D. melanogaster (14.4% v.s. 13.9%) but the difference was large and significant when considering only polymorphic loci (37.2% v.s. 26.1%). (5) The species-wise pooled populations of these two species showed similar results (all loci = 18.3% v.s. 20.0%, polymorphic loci = 47.2% v.s. 37.6%). (6) An average population of D. simulans had more low-frequency alleles than D. melanogaster, and the D. simulans alleles were found widely distributed in all populations whereas the D. melanogaster alleles were limited to local populations. As a results of this, pooled populations of D. melanogaster showed more polymorphic loci than those of D. simulans

  1. 21 CFR 312.315 - Intermediate-size patient populations.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 5 2013-04-01 2013-04-01 false Intermediate-size patient populations. 312.315... for Treatment Use § 312.315 Intermediate-size patient populations. Under this section, FDA may permit an investigational drug to be used for the treatment of a patient population smaller than that...

  2. 21 CFR 312.315 - Intermediate-size patient populations.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 5 2014-04-01 2014-04-01 false Intermediate-size patient populations. 312.315... for Treatment Use § 312.315 Intermediate-size patient populations. Under this section, FDA may permit an investigational drug to be used for the treatment of a patient population smaller than that...

  3. 21 CFR 312.315 - Intermediate-size patient populations.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 5 2012-04-01 2012-04-01 false Intermediate-size patient populations. 312.315... for Treatment Use § 312.315 Intermediate-size patient populations. Under this section, FDA may permit an investigational drug to be used for the treatment of a patient population smaller than that...

  4. 21 CFR 312.315 - Intermediate-size patient populations.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 5 2011-04-01 2011-04-01 false Intermediate-size patient populations. 312.315... for Treatment Use § 312.315 Intermediate-size patient populations. Under this section, FDA may permit an investigational drug to be used for the treatment of a patient population smaller than that...

  5. 21 CFR 312.315 - Intermediate-size patient populations.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 5 2010-04-01 2010-04-01 false Intermediate-size patient populations. 312.315... for Treatment Use § 312.315 Intermediate-size patient populations. Under this section, FDA may permit an investigational drug to be used for the treatment of a patient population smaller than that...

  6. Sample-size requirements for evaluating population size structure

    USGS Publications Warehouse

    Vokoun, J.C.; Rabeni, C.F.; Stanovick, J.S.

    2001-01-01

    A method with an accompanying computer program is described to estimate the number of individuals needed to construct a sample length-frequency with a given accuracy and precision. First, a reference length-frequency assumed to be accurate for a particular sampling gear and collection strategy was constructed. Bootstrap procedures created length-frequencies with increasing sample size that were randomly chosen from the reference data and then were compared with the reference length-frequency by calculating the mean squared difference. Outputs from two species collected with different gears and an artificial even length-frequency are used to describe the characteristics of the method. The relations between the number of individuals used to construct a length-frequency and the similarity to the reference length-frequency followed a negative exponential distribution and showed the importance of using 300-400 individuals whenever possible.

  7. Naturalization of plant populations: the role of cultivation and population size and density.

    PubMed

    Minton, Mark S; Mack, Richard N

    2010-10-01

    Field experimentation is required to assess the effects of environmental stochasticity on small immigrant plant populations-a widely understood but largely unexplored aspect of predicting any species' likelihood of naturalization and potential invasion. Cultivation can mitigate this stochasticity, although the outcome for a population under cultivation nevertheless varies enormously from extinction to persistence. Using factorial experiments, we investigated the effects of population size, density, and cultivation (irrigation) on the fate of founder populations for four alien species with different life history characteristics (Echinochloa frumentacea, Fagopyrum esculentum, Helianthus annuus, and Trifolium incarnatum) in eastern Washington, USA. The fate of founder populations was highly variable within and among the 3 years of experimentation and illustrates the often precarious environment encountered by plant immigrants. Larger founder populations produced more seeds (P < 0.001); the role of founder population size, however, differed among years. Irrigation resulted in higher percent survival (P < 0.001) and correspondingly larger net reproductive rate (R(0); P < 0.001). But the minimum level of irrigation for establishment, R(0) > 1, differed among years and species. Sowing density did not affect the likelihood of establishment for any species. Our results underscore the importance of environmental stochasticity in determining the fate of founder populations and the potential of cultivation and large population size in countering the long odds against naturalization. Any implementation of often proposed post-immigration field trials to assess the risk of an alien species becoming naturalized, a requisite step toward invasion, will need to assess different sizes of founder populations and the extent and character of cultivation (intentional or unintentional) that the immigrants might receive.

  8. NeEstimator v2: re-implementation of software for the estimation of contemporary effective population size (Ne ) from genetic data.

    PubMed

    Do, C; Waples, R S; Peel, D; Macbeth, G M; Tillett, B J; Ovenden, J R

    2014-01-01

    NeEstimator v2 is a completely revised and updated implementation of software that produces estimates of contemporary effective population size, using several different methods and a single input file. NeEstimator v2 includes three single-sample estimators (updated versions of the linkage disequilibrium and heterozygote-excess methods, and a new method based on molecular coancestry), as well as the two-sample (moment-based temporal) method. New features include the following: (i) an improved method for accounting for missing data; (ii) options for screening out rare alleles; (iii) confidence intervals for all methods; (iv) the ability to analyse data sets with large numbers of genetic markers (10 000 or more); (v) options for batch processing large numbers of different data sets, which will facilitate cross-method comparisons using simulated data; and (vi) correction for temporal estimates when individuals sampled are not removed from the population (Plan I sampling). The user is given considerable control over input data and composition, and format of output files. The freely available software has a new JAVA interface and runs under MacOS, Linux and Windows.

  9. A Draft De Novo Genome Assembly for the Northern Bobwhite (Colinus virginianus) Reveals Evidence for a Rapid Decline in Effective Population Size Beginning in the Late Pleistocene

    PubMed Central

    Halley, Yvette A.; Dowd, Scot E.; Decker, Jared E.; Seabury, Paul M.; Bhattarai, Eric; Johnson, Charles D.; Rollins, Dale; Tizard, Ian R.; Brightsmith, Donald J.; Peterson, Markus J.; Taylor, Jeremy F.; Seabury, Christopher M.

    2014-01-01

    Wild populations of northern bobwhites (Colinus virginianus; hereafter bobwhite) have declined across nearly all of their U.S. range, and despite their importance as an experimental wildlife model for ecotoxicology studies, no bobwhite draft genome assembly currently exists. Herein, we present a bobwhite draft de novo genome assembly with annotation, comparative analyses including genome-wide analyses of divergence with the chicken (Gallus gallus) and zebra finch (Taeniopygia guttata) genomes, and coalescent modeling to reconstruct the demographic history of the bobwhite for comparison to other birds currently in decline (i.e., scarlet macaw; Ara macao). More than 90% of the assembled bobwhite genome was captured within <40,000 final scaffolds (N50 = 45.4 Kb) despite evidence for approximately 3.22 heterozygous polymorphisms per Kb, and three annotation analyses produced evidence for >14,000 unique genes and proteins. Bobwhite analyses of divergence with the chicken and zebra finch genomes revealed many extremely conserved gene sequences, and evidence for lineage-specific divergence of noncoding regions. Coalescent models for reconstructing the demographic history of the bobwhite and the scarlet macaw provided evidence for population bottlenecks which were temporally coincident with human colonization of the New World, the late Pleistocene collapse of the megafauna, and the last glacial maximum. Demographic trends predicted for the bobwhite and the scarlet macaw also were concordant with how opposing natural selection strategies (i.e., skewness in the r-/K-selection continuum) would be expected to shape genome diversity and the effective population sizes in these species, which is directly relevant to future conservation efforts. PMID:24621616

  10. Microstructure versus substructure size effect

    NASA Astrophysics Data System (ADS)

    Ghassemali, Ehsan; Jarfors, Anders E. W.; Tan, Ming-Jen; Wah, Chua Beng

    2016-10-01

    In metal deformation, size effect is generally attributed to the interactive effect of grain size and specimen dimension. This work shows, however, that relative substructure dimensions should also be considered. Micro-compression tests on the micro-pins having different grain sizes revealed no significant size effect with respect to the mechanical behavior, even if the number of grains over the diameter of the micro-pins falls below its critical value. To justify the reason laying under this fact, a recovery annealing cycle was applied on the micro-pins to change the substructure properties without altering the mean grain size. A surprising drop in the flow stress of the recovery-annealed micro-pins implied the importance of considering subgrain size rather than grain size over the diameter of component for the size effect investigation.

  11. Common Language Effect Size for Multiple Treatment Comparisons

    ERIC Educational Resources Information Center

    Liu, Xiaofeng Steven

    2015-01-01

    Researchers who need to explain treatment effects to laypeople can translate Cohen's effect size (standardized mean difference) to a common language effect size--a probability of a random observation from one population being larger than a random observation from the other population. This common language effect size can be extended to represent…

  12. Common Language Effect Size for Multiple Treatment Comparisons

    ERIC Educational Resources Information Center

    Liu, Xiaofeng Steven

    2015-01-01

    Researchers who need to explain treatment effects to laypeople can translate Cohen's effect size (standardized mean difference) to a common language effect size--a probability of a random observation from one population being larger than a random observation from the other population. This common language effect size can be extended to represent…

  13. Annotated Draft Genome Assemblies for the Northern Bobwhite (Colinus virginianus) and the Scaled Quail (Callipepla squamata) Reveal Disparate Estimates of Modern Genome Diversity and Historic Effective Population Size

    PubMed Central

    Oldeschulte, David L.; Halley, Yvette A.; Wilson, Miranda L.; Bhattarai, Eric K.; Brashear, Wesley; Hill, Joshua; Metz, Richard P.; Johnson, Charles D.; Rollins, Dale; Peterson, Markus J.; Bickhart, Derek M.; Decker, Jared E.; Sewell, John F.; Seabury, Christopher M.

    2017-01-01

    Northern bobwhite (Colinus virginianus; hereafter bobwhite) and scaled quail (Callipepla squamata) populations have suffered precipitous declines across most of their US ranges. Illumina-based first- (v1.0) and second- (v2.0) generation draft genome assemblies for the scaled quail and the bobwhite produced N50 scaffold sizes of 1.035 and 2.042 Mb, thereby producing a 45-fold improvement in contiguity over the existing bobwhite assembly, and ≥90% of the assembled genomes were captured within 1313 and 8990 scaffolds, respectively. The scaled quail assembly (v1.0 = 1.045 Gb) was ∼20% smaller than the bobwhite (v2.0 = 1.254 Gb), which was supported by kmer-based estimates of genome size. Nevertheless, estimates of GC content (41.72%; 42.66%), genome-wide repetitive content (10.40%; 10.43%), and MAKER-predicted protein coding genes (17,131; 17,165) were similar for the scaled quail (v1.0) and bobwhite (v2.0) assemblies, respectively. BUSCO analyses utilizing 3023 single-copy orthologs revealed a high level of assembly completeness for the scaled quail (v1.0; 84.8%) and the bobwhite (v2.0; 82.5%), as verified by comparison with well-established avian genomes. We also detected 273 putative segmental duplications in the scaled quail genome (v1.0), and 711 in the bobwhite genome (v2.0), including some that were shared among both species. Autosomal variant prediction revealed ∼2.48 and 4.17 heterozygous variants per kilobase within the scaled quail (v1.0) and bobwhite (v2.0) genomes, respectively, and estimates of historic effective population size were uniformly higher for the bobwhite across all time points in a coalescent model. However, large-scale declines were predicted for both species beginning ∼15–20 KYA. PMID:28717047

  14. Comparing population size estimators for plethodontid salamanders

    USGS Publications Warehouse

    Bailey, L.L.; Simons, T.R.; Pollock, K.H.

    2004-01-01

    Despite concern over amphibian declines, few studies estimate absolute abundances because of logistic and economic constraints and previously poor estimator performance. Two estimation approaches recommended for amphibian studies are mark-recapture and depletion (or removal) sampling. We compared abundance estimation via various mark-recapture and depletion methods, using data from a three-year study of terrestrial salamanders in Great Smoky Mountains National Park. Our results indicate that short-term closed-population, robust design, and depletion methods estimate surface population of salamanders (i.e., those near the surface and available for capture during a given sampling occasion). In longer duration studies, temporary emigration violates assumptions of both open- and closed-population mark-recapture estimation models. However, if the temporary emigration is completely random, these models should yield unbiased estimates of the total population (superpopulation) of salamanders in the sampled area. We recommend using Pollock's robust design in mark-recapture studies because of its flexibility to incorporate variation in capture probabilities and to estimate temporary emigration probabilities.

  15. Size Effect in Continuum Modeling

    SciTech Connect

    Lu, Wei-Yang; James W. Foulk; Huestis, Edwin M.; Connelly, Kevin; Song, Bo; Yang, Nancy Y. C.

    2008-09-01

    The mechanical properties of some materials (Cu, Ni, Ag, etc.) have been shown to develop strong dependence on the geometric dimensions, resulting in a size effect. Several theories have been proposed to model size effects, but have been based on very few experiments conducted at appropriate scales. Some experimental results implied that size effects are caused by increasing strain gradients and have been used to confirm many strain gradient theories. On the other hand, some recent experiments show that a size effect exists in the absence of strain gradients. This report describes a brief analytical and experimental study trying to clarify the material and experimental issues surrounding the most influential size-effect experiments by Fleck et al (1994). This effort is to understand size effects intended to further develop predictive models.

  16. Estimating hidden population size using Respondent-Driven Sampling data

    PubMed Central

    Handcock, Mark S.; Gile, Krista J.; Mar, Corinne M.

    2015-01-01

    Respondent-Driven Sampling (RDS) is n approach to sampling design and inference in hard-to-reach human populations. It is often used in situations where the target population is rare and/or stigmatized in the larger population, so that it is prohibitively expensive to contact them through the available frames. Common examples include injecting drug users, men who have sex with men, and female sex workers. Most analysis of RDS data has focused on estimating aggregate characteristics, such as disease prevalence. However, RDS is often conducted in settings where the population size is unknown and of great independent interest. This paper presents an approach to estimating the size of a target population based on data collected through RDS. The proposed approach uses a successive sampling approximation to RDS to leverage information in the ordered sequence of observed personal network sizes. The inference uses the Bayesian framework, allowing for the incorporation of prior knowledge. A flexible class of priors for the population size is used that aids elicitation. An extensive simulation study provides insight into the performance of the method for estimating population size under a broad range of conditions. A further study shows the approach also improves estimation of aggregate characteristics. Finally, the method demonstrates sensible results when used to estimate the size of known networked populations from the National Longitudinal Study of Adolescent Health, and when used to estimate the size of a hard-to-reach population at high risk for HIV. PMID:26180577

  17. The effects of predation by wading birds (Ardeidae) and blue crabs ( Callinectes sapidus) on the population size structure of the common mummichog, Fundulus heteroclitus

    NASA Astrophysics Data System (ADS)

    Kneib, R. T.

    1982-02-01

    Preliminary observations suggested that predation by herons and egretsaffected the size structure of a mummichog ( Fundulus heteroclitus) population in Tar Landing Marsh, North Carolina. The hypothesis was tested by placing 300 mummichogs represented equally in three size classes into each half of an enclosed, divided, high marsh pool. Nylon cord was strung in a grid over one side to inhibit predation by wading birds. Although mummichog losses were higher in the side of the pool which was open to bird predation, the same trend in size-specific losses also occurred in the bird-exclusion side. Repeating the experiment after the removal of several blue crabs ( Callinectes sapidus) improved mummichog survivorship and suggested that crabs and not birds were responsible for the fish losses previously observed. In a final experiment, birds were excluded and crabs were removed from one side but added to the other side of the pool. After 24 days losses due to C. sapidus occurred in all mummichog size classes, but size-specific predation by blue crabs produced the highest losses (90%) among the largest (>70 mm total length) fish. Blue crab predation on mummichog populations may influence the community structure of salt marsh infauna and may also function in the movement of marsh production to open coastal waters.

  18. Evolutionary dynamics with fluctuating population sizes and strong mutualism

    NASA Astrophysics Data System (ADS)

    Chotibut, Thiparat; Nelson, David R.

    2015-08-01

    Game theory ideas provide a useful framework for studying evolutionary dynamics in a well-mixed environment. This approach, however, typically enforces a strictly fixed overall population size, deemphasizing natural growth processes. We study a competitive Lotka-Volterra model, with number fluctuations, that accounts for natural population growth and encompasses interaction scenarios typical of evolutionary games. We show that, in an appropriate limit, the model describes standard evolutionary games with both genetic drift and overall population size fluctuations. However, there are also regimes where a varying population size can strongly influence the evolutionary dynamics. We focus on the strong mutualism scenario and demonstrate that standard evolutionary game theory fails to describe our simulation results. We then analytically and numerically determine fixation probabilities as well as mean fixation times using matched asymptotic expansions, taking into account the population size degree of freedom. These results elucidate the interplay between population dynamics and evolutionary dynamics in well-mixed systems.

  19. Genetic estimates of annual reproductive success in male brown bears: the effects of body size, age, internal relatedness and population density.

    PubMed

    Zedrosser, Andreas; Bellemain, Eva; Taberlet, Pierre; Swenson, Jon E

    2007-03-01

    1. We studied male yearly reproductive success (YRS) and its determinants (phenotypic characteristics, age, population density) in two Scandinavian brown bear populations, using molecular techniques to determine paternity. 2. We found a significant difference in male YRS between the study areas, with lower YRS in the south than in the north. 3. In general, older and larger males had higher YRS. Older males may be more experienced in competition for reproduction (male dominance). Large body size is of direct benefit in male-male competition and of advantage in endurance competition for the access to females. 4. Age was relatively more important for YRS in the north and body size was more important in the south, due perhaps to differences in male age structure due to illegal killing. A single old male dominated the reproduction in the north during the study, which resulted most probably in the relatively higher importance of age in the north. In the south, with a more even male age structure, no single male was able to dominate, probably resulting in a more intense competition among males, with body size as the deciding factor. 5. Male YRS was correlated positively with population density. This may be related to the structure of the expanding bear population, with female densities declining towards the population edge. 6. Internal relatedness, a measure of genetic heterozygosity, was correlated negatively with YRS, suggesting that outbred individuals have a higher YRS. Individual heterozygosity at key or many loci may reflect male physical qualities and condition-sensitive traits, which may benefit males directly in contest or in sperm competition.

  20. Estimation of population size using open capture-recapture models

    USGS Publications Warehouse

    McDonald, T.L.; Amstrup, Steven C.

    2001-01-01

    One of the most important needs for wildlife managers is an accurate estimate of population size. Yet, for many species, including most marine species and large mammals, accurate and precise estimation of numbers is one of the most difficult of all research challenges. Open-population capture-recapture models have proven useful in many situations to estimate survival probabilities but typically have not been used to estimate population size. We show that open-population models can be used to estimate population size by developing a Horvitz-Thompson-type estimate of population size and an estimator of its variance. Our population size estimate keys on the probability of capture at each trap occasion and therefore is quite general and can be made a function of external covariates measured during the study. Here we define the estimator and investigate its bias, variance, and variance estimator via computer simulation. Computer simulations make extensive use of real data taken from a study of polar bears (Ursus maritimus) in the Beaufort Sea. The population size estimator is shown to be useful because it was negligibly biased in all situations studied. The variance estimator is shown to be useful in all situations, but caution is warranted in cases of extreme capture heterogeneity.

  1. Determining size and dispersion of minimum viable populations for land management planning and species conservation

    NASA Astrophysics Data System (ADS)

    Lehmkuhl, John F.

    1984-03-01

    The concept of minimum populations of wildlife and plants has only recently been discussed in the literature. Population genetics has emerged as a basic underlying criterion for determining minimum population size. This paper presents a genetic framework and procedure for determining minimum viable population size and dispersion strategies in the context of multiple-use land management planning. A procedure is presented for determining minimum population size based on maintenance of genetic heterozygosity and reduction of inbreeding. A minimum effective population size ( N e ) of 50 breeding animals is taken from the literature as the minimum shortterm size to keep inbreeding below 1% per generation. Steps in the procedure adjust N e to account for variance in progeny number, unequal sex ratios, overlapping generations, population fluctuations, and period of habitat/population constraint. The result is an approximate census number that falls within a range of effective population size of 50 500 individuals. This population range defines the time range of short- to long-term population fitness and evolutionary potential. The length of the term is a relative function of the species generation time. Two population dispersion strategies are proposed: core population and dispersed population.

  2. Economic consequences of population size, structure and growth.

    PubMed

    Lee, R

    1983-01-01

    There seems to be 4 major approaches to conceptualizing and modeling demographic influences on economic and social welfare. These approaches are combined in various ways to construct richer and more comprehensive models. The basic approaches are: demographic influences on household or family behavior; population growth and reproducible capital; population size and fixed factors; and population and advantages of scale. These 4 models emphasize the supply side effects of population. A few of the ways in which these theories have been combined are sketched. Neoclassical growth models often have been combined with age distributed populations of individuals (or households), assumed to pursue optimal life cycle consumption and saving. In some well known development models, neoclassical growth models for the modern sector are linked by labor markets and migration to fixed factor (land) models of the traditional (agricultural) sector. A whole series of macro simulation models for developed and developing countries was based on single sector neoclassical growth models with age distributed populations. Yet, typically the household level foundations of assumed age distribution effects were not worked out. Simon's (1977) simulation models are in a class by themselves, for they are the only models that attempt to incorporate all the kinds of effects discussed. The economic demography of the individual and family cycle, as it is affected by regimes of fertility, mortality, and nuptiality, taken as given, are considered. The examination touches on many of the purported consequences of aggregate population growth and age composition, since so many of these are based implicitly or explicitly on assertions about micro level behavior. Demographic influences on saving and consumption, on general labor supply and female labor supply, and on problems of youth and old age dependency frequently fall in this category. Finally, attention is focused specifically on macro economic issues in

  3. Both population size and patch quality affect local extinctions and colonizations.

    PubMed

    Franzén, Markus; Nilsson, Sven G

    2010-01-07

    Currently, the habitat of many species is fragmented, resulting in small local populations with individuals occasionally dispersing between the remaining habitat patches. In a solitary bee metapopulation, extinction probability was related to both local bee population sizes and pollen resources measured as host plant population size. Patch size, on the other hand, had no additional predictive power. The turnover rate of local bee populations in 63 habitat patches over 4 years was high, with 72 extinction events and 31 colonization events, but the pollen plant population was stable with no extinctions or colonizations. Both pollen resources and bee populations had strong and independent effects on extinction probability, but connectivity was not of importance. Colonizations occurred more frequently within larger host plant populations. For metapopulation survival of the bee, large pollen plant populations are essential, independent of current bee population size.

  4. Population size, habitat fragmentation, and the nature of adaptive variation in a stream fish.

    PubMed

    Fraser, Dylan J; Debes, Paul V; Bernatchez, Louis; Hutchings, Jeffrey A

    2014-09-07

    Whether and how habitat fragmentation and population size jointly affect adaptive genetic variation and adaptive population differentiation are largely unexplored. Owing to pronounced genetic drift, small, fragmented populations are thought to exhibit reduced adaptive genetic variation relative to large populations. Yet fragmentation is known to increase variability within and among habitats as population size decreases. Such variability might instead favour the maintenance of adaptive polymorphisms and/or generate more variability in adaptive differentiation at smaller population size. We investigated these alternative hypotheses by analysing coding-gene, single-nucleotide polymorphisms associated with different biological functions in fragmented brook trout populations of variable sizes. Putative adaptive differentiation was greater between small and large populations or among small populations than among large populations. These trends were stronger for genetic population size measures than demographic ones and were present despite pronounced drift in small populations. Our results suggest that fragmentation affects natural selection and that the changes elicited in the adaptive genetic composition and differentiation of fragmented populations vary with population size. By generating more variable evolutionary responses, the alteration of selective pressures during habitat fragmentation may affect future population persistence independently of, and perhaps long before, the effects of demographic and genetic stochasticity are manifest. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

  5. Asymmetric competition causes multimodal size distributions in spatially structured populations.

    PubMed

    Velázquez, Jorge; Allen, Robert B; Coomes, David A; Eichhorn, Markus P

    2016-01-27

    Plant sizes within populations often exhibit multimodal distributions, even when all individuals are the same age and have experienced identical conditions. To establish the causes of this, we created an individual-based model simulating the growth of trees in a spatially explicit framework, which was parametrized using data from a long-term study of forest stands in New Zealand. First, we demonstrate that asymmetric resource competition is a necessary condition for the formation of multimodal size distributions within cohorts. By contrast, the legacy of small-scale clustering during recruitment is transient and quickly overwhelmed by density-dependent mortality. Complex multi-layered size distributions are generated when established individuals are restricted in the spatial domain within which they can capture resources. The number of modes reveals the effective number of direct competitors, while the separation and spread of modes are influenced by distances among established individuals. Asymmetric competition within local neighbourhoods can therefore generate a range of complex size distributions within even-aged cohorts. © 2016 The Author(s).

  6. Asymmetric competition causes multimodal size distributions in spatially structured populations

    PubMed Central

    Velázquez, Jorge; Allen, Robert B.; Coomes, David A.; Eichhorn, Markus P.

    2016-01-01

    Plant sizes within populations often exhibit multimodal distributions, even when all individuals are the same age and have experienced identical conditions. To establish the causes of this, we created an individual-based model simulating the growth of trees in a spatially explicit framework, which was parametrized using data from a long-term study of forest stands in New Zealand. First, we demonstrate that asymmetric resource competition is a necessary condition for the formation of multimodal size distributions within cohorts. By contrast, the legacy of small-scale clustering during recruitment is transient and quickly overwhelmed by density-dependent mortality. Complex multi-layered size distributions are generated when established individuals are restricted in the spatial domain within which they can capture resources. The number of modes reveals the effective number of direct competitors, while the separation and spread of modes are influenced by distances among established individuals. Asymmetric competition within local neighbourhoods can therefore generate a range of complex size distributions within even-aged cohorts. PMID:26817778

  7. Changes in breeding phenology and population size of birds.

    PubMed

    Dunn, Peter O; Møller, Anders P

    2014-05-01

    Although the phenology of numerous organisms has advanced significantly in response to recent climate change, the life-history and population consequences of earlier reproduction remain poorly understood. We analysed extensive data on temporal change in laying date and clutch size of birds from Europe and North America to test whether these changes were related to recent trends in population size. Across studies, laying date advanced significantly, while clutch size did not change. However, within populations, changes in laying date and clutch size were positively correlated, implying that species which advanced their laying date the most were also those that increased their clutch size the most. Greater advances in laying date were associated with species that had multiple broods per season, lived in nonagricultural habitats and were herbivorous or predatory. The duration of the breeding season increased for multibrooded species and decreased for single-brooded species. Changes in laying date and clutch size were not related to changes in population size (for resident or migratory species). This suggests that, across a wide variety of species, mismatches in the timing of egg laying or numbers of offspring have had relatively little influence on population size compared with other aspects of phenology and life history. © 2013 The Authors. Journal of Animal Ecology © 2013 British Ecological Society.

  8. Determination of the optimal sample size for a clinical trial accounting for the population size.

    PubMed

    Stallard, Nigel; Miller, Frank; Day, Simon; Hee, Siew Wan; Madan, Jason; Zohar, Sarah; Posch, Martin

    2017-07-01

    The problem of choosing a sample size for a clinical trial is a very common one. In some settings, such as rare diseases or other small populations, the large sample sizes usually associated with the standard frequentist approach may be infeasible, suggesting that the sample size chosen should reflect the size of the population under consideration. Incorporation of the population size is possible in a decision-theoretic approach either explicitly by assuming that the population size is fixed and known, or implicitly through geometric discounting of the gain from future patients reflecting the expected population size. This paper develops such approaches. Building on previous work, an asymptotic expression is derived for the sample size for single and two-arm clinical trials in the general case of a clinical trial with a primary endpoint with a distribution of one parameter exponential family form that optimizes a utility function that quantifies the cost and gain per patient as a continuous function of this parameter. It is shown that as the size of the population, N, or expected size, N∗ in the case of geometric discounting, becomes large, the optimal trial size is O(N1/2) or O(N∗1/2). The sample size obtained from the asymptotic expression is also compared with the exact optimal sample size in examples with responses with Bernoulli and Poisson distributions, showing that the asymptotic approximations can also be reasonable in relatively small sample sizes. © 2016 The Author. Biometrical Journal published by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. Variability levels, population size and structure of American and European Drosophila montana populations.

    PubMed

    Vieira, J; Hoikkala, A

    2001-04-01

    The level and patterns of nucleotide diversity have been characterized for two X-linked loci, fused (fu; a region of 2362 bp) and suppressor of sable (su(s); a region of 413 bp), in one European and one American D. montana population. Sequence variation at these loci shows that the two populations are divergent, although they may not be completely isolated. Data on the level of silent site variability at su(s) (1.1% and 0.5% for the European and American populations, respectively) suggest that the effective population sizes of the two populations may be similar. At the fused locus, one European sequence was highly divergent and may have resulted from gene conversion, and was excluded from the analysis. With this sequence removed, the level of silent site variability was significantly lower in the European population (0.28%) than in the American population (2.3%), which suggests a selective sweep at or near fu in the former population.

  10. Size effect in thermoelectric materials

    NASA Astrophysics Data System (ADS)

    Mao, Jun; Liu, Zihang; Ren, Zhifeng

    2016-12-01

    Thermoelectric applications have attracted increasing interest recently due to its capability of converting waste heat into electricity without hazardous emissions. Materials with enhanced thermoelectric performance have been reported in recent two decades. The revival of research for thermoelectric materials began in early 1990s when the size effect is considered. Low-dimensional materials with exceptionally high thermoelectric figure of merit (ZT) have been presented, which broke the limit of ZT around unity. The idea of size effect in thermoelectric materials even inspired the later nanostructuring and band engineering strategies, which effectively enhanced the thermoelectric performance of bulk materials. In this overview, the size effect in low-dimensional thermoelectric materials is reviewed. We first discuss the quantum confinement effect on carriers, including the enhancement of electronic density of states, semimetal to semiconductor transition and carrier pocket engineering. Then, the effect of assumptions on theoretical calculations is presented. Finally, the effect of phonon confinement and interface scattering on lattice thermal conductivity is discussed.

  11. Population size is weakly related to quantitative genetic variation and trait differentiation in a stream fish.

    PubMed

    Wood, Jacquelyn L A; Tezel, Defne; Joyal, Destin; Fraser, Dylan J

    2015-09-01

    How population size influences quantitative genetic variation and differentiation among natural, fragmented populations remains unresolved. Small, isolated populations might occupy poor quality habitats and lose genetic variation more rapidly due to genetic drift than large populations. Genetic drift might furthermore overcome selection as population size decreases. Collectively, this might result in directional changes in additive genetic variation (VA ) and trait differentiation (QST ) from small to large population size. Alternatively, small populations might exhibit larger variation in VA and QST if habitat fragmentation increases variability in habitat types. We explored these alternatives by investigating VA and QST using nine fragmented populations of brook trout varying 50-fold in census size N (179-8416) and 10-fold in effective number of breeders, Nb (18-135). Across 15 traits, no evidence was found for consistent differences in VA and QST with population size and almost no evidence for increased variability of VA or QST estimates at small population size. This suggests that (i) small populations of some species may retain adaptive potential according to commonly adopted quantitative genetic measures and (ii) populations of varying sizes experience a variety of environmental conditions in nature, however extremely large studies are likely required before any firm conclusions can be made. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

  12. Relationship of habitat variability to population size in a stream fish.

    PubMed

    Wood, Jacquelyn L A; Belmar-Lucero, Sebastian; Hutchings, I Jeffrey A; Fraser, Dylan J

    2014-07-01

    The relationship between habitat variability and population size in fragmented habitats is poorly understood, yet might have important evolutionary consequences. For instance, fragmentation could (1) shift habitat characteristics, and by extension, selective regimes, in a consistent direction as populations and the fragments they occupy are reduced in size (directional hypothesis): or (2) increase variability in habitats among similarly sized populations as fragment size decreases (variable hypothesis). We investigated these alternatives based on multiyear habitat, demographic, and genetic data from 19 fragmented populations of a stream fish varying in census size (N) and effective number of breeders (N(b)). Mean habitat parameters were significantly related to N and N(b), but the forms of the relationships varied, and there was no evidence of consistent directional differences in habitat parameters from small to large population size. Small populations exhibited a wider range of variances in habitat parameters than large populations, and to a lesser extent, small populations also had greater variability in mean habitat parameters, possibly signaling more diverse selective regimes. These results suggest that many different environments are associated with small population size in nature, counter to the frequently cited assumption that small populations tend to occur only in marginal environments. In addition to well-documented demographic and genetic stochasticity operating within small populations, our work raises the possibility that small populations exhibit more variable and potentially less predictable evolutionary responses to future environmental change.

  13. Using molecular markers with high mutation rates to obtain estimates of relative population size and to distinguish the effects of gene flow and mutation: a demonstration using data from endemic Mauritian skinks.

    PubMed

    Nichols, R A; Freeman, K L M

    2004-04-01

    We propose a method of analysing genetic data to obtain separate estimates of the size (N(p)) and migration rate (m(p)) for the sampled populations, without precise prior knowledge of mutation rates at each locus ( micro(L)). The effects of migration and mutation can be distinguished because high migration has the effect of reducing genetic differentiation across all loci, whereas a high mutation rate will only affect the locus in question. The method also takes account of any differences between the spectra of immigrant alleles and of new mutant alleles. If the genetic data come from a range of population sizes, and the loci have a range of mutation rates, it is possible to estimate the relative sizes of the different N(p) values, and likewise the m(p) and the micro(L). Microsatellite loci may also be particularly appropriate because loci with a high mutation rate can reach mutation-drift-migration equilibrium more quickly, and because the spectra of mutants arriving in a population can be particularly distinct from the immigrants. We demonstrate this principle using a microsatellite data set from Mauritian skinks. The method identifies low gene flow between a putative new species and populations of its sister species, whereas the differentiation of two other populations is attributed to small population size. These distinct interpretations were not readily apparent from conventional measures of genetic differentiation and gene diversity. When the method is evaluated using simulated data sets, it correctly distinguishes low gene flow from small population size. Loci that are not at mutation-migration-drift equilibrium can distort the parameter estimates slightly. We discuss strategies for detecting and overcoming this effect.

  14. The Relationship between the Proportional Size of the Special Education Population and Academic Achievement

    ERIC Educational Resources Information Center

    Harper, Patricia Kenner

    2013-01-01

    This investigation addressed the hypothesized effects of the proportional size of a district's special education population on the overall student achievement in selected school districts in Texas. The size of a district's special education population (independent variable) was compared to districts' achievement (dependent variables) in order to…

  15. Estimating population size with correlated sampling unit estimates

    Treesearch

    David C. Bowden; Gary C. White; Alan B. Franklin; Joseph L. Ganey

    2003-01-01

    Finite population sampling theory is useful in estimating total population size (abundance) from abundance estimates of each sampled unit (quadrat). We develop estimators that allow correlated quadrat abundance estimates, even for quadrats in different sampling strata. Correlated quadrat abundance estimates based on mark–recapture or distance sampling methods occur...

  16. Flower size variation in Rosmarinus officinalis: individuals, populations and habitats.

    PubMed

    Herrera, Javier

    2005-02-01

    Flowers are relatively invariant organs within species, but quantitative variation often exists among conspecifics. These variations represent the raw material that natural selection can magnify, eventually resulting in morphological divergence and diversification. This paper investigates floral variability in Rosmarinus officinalis, a Mediterranean shrub. Nine populations were selected in three major southern Spanish habitats (coast, lowland and mountains) along an elevation gradient. Flower samples from randomly chosen plants were collected from each population, and a total of 641 flowers from 237 shrubs were weighed while still fresh to the nearest 0.1 mg. Leaves from the same plants were also measured. Variations among habitats, sites and plants were explored with general linear model ANOVA. Leaf-flower covariation was also investigated. Most (58%) mass in flowers was accounted for by the corolla, whose linear dimensions correlated directly with flower mass. Averaged over plants, the mass of a flower varied between 12 mg and 38 mg. Habitat, site (within habitat) and shrub identity had significant effects on mass variance. Flowers from the coast were the smallest (17 mg) and those from the mountains the largest (25 mg on average). A pattern of continuously increasing flower size with elevation emerged which was largely uncoupled from the geographical pattern of leaf size variation. As regards flower size, a great potential to local differentiation exists in Rosmarinus. Observed divergences accord with a regime of large-bodied pollinator selection in the mountains, but also with resource-cost hypotheses on floral evolution that postulate that reduced corollas are advantageous under prevailingly stressful conditions.

  17. Body size distributions of the pale grass blue butterfly in Japan: Size rules and the status of the Fukushima population

    NASA Astrophysics Data System (ADS)

    Taira, Wataru; Iwasaki, Mayo; Otaki, Joji M.

    2015-07-01

    The body size of the pale grass blue butterfly, Zizeeria maha, has been used as an environmental indicator of radioactive pollution caused by the Fukushima nuclear accident. However, geographical and temporal size distributions in Japan and temperature effects on size have not been established in this species. Here, we examined the geographical, temporal, and temperature-dependent changes of the forewing size of Z. maha argia in Japan. Butterflies collected in 2012 and 2013 from multiple prefectures throughout Japan demonstrated an inverse relationship of latitude and forewing size, which is the reverse of Bergmann’s cline. The Fukushima population was significantly larger than the Aomori and Miyagi populations and exhibited no difference from most of the other prefectural populations. When monitored at a single geographic locality every other month, forewing sizes were the largest in April and the smallest in August. Rearing larvae at a constant temperature demonstrated that forewing size followed the temperature-size rule. Therefore, the converse Bergmann’s rule and the temperature-size rule coexist in this multivoltine species. Our study establishes this species as a useful environmental indicator and supports the idea that the size reduction observed only in Fukushima Prefecture in 2011 was caused by the environmental stress of radioactive pollution.

  18. Body size distributions of the pale grass blue butterfly in Japan: Size rules and the status of the Fukushima population

    PubMed Central

    Taira, Wataru; Iwasaki, Mayo; Otaki, Joji M.

    2015-01-01

    The body size of the pale grass blue butterfly, Zizeeria maha, has been used as an environmental indicator of radioactive pollution caused by the Fukushima nuclear accident. However, geographical and temporal size distributions in Japan and temperature effects on size have not been established in this species. Here, we examined the geographical, temporal, and temperature-dependent changes of the forewing size of Z. maha argia in Japan. Butterflies collected in 2012 and 2013 from multiple prefectures throughout Japan demonstrated an inverse relationship of latitude and forewing size, which is the reverse of Bergmann’s cline. The Fukushima population was significantly larger than the Aomori and Miyagi populations and exhibited no difference from most of the other prefectural populations. When monitored at a single geographic locality every other month, forewing sizes were the largest in April and the smallest in August. Rearing larvae at a constant temperature demonstrated that forewing size followed the temperature-size rule. Therefore, the converse Bergmann’s rule and the temperature-size rule coexist in this multivoltine species. Our study establishes this species as a useful environmental indicator and supports the idea that the size reduction observed only in Fukushima Prefecture in 2011 was caused by the environmental stress of radioactive pollution. PMID:26197998

  19. Simulated effect of pig-population density on epidemic size and choice of control strategy for classical swine fever epidemics in The Netherlands.

    PubMed

    Mangen, M-J J; Nielen, M; Burrell, A M

    2002-12-18

    We examined the importance of pig-population density in the area of an outbreak of classical swine fever (CSF) for the spread of the infection and the choice of control measures. A spatial, stochastic, dynamic epidemiological simulation model linked to a sector-level market-and-trade model for The Netherlands were used. Outbreaks in sparsely and densely populated areas were compared under four different control strategies and with two alternative trade assumptions. The obligatory control strategy required by current EU legislation was predicted to be enough to eradicate an epidemic starting in an area with sparse pig population. By contrast, additional control measures would be necessary if the outbreak began in an area with high pig density. The economic consequences of using preventive slaughter rather than emergency vaccination as an additional control measure depended strongly on the reactions of trading partners. Reducing the number of animal movements significantly reduced the size and length of epidemics in areas with high pig density. The phenomenon of carrier piglets was included in the model with realistic probabilities of infection by this route, but it made a negligible contribution to the spread of the infection.

  20. Effect of Bactericides on Population Sizes and Spread of Clavibacter michiganensis subsp. michiganensis on Tomatoes in the Greenhouse and on Disease Development and Crop Yield in the Field.

    PubMed

    Hausbeck, M K; Bell, J; Medina-Mora, C; Podolsky, R; Fulbright, D W

    2000-01-01

    ABSTRACT Chemical applications, with the exception of mancozeb, reduced population sizes and spread of Clavibacter michiganensis subsp. michiganensis among tomato seedlings in the greenhouse and impacted subsequent plant development and yield in the field. While applications of copper hydroxide, copper hydroxide/mancozeb, copper hydroxide/mancozeb (premixed 12 h before spraying), streptomycin, and streptomycin/copper hydroxide to seedlings in the greenhouse did not differ significantly from the inoculated control, the trend was for these treatments to increase the survival of inoculated transplants in the field in comparison to the inoculated control. In the field, inoculated controls produced yields that were 63% (1995) and 51% (1996) of those produced by uninoculated controls. In both years, with the exception of mancozeb in 1995, all treatments resulted in yields similar to those obtained with the uninoculated control. Plant survival and yield in the field were severely affected when transplants had a pathogen population of >/= x 10(8) CFU/g of tissue. All treatments, with the exception of mancozeb, limited C. michiganensis subsp. michiganensis populations to <5.0 x 10(5). None of the treatments significantly reduced the incidence of fruit spotting compared with that of the inoculated control.

  1. Reliability of Different Mark-Recapture Methods for Population Size Estimation Tested against Reference Population Sizes Constructed from Field Data

    PubMed Central

    Grimm, Annegret; Gruber, Bernd; Henle, Klaus

    2014-01-01

    Reliable estimates of population size are fundamental in many ecological studies and biodiversity conservation. Selecting appropriate methods to estimate abundance is often very difficult, especially if data are scarce. Most studies concerning the reliability of different estimators used simulation data based on assumptions about capture variability that do not necessarily reflect conditions in natural populations. Here, we used data from an intensively studied closed population of the arboreal gecko Gehyra variegata to construct reference population sizes for assessing twelve different population size estimators in terms of bias, precision, accuracy, and their 95%-confidence intervals. Two of the reference populations reflect natural biological entities, whereas the other reference populations reflect artificial subsets of the population. Since individual heterogeneity was assumed, we tested modifications of the Lincoln-Petersen estimator, a set of models in programs MARK and CARE-2, and a truncated geometric distribution. Ranking of methods was similar across criteria. Models accounting for individual heterogeneity performed best in all assessment criteria. For populations from heterogeneous habitats without obvious covariates explaining individual heterogeneity, we recommend using the moment estimator or the interpolated jackknife estimator (both implemented in CAPTURE/MARK). If data for capture frequencies are substantial, we recommend the sample coverage or the estimating equation (both models implemented in CARE-2). Depending on the distribution of catchabilities, our proposed multiple Lincoln-Petersen and a truncated geometric distribution obtained comparably good results. The former usually resulted in a minimum population size and the latter can be recommended when there is a long tail of low capture probabilities. Models with covariates and mixture models performed poorly. Our approach identified suitable methods and extended options to evaluate the

  2. The critical domain size of stochastic population models.

    PubMed

    Reimer, Jody R; Bonsall, Michael B; Maini, Philip K

    2017-02-01

    Identifying the critical domain size necessary for a population to persist is an important question in ecology. Both demographic and environmental stochasticity impact a population's ability to persist. Here we explore ways of including this variability. We study populations with distinct dispersal and sedentary stages, which have traditionally been modelled using a deterministic integrodifference equation (IDE) framework. Individual-based models (IBMs) are the most intuitive stochastic analogues to IDEs but yield few analytic insights. We explore two alternate approaches; one is a scaling up to the population level using the Central Limit Theorem, and the other a variation on both Galton-Watson branching processes and branching processes in random environments. These branching process models closely approximate the IBM and yield insight into the factors determining the critical domain size for a given population subject to stochasticity.

  3. Effect Size in Clinical Phonology

    ERIC Educational Resources Information Center

    Gierut, Judith A.; Morrisette, Michele L.

    2011-01-01

    The purpose of this article is to motivate the use of effect size (ES) for single-subject research in clinical phonology, with an eye towards meta-analyses of treatment effects for children with phonological disorders. Standard mean difference (SMD) is introduced and illustrated as one ES well suited to the multiple baseline (MBL) design and…

  4. Effect Size in Clinical Phonology

    ERIC Educational Resources Information Center

    Gierut, Judith A.; Morrisette, Michele L.

    2011-01-01

    The purpose of this article is to motivate the use of effect size (ES) for single-subject research in clinical phonology, with an eye towards meta-analyses of treatment effects for children with phonological disorders. Standard mean difference (SMD) is introduced and illustrated as one ES well suited to the multiple baseline (MBL) design and…

  5. Does population size affect genetic diversity? A test with sympatric lizard species

    PubMed Central

    Hague, M T J; Routman, E J

    2016-01-01

    Genetic diversity is a fundamental requirement for evolution and adaptation. Nonetheless, the forces that maintain patterns of genetic variation in wild populations are not completely understood. Neutral theory posits that genetic diversity will increase with a larger effective population size and the decreasing effects of drift. However, the lack of compelling evidence for a relationship between genetic diversity and population size in comparative studies has generated some skepticism over the degree that neutral sequence evolution drives overall patterns of diversity. The goal of this study was to measure genetic diversity among sympatric populations of related lizard species that differ in population size and other ecological factors. By sampling related species from a single geographic location, we aimed to reduce nuisance variance in genetic diversity owing to species differences, for example, in mutation rates or historical biogeography. We compared populations of zebra-tailed lizards and western banded geckos, which are abundant and short-lived, to chuckwallas and desert iguanas, which are less common and long-lived. We assessed population genetic diversity at three protein-coding loci for each species. Our results were consistent with the predictions of neutral theory, as the abundant species almost always had higher levels of haplotype diversity than the less common species. Higher population genetic diversity in the abundant species is likely due to a combination of demographic factors, including larger local population sizes (and presumably effective population sizes), faster generation times and high rates of gene flow with other populations. PMID:26306730

  6. Does population size affect genetic diversity? A test with sympatric lizard species.

    PubMed

    Hague, M T J; Routman, E J

    2016-01-01

    Genetic diversity is a fundamental requirement for evolution and adaptation. Nonetheless, the forces that maintain patterns of genetic variation in wild populations are not completely understood. Neutral theory posits that genetic diversity will increase with a larger effective population size and the decreasing effects of drift. However, the lack of compelling evidence for a relationship between genetic diversity and population size in comparative studies has generated some skepticism over the degree that neutral sequence evolution drives overall patterns of diversity. The goal of this study was to measure genetic diversity among sympatric populations of related lizard species that differ in population size and other ecological factors. By sampling related species from a single geographic location, we aimed to reduce nuisance variance in genetic diversity owing to species differences, for example, in mutation rates or historical biogeography. We compared populations of zebra-tailed lizards and western banded geckos, which are abundant and short-lived, to chuckwallas and desert iguanas, which are less common and long-lived. We assessed population genetic diversity at three protein-coding loci for each species. Our results were consistent with the predictions of neutral theory, as the abundant species almost always had higher levels of haplotype diversity than the less common species. Higher population genetic diversity in the abundant species is likely due to a combination of demographic factors, including larger local population sizes (and presumably effective population sizes), faster generation times and high rates of gene flow with other populations.

  7. Precision of recombination frequency estimates after random intermating with finite population sizes.

    PubMed

    Frisch, Matthias; Melchinger, Albrecht E

    2008-01-01

    Random intermating of F2 populations has been suggested for obtaining precise estimates of recombination frequencies between tightly linked loci. In a simulation study, sampling effects due to small population sizes in the intermating generations were found to abolish the advantages of random intermating that were reported in previous theoretical studies considering an infinite population size. We propose a mating scheme for intermating with planned crosses that yields more precise estimates than those under random intermating.

  8. The size distribution of conspecific populations: the peoples of New Guinea.

    PubMed Central

    Novotny, V; Drozd, P

    2000-01-01

    The size distribution of the language populations in New Guinea, which represent over 15% of the world's languages, is analysed using models analogous to the resource division models of species abundance distribution in ecological communities. A model distribution of resource segments reflecting population size is created by repeated selection of an existing resource segment and its division into two. We found that any dependency of the selection probability on the size of the segment generated negatively skewed abundance distributions after log transformation. Asymmetric segment division further exacerbated the negative skewness. Size-independent selection produced lognormal abundance distributions, irrespective of the segment division method. Size-dependent selection and asymmetric division were deemed reasonable assumptions since large language populations are more likely to generate isolates, which develop into new populations, than small ones, and these isolates are likely to be small relative to the progenitor population. A negatively skewed distribution of the log-transformed population sizes was therefore expected. However, the observed distributions were lognormal, scale invariant for areas containing between 100 and over 1000 language populations. The dynamics of language differentiation, as reflected by the models, may therefore be unimportant relative to the effect of variable growth rates among populations. All lognormal distributions from resource division models had a higher variance than the observed one, where half of the 1053 populations had between 350 and 3000 individuals. The possible mechanisms maintaining such a low variance around a modal population size of 1000 are discussed. PMID:10853740

  9. Estimated portion sizes in a school-aged population.

    PubMed

    Patel, Sumaiya; Vyas, Avni; Custovic, Adnan; Murray, Clare S

    2012-12-01

    To produce study-specific portion sizes for 11-year-old children in a population-based birth cohort and to compare these study-specific portion sizes with previously published children's portion sizes, to assess their relevance today. Two multiple-pass 24 h dietary recalls were taken. The Food Standard Agency's photographic food atlas was used to quantify intakes. Study-specific food portion sizes were calculated for each food group. Portion sizes were calculated for all children and separately for boys and girls. The nutrient intake from the 24 h dietary recalls was analysed using study-specific and published portion sizes for individual participants. Agreement was assessed using Pearson's correlation, intra-class correlation coefficients and the Bland-Altman method. Birth cohort study, UK. Children (mean age 11.3 years, n 264) and parents/guardians. A total of 124 food portion sizes were calculated. Differences in portion weights between boys and girls were seen only for seven food items. There was a significant positive relationship (P < 0.001) between intakes of each nutrient as determined by the two sets of portion sizes. Correlation coefficients ranged from 0.77 (protein) to 0.98 (β-carotene). The intra-class correlation coefficients showed good agreement between nutrient intakes determined by the study-specific and published portion sizes (P < 0.001). Nutrient intakes calculated using portion sizes from our population were similar to those calculated from portion size data collected in a national survey, despite being collected over a decade later. The present study adds to the small amount of evidence regarding portion sizes in UK children and shows agreement with previously published paediatric portion sizes.

  10. Sample Size Calculations for Population Size Estimation Studies Using Multiplier Methods With Respondent-Driven Sampling Surveys.

    PubMed

    Fearon, Elizabeth; Chabata, Sungai T; Thompson, Jennifer A; Cowan, Frances M; Hargreaves, James R

    2017-09-14

    While guidance exists for obtaining population size estimates using multiplier methods with respondent-driven sampling surveys, we lack specific guidance for making sample size decisions. To guide the design of multiplier method population size estimation studies using respondent-driven sampling surveys to reduce the random error around the estimate obtained. The population size estimate is obtained by dividing the number of individuals receiving a service or the number of unique objects distributed (M) by the proportion of individuals in a representative survey who report receipt of the service or object (P). We have developed an approach to sample size calculation, interpreting methods to estimate the variance around estimates obtained using multiplier methods in conjunction with research into design effects and respondent-driven sampling. We describe an application to estimate the number of female sex workers in Harare, Zimbabwe. There is high variance in estimates. Random error around the size estimate reflects uncertainty from M and P, particularly when the estimate of P in the respondent-driven sampling survey is low. As expected, sample size requirements are higher when the design effect of the survey is assumed to be greater. We suggest a method for investigating the effects of sample size on the precision of a population size estimate obtained using multipler methods and respondent-driven sampling. Uncertainty in the size estimate is high, particularly when P is small, so balancing against other potential sources of bias, we advise researchers to consider longer service attendance reference periods and to distribute more unique objects, which is likely to result in a higher estimate of P in the respondent-driven sampling survey.

  11. An examination of positive selection and changing effective population size in Angus and Holstein cattle populations (Bos taurus) using a high density SNP genotyping platform and the contribution of ancient polymorphism to genomic diversity in Domestic cattle

    PubMed Central

    MacEachern, Sean; Hayes, Ben; McEwan, John; Goddard, Mike

    2009-01-01

    Background Identifying recent positive selection signatures in domesticated animals could provide information on genome response to strong directional selection from domestication and artificial selection. With the completion of the cattle genome, private companies are now providing large numbers of polymorphic markers for probing variation in domestic cattle (Bos taurus). We analysed over 7,500 polymorphic single nucleotide polymorphisms (SNP) in beef (Angus) and dairy (Holstein) cattle and outgroup species Bison, Yak and Banteng in an indirect test of inbreeding and positive selection in Domestic cattle. Results Outgroup species: Bison, Yak and Banteng, were genotyped with high levels of success (90%) and used to determine ancestral and derived allele states in domestic cattle. Frequency spectrums of the derived alleles in Angus and Holstein were examined using Fay and Wu's H test. Significant divergences from the predicted frequency spectrums expected under neutrality were identified. This appeared to be the result of combined influences of positive selection, inbreeding and ascertainment bias for moderately frequent SNP. Approximately 10% of all polymorphisms identified as segregating in B. taurus were also segregating in Bison, Yak or Banteng; highlighting a large number of polymorphisms that are ancient in origin. Conclusion These results suggest that a large effective population size (Ne) of approximately 90,000 or more existed in B. taurus since they shared a common ancestor with Bison, Yak and Banteng ~1–2 million years ago (MYA). More recently Ne decreased sharply probably associated with domestication. This may partially explain the paradox of high levels of polymorphism in Domestic cattle and the relatively small recent Ne in this species. The period of inbreeding caused Fay and Wu's H statistic to depart from its expectation under neutrality mimicking the effect of selection. However, there was also evidence for selection, because high frequency

  12. The Small Size Debris Population at GEO from Optical Observations

    NASA Technical Reports Server (NTRS)

    Seitzer, Patrick; Barker, Ed; Buckalew, Brent; Burkhardt, Andrew; Cowardin, Heather; Frith, James; Kaleida, Catherine; Lederer, Susan M.; Lee, Chris H.

    2017-01-01

    We have observed the geosynchronous orbit (GEO) debris population at sizes smaller than 10 cm using optical observations with the 6.5-m Magellan telescope 'Walter Baade' at the Las Campanas Observatory in Chile. The IMACS f/2 imaging camera with a 0.5-degree diameter field of view has been used in small area surveys of the GEO regime to study the population of optically faint GEO debris. The goal is to estimate the population of GEO debris that is fainter than can be studied with 1-meter class telescopes. A significant population of objects fainter than R = 19th magnitude has been found. These objects have observed with angular rates consistent with circular orbits and orbital inclinations up to 15 degrees at GEO. A sizeable number of these objects have significant brightness variations ("flashes") during the 5-second exposure, which suggest rapid changes in the albedo-projected size product.

  13. Bayesian Optimization Algorithm, Population Sizing, and Time to Convergence

    SciTech Connect

    Pelikan, M.; Goldberg, D.E.; Cantu-Paz, E.

    2000-01-19

    This paper analyzes convergence properties of the Bayesian optimization algorithm (BOA). It settles the BOA into the framework of problem decomposition used frequently in order to model and understand the behavior of simple genetic algorithms. The growth of the population size and the number of generations until convergence with respect to the size of a problem is theoretically analyzed. The theoretical results are supported by a number of experiments.

  14. Dispatch centres: what is the right population catchment size?

    PubMed

    Dami, Fabrice; Fuchs, Vincent; Hugli, Olivier

    2015-04-09

    Literature on medical dispatch is growing, focusing mainly on efficiency (under and overtriage) and dispatch-assisted CPR. But the issue of population catchment size, functional costs and rationalization is rarely addressed. If we can observe a trend toward a decreasing number of dispatch centres in many European countries, there is today no evidence on what is the right catchment size to reach the best balance between quality of services and costs.

  15. Obesity and body size perceptions in a Spanish Roma population.

    PubMed

    Poveda, Alaitz; Ibáñez, María Eugenia; Rebato, Esther

    2014-01-01

    Roma people are particularly vulnerable to developing overweight and obesity. Self-perception of body image may influence the prevalence of obesity in this ethnic minority. The objectives of this study are to estimate the prevalence of obesity, to analyse body size perceptions and preferences and to assess the relationship between body size perceptions and obesity in the Roma population. The analyses were carried out on 372 men, women and children from the Roma population residing in the Greater Bilbao region (Basque Country, Spain). In adults, a standard figural scale was used to analyse body size perceptions and preferences in this ethnic minority. Overall 51.7% of adult and 24.4% of minor Roma individuals were obese. Both Roma men and women had inaccurate self-perceptions of their body size. Significant differences on body size perceptions were detected based on age, sex, nutritional status and socioeconomic characteristics. This Roma population presents one of the highest rates of obesity worldwide. Although a certain awareness of the correct weight status was appreciated, the inability of Roma individuals to see themselves as overweight or obese may be a significant factor on the high prevalence of obesity in this population.

  16. [Teeth size reduction in the prehistoric populations in Serbia].

    PubMed

    Pajević, Tina; Sessa, Tijana; Juloski, Jovana; Glišić, Branislav

    2012-01-01

    Anthropological studies show craniofacial changes with a reduction in teeth size during evolution of the human population. The objective was to measure and compare the sizes of teeth in the population of the Mesolithic-Neolithic sites in the Iron Gate Gorge and the population from the Early Bronze Age site of Mokrin. The study included teeth without advanced wear near the pulp. The material was divided according to the site of the skeletal population in two groups. Group 1 comprised 107 teeth from the Mesolithic-Neolithic sites Lepenski Vir and Vlasac. Group 2 included 158 teeth from the Mokrin graveyard dated in the Early Bronze Age. The mesio-distal diameter was measured in all teeth, while the vestibulo-oral diameter was measured in the molars only. Using the two-factor analysis of variance, the influence of sex, site and their interaction on the size of the teeth were investigated. The vestibulo-oral diameter of the upper third molar was significantly higher in males compared to females. The comparison between the groups showed that the vestibulooral diameter of the lower first molar was significantly higher in group 1. The present difference in teeth size indicates the existence of reduction during the prehistoric times. However, the time period between the populations studied is probably too short to be manifested on a large number of teeth.

  17. Universal Asymptotic Clone Size Distribution for General Population Growth.

    PubMed

    Nicholson, Michael D; Antal, Tibor

    2016-11-01

    Deterministically growing (wild-type) populations which seed stochastically developing mutant clones have found an expanding number of applications from microbial populations to cancer. The special case of exponential wild-type population growth, usually termed the Luria-Delbrück or Lea-Coulson model, is often assumed but seldom realistic. In this article, we generalise this model to different types of wild-type population growth, with mutants evolving as a birth-death branching process. Our focus is on the size distribution of clones-that is the number of progeny of a founder mutant-which can be mapped to the total number of mutants. Exact expressions are derived for exponential, power-law and logistic population growth. Additionally, for a large class of population growth, we prove that the long-time limit of the clone size distribution has a general two-parameter form, whose tail decays as a power-law. Considering metastases in cancer as the mutant clones, upon analysing a data-set of their size distribution, we indeed find that a power-law tail is more likely than an exponential one.

  18. Andean Condor (Vultur gryphus) in Ecuador: Geographic Distribution, Population Size and Extinction Risk

    PubMed Central

    Naveda-Rodríguez, Adrián; Vargas, Félix Hernán; Kohn, Sebastián; Zapata-Ríos, Galo

    2016-01-01

    The Andean Condor (Vultur gryphus) in Ecuador is classified as Critically Endangered. Before 2015, standardized and systematic estimates of geographic distribution, population size and structure were not available for this species, hampering the assessment of its current status and hindering the design and implementation of effective conservation actions. In this study, we performed the first quantitative assessment of geographic distribution, population size and population viability of Andean Condor in Ecuador. We used a methodological approach that included an ecological niche model to study geographic distribution, a simultaneous survey of 70 roosting sites to estimate population size and a population viability analysis (PVA) for the next 100 years. Geographic distribution in the form of extent of occurrence was 49 725 km2. During a two-day census, 93 Andean Condors were recorded and a population of 94 to 102 individuals was estimated. In this population, adult-to-immature ratio was 1:0.5. In the modeled PVA scenarios, the probability of extinction, mean time to extinction and minimum population size varied from zero to 100%, 63 years and 193 individuals, respectively. Habitat loss is the greatest threat to the conservation of Andean Condor populations in Ecuador. Population size reduction in scenarios that included habitat loss began within the first 15 years of this threat. Population reinforcement had no effects on the recovery of Andean Condor populations given the current status of the species in Ecuador. The population size estimate presented in this study is the lower than those reported previously in other countries where the species occur. The inferences derived from the population viability analysis have implications for Condor management in Ecuador. This study highlights the need to redirect efforts from captive breeding and population reinforcement to habitat conservation. PMID:26986004

  19. Andean Condor (Vultur gryphus) in Ecuador: Geographic Distribution, Population Size and Extinction Risk.

    PubMed

    Naveda-Rodríguez, Adrián; Vargas, Félix Hernán; Kohn, Sebastián; Zapata-Ríos, Galo

    2016-01-01

    The Andean Condor (Vultur gryphus) in Ecuador is classified as Critically Endangered. Before 2015, standardized and systematic estimates of geographic distribution, population size and structure were not available for this species, hampering the assessment of its current status and hindering the design and implementation of effective conservation actions. In this study, we performed the first quantitative assessment of geographic distribution, population size and population viability of Andean Condor in Ecuador. We used a methodological approach that included an ecological niche model to study geographic distribution, a simultaneous survey of 70 roosting sites to estimate population size and a population viability analysis (PVA) for the next 100 years. Geographic distribution in the form of extent of occurrence was 49 725 km2. During a two-day census, 93 Andean Condors were recorded and a population of 94 to 102 individuals was estimated. In this population, adult-to-immature ratio was 1:0.5. In the modeled PVA scenarios, the probability of extinction, mean time to extinction and minimum population size varied from zero to 100%, 63 years and 193 individuals, respectively. Habitat loss is the greatest threat to the conservation of Andean Condor populations in Ecuador. Population size reduction in scenarios that included habitat loss began within the first 15 years of this threat. Population reinforcement had no effects on the recovery of Andean Condor populations given the current status of the species in Ecuador. The population size estimate presented in this study is the lower than those reported previously in other countries where the species occur. The inferences derived from the population viability analysis have implications for Condor management in Ecuador. This study highlights the need to redirect efforts from captive breeding and population reinforcement to habitat conservation.

  20. Effect size in clinical phonology.

    PubMed

    Gierut, Judith A; Morrisette, Michele L

    2011-11-01

    The purpose of this article is to motivate the use of effect size (ES) for single-subject research in clinical phonology, with an eye towards meta-analyses of treatment effects for children with phonological disorders. Standard mean difference (SMD) is introduced and illustrated as one ES well suited to the multiple baseline (MBL) design and evaluation of generalization learning, both of which are key to experimental studies in clinical phonology.

  1. Effect size in clinical phonology

    PubMed Central

    Gierut, Judith A.; Morrisette, Michele L.

    2012-01-01

    The purpose of this article is to motivate the use of effect size (ES) for single-subject research in clinical phonology, with an eye towards meta-analyses of treatment effects for children with phonological disorders. Standard mean difference (SMD) is introduced and illustrated as one ES well suited to the multiple baseline (MBL) design and evaluation of generalization learning, both of which are key to experimental studies in clinical phonology. PMID:21787149

  2. The elusive minimum viable population size for white sturgeon

    SciTech Connect

    Jager, Yetta; Lepla, Ken B.; Van Winkle, Webb; James, Mr Brad; McAdam, Dr Steve

    2010-01-01

    Biological conservation of sturgeon populations is a concern for many species. Those responsible for managing the white sturgeon (Acipenser transmontanus) and similar species are interested in identifying extinction thresholds to avoid. Two thresholds that exist in theory are the minimum viable population size (MVP) and minimum amount of suitable habitat. In this paper, we present both model and empirical estimates of these thresholds. We modified a population viability analysis (PVA) model for white sturgeon to include two new Allee mechanisms. Despite this, PVA-based MVP estimates were unrealistically low compared with empirical estimates unless opportunities for spawning were assumed to be less frequent. PVA results revealed a trade-off between MVP and habitat thresholds; smaller populations persisted in longer river segments and vice versa. Our empirical analyses suggested (1) a MVP range based on population trends from 1,194 to 27,700 individuals, and (2) a MVP estimate of 4,000 individuals based on recruitment. Long-term historical population surveys are needed for more populations to pinpoint an MVP based on trends, whereas the available data were sufficient to estimate MVP based on recruitment. Beyond the MVP, we developed a hierarchical model for population status based on empirical data. Metapopulation support was the most important predictor of population health, followed by the length of free-flowing habitat, with habitat thresholds at 26 and 150 km. Together, these results suggest that habitat and connectivity are important determinants of population status that likely influence the site-specific MVP thresholds.

  3. Effects of Body Size and Gender on the Population Pharmacokinetics of Artesunate and Its Active Metabolite Dihydroartemisinin in Pediatric Malaria Patients

    PubMed Central

    Morris, Carrie A.; Tan, Beesan; Duparc, Stephan; Borghini-Fuhrer, Isabelle; Jung, Donald; Shin, Chang-Sik

    2013-01-01

    Despite the important role of the antimalarial artesunate and its active metabolite dihydroartemisinin (DHA) in malaria treatment efforts, there are limited data on the pharmacokinetics of these agents in pediatric patients. This study evaluated the effects of body size and gender on the pharmacokinetics of artesunate-DHA using data from pediatric and adult malaria patients. Nonlinear mixed-effects modeling was used to obtain a base model consisting of first-order artesunate absorption and one-compartment models for artesunate and for DHA. Various methods of incorporating effects of body size descriptors on clearance and volume parameters were tested. An allometric scaling model for weight and a linear body surface area (BSA) model were deemed optimal. The apparent clearance and volume of distribution of DHA obtained with the allometric scaling model, normalized to a 38-kg patient, were 63.5 liters/h and 65.1 liters, respectively. Estimates for the linear BSA model were similar. The 95% confidence intervals for the estimated gender effects on clearance and volume parameters for artesunate fell outside the predefined no-relevant-clinical-effect interval of 0.75 to 1.25. However, the effect of gender on apparent DHA clearance was almost entirely contained within this interval, suggesting a lack of an influence of gender on this parameter. Overall, the pharmacokinetics of artesunate and DHA following oral artesunate administration can be described for pediatric patients using either an allometric scaling or linear BSA model. Both models predict that, for a given artesunate dose in mg/kg of body weight, younger children are expected to have lower DHA exposure than older children or adults. PMID:24041884

  4. Acceptability of the Kalman filter to monitor pronghorn population size

    Treesearch

    Raymond L. Czaplewski

    1986-01-01

    Pronghorn antelope are important components of grassland and steppe ecosystems in Wyoming. Monitoring data on the size and population dynamics of these herds are expensive and gathered only a few times each year. Reliable data include estimates of animals harvested and proportion of bucks, does, and fawns. A deterministic simulation model has been used to improve...

  5. Estimating total population size for adult female sea turtles: Accounting for non-nesters

    USGS Publications Warehouse

    Kendall, W.L.; Richardson, J.I.; Rees, Alan F.

    2008-01-01

    Assessment of population size and changes therein is important to sea turtle management and population or life history research. Investigators might be interested in testing hypotheses about the effect of current population size or density (number of animals per unit resource) on future population processes. Decision makers might want to determine a level of allowable take of individual turtles of specified life stage. Nevertheless, monitoring most stages of sea turtle life histories is difficult, because obtaining access to individuals is difficult. Although in-water assessments are becoming more common, nesting females and their hatchlings remain the most accessible life stages. In some cases adult females of a given nesting population are sufficiently philopatric that the population itself can be well defined. If a well designed tagging study is conducted on this population, survival, breeding probability, and the size of the nesting population in a given year can be estimated. However, with published statistical methodology the size of the entire breeding population (including those females skipping nesting in that year) cannot be estimated without assuming that each adult female in this population has the same probability of nesting in a given year (even those that had just nested in the previous year). We present a method for estimating the total size of a breeding population (including nesters those skipping nesting) from a tagging study limited to the nesting population, allowing for the probability of nesting in a given year to depend on an individual's nesting status in the previous year (i.e., a Markov process). From this we further develop estimators for rate of growth from year to year in both nesting population and total breeding population, and the proportion of the breeding population that is breeding in a given year. We also discuss assumptions and apply these methods to a breeding population of hawksbill sea turtles (Eretmochelys imbricata) from

  6. Overdominant alleles in a population of variable size.

    PubMed Central

    Slatkin, M; Muirhead, C A

    1999-01-01

    An approximate method is developed to predict the number of strongly overdominant alleles in a population of which the size varies with time. The approximation relies on the strong-selection weak-mutation (SSWM) method introduced by J. H. Gillespie and leads to a Markov chain model that describes the number of common alleles in the population. The parameters of the transition matrix of the Markov chain depend in a simple way on the population size. For a population of constant size, the Markov chain leads to results that are nearly the same as those of N. Takahata. The Markov chain allows the prediction of the numbers of common alleles during and after a population bottleneck and the numbers of alleles surviving from before a bottleneck. This method is also adapted to modeling the case in which there are two classes of alleles, with one class causing a reduction in fitness relative to the other class. Very slight selection against one class can strongly affect the relative frequencies of the two classes and the relative ages of alleles in each class. PMID:10353917

  7. Size specific predation by herons and its effect on the sex-ratio of natural populations of the mosquito fish Gambusia affinis baird and girard.

    PubMed

    Britton, Robert H; Moser, Michael E

    1982-01-01

    Sex-ratios of Gambusia affinis populations in freshwater marshes in the Camargue (Rhône Delta), are highly biased in favour of males, whereas the sex-ratios in ditches are close to unity. Studies of the diet of free living birds and experimental studies on prey size selection in captivity show that the abnormal sex-ratios in marshes can be attributed to differential heron predation. Ditches are relatively free from predation. Mature female Gambusia are larger, and have an energy content 5-25 times greater than that of mature males. Handling times of Grey Heron (Ardea cinerea) and Little Egret (Egretta garzetta) are only slightly longer for female Gambusia than males. Hence, females represent a much more profitable prey.Analysis of nestling regurgitates show that Gambusia makes up a considerable proportion of the diet of four species of Camargue herons, and that the majority of Gambusia taken are females. Under experimental conditions, captive herons consume almost exclusively female fish, even when offered in ratios where they are heavily outnumbered by males.The relevance of these results to optimal diet theory is discussed.

  8. Reductive genome evolution at both ends of the bacterial population size spectrum.

    PubMed

    Batut, Bérénice; Knibbe, Carole; Marais, Gabriel; Daubin, Vincent

    2014-12-01

    Bacterial genomes show substantial variations in size. The smallest bacterial genomes are those of endocellular symbionts of eukaryotic hosts, which have undergone massive genome reduction and show patterns that are consistent with the degenerative processes that are predicted to occur in species with small effective population sizes. However, similar genome reduction is found in some free-living marine cyanobacteria that are characterized by extremely large populations. In this Opinion article, we discuss the different hypotheses that have been proposed to account for this reductive genome evolution at both ends of the bacterial population size spectrum.

  9. Noninvasive genetics provides insights into the population size and genetic diversity of an Amur tiger population in China.

    PubMed

    Wang, Dan; Hu, Yibo; Ma, Tianxiao; Nie, Yonggang; Xie, Yan; Wei, Fuwen

    2016-01-01

    Understanding population size and genetic diversity is critical for effective conservation of endangered species. The Amur tiger (Panthera tigris altaica) is the largest felid and a flagship species for wildlife conservation. Due to habitat loss and human activities, available habitat and population size are continuously shrinking. However, little is known about the true population size and genetic diversity of wild tiger populations in China. In this study, we collected 55 fecal samples and 1 hair sample to investigate the population size and genetic diversity of wild Amur tigers in Hunchun National Nature Reserve, Jilin Province, China. From the samples, we determined that 23 fecal samples and 1 hair sample were from 7 Amur tigers: 2 males, 4 females and 1 individual of unknown sex. Interestingly, 2 fecal samples that were presumed to be from tigers were from Amur leopards, highlighting the significant advantages of noninvasive genetics over traditional methods in studying rare and elusive animals. Analyses from this sample suggested that the genetic diversity of wild Amur tigers is much lower than that of Bengal tigers, consistent with previous findings. Furthermore, the genetic diversity of this Hunchun population in China was lower than that of the adjoining subpopulation in southwest Primorye Russia, likely due to sampling bias. Considering the small population size and relatively low genetic diversity, it is urgent to protect this endangered local subpopulation in China. © 2015 International Society of Zoological Sciences, Institute of Zoology/Chinese Academy of Sciences and John Wiley & Sons Australia, Ltd.

  10. Size-specific sensitivity: Applying a new structured population model

    SciTech Connect

    Easterling, M.R.; Ellner, S.P.; Dixon, P.M.

    2000-03-01

    Matrix population models require the population to be divided into discrete stage classes. In many cases, especially when classes are defined by a continuous variable, such as length or mass, there are no natural breakpoints, and the division is artificial. The authors introduce the integral projection model, which eliminates the need for division into discrete classes, without requiring any additional biological assumptions. Like a traditional matrix model, the integral projection model provides estimates of the asymptotic growth rate, stable size distribution, reproductive values, and sensitivities of the growth rate to changes in vital rates. However, where the matrix model represents the size distributions, reproductive value, and sensitivities as step functions (constant within a stage class), the integral projection model yields smooth curves for each of these as a function of individual size. The authors describe a method for fitting the model to data, and they apply this method to data on an endangered plant species, northern monkshood (Aconitum noveboracense), with individuals classified by stem diameter. The matrix and integral models yield similar estimates of the asymptotic growth rate, but the reproductive values and sensitivities in the matrix model are sensitive to the choice of stage classes. The integral projection model avoids this problem and yields size-specific sensitivities that are not affected by stage duration. These general properties of the integral projection model will make it advantageous for other populations where there is no natural division of individuals into stage classes.

  11. A Model for Cell Population Size Control Using Asymmetric Division

    PubMed Central

    Hamidi, Mani; Emberly, Eldon

    2013-01-01

    In multicellular organisms one can find examples where a growing tissue divides up until some final fixed cell number. Asymmetric division plays a prevalent feature in tissue differentiation in these organisms, where the daughters of each asymmetric division inherit unequal amounts of a fate determining molecule and as a result follow different developmental fates. In some tissues the accumulation or decrease of cell cycle regulators acts as an intrinsic timing mechanism governing proliferation. Here we present a minimal model based on asymmetric division and dilution of a cell-cycle regulator that can generate any final population size that might be needed. We show that within the model there are a variety of growth mechanisms from linear to non-linear that can lead to the same final cell count. Interestingly, when we include noise at division we find that there are special final cell population sizes that can be generated with high confidence that are flanked by population sizes that are less robust to division noise. When we include further perturbations in the division process we find that these special populations can remain relatively stable and in some cases even improve in their fidelity. PMID:24040230

  12. Extinction risk of a density-dependent population estimated from a time series of population size.

    PubMed

    Hakoyama, H; Iwasa, Y

    2000-06-07

    Environmental threats, such as habitat size reduction or environmental pollution, may not cause immediate extinction of a population but shorten the expected time to extinction. We develop a method to estimate the mean time to extinction for a density-dependent population with environmental fluctuation. We first derive a formula for a stochastic differential equation model (canonical model) of a population with logistic growth with environmental and demographic stochasticities. We then study an approximate maximum likelihood (AML) estimate of three parameters (intrinsic growth rate r, carrying capacity K, and environmental stochasticity sigma(2)(e)) from a time series of population size. The AML estimate of r has a significant bias, but by adopting the Monte Carlo method, we can remove the bias very effectively (bias-corrected estimate). We can also determine the confidence interval of the parameter based on the Monte Carlo method. If the length of the time series is moderately long (with 40-50 data points), parameter estimation with the Monte Carlo sampling bias correction has a relatively small variance. However, if the time series is short (less than or equal to 10 data points), the estimate has a large variance and is not reliable. If we know the intrinsic growth rate r, however, the estimate of K and sigma(2)(e)and the mean extinction time T are reliable even if only a short time series is available. We illustrate the method using data for a freshwater fish, Japanese crucian carp (Carassius auratus subsp.) in Lake Biwa, in which the growth rate and environmental noise of crucian carp are estimated using fishery records.

  13. Genetic Diversity in Introduced Populations with an Allee Effect

    PubMed Central

    Wittmann, Meike J.; Gabriel, Wilfried; Metzler, Dirk

    2014-01-01

    A phenomenon that strongly influences the demography of small introduced populations and thereby potentially their genetic diversity is the demographic Allee effect, a reduction in population growth rates at small population sizes. We take a stochastic modeling approach to investigate levels of genetic diversity in populations that successfully overcame either a strong Allee effect, in which populations smaller than a certain critical size are expected to decline, or a weak Allee effect, in which the population growth rate is reduced at small sizes but not negative. Our results indicate that compared to successful populations without an Allee effect, successful populations with a strong Allee effect tend to (1) derive from larger founder population sizes and thus have a higher initial amount of genetic variation, (2) spend fewer generations at small population sizes where genetic drift is particularly strong, and (3) spend more time around the critical population size and thus experience more genetic drift there. In the case of multiple introduction events, there is an additional increase in diversity because Allee-effect populations tend to derive from a larger number of introduction events than other populations. Altogether, a strong Allee effect can either increase or decrease genetic diversity, depending on the average founder population size. By contrast, a weak Allee effect tends to decrease genetic diversity across the entire range of founder population sizes. Finally, we show that it is possible in principle to infer critical population sizes from genetic data, although this would require information from many independently introduced populations. PMID:25009147

  14. A survey of FRAXE allele sizes in three populations

    SciTech Connect

    Zhong, N.; Ju, W.; Curley, D.

    1996-08-09

    FRAXE is a fragile site located at Xq27-8, which contains polymorphic triplet GCC repeats associated with a CpG island. Similar to FRAXA, expansion of the GCC repeats results in an abnormal methylation of the CpG island and is associated with a mild mental retardation syndrome (FRAXE-MR). We surveyed the GCC repeat alleles of FRAXE from 3 populations. A total of 665 X chromosomes including 416 from a New York Euro-American sample (259 normal and 157 with FRAXA mutations), 157 from a Chinese sample (144 normal and 13 FRAXA), and 92 from a Finnish sample (56 normal and 36 FRAXA) were analyzed by polymerase chain reaction. Twenty-seven alleles, ranging from 4 to 39 GCC repeats, were observed. The modal repeat number was 16 in the New York and Finnish samples and accounted for 24% of all the chromosomes tested (162/665). The modal repeat number in the Chinese sample was 18. A founder effect for FRAXA was suggested among the Finnish FRAXA samples in that 75% had the FRAXE 16 repeat allele versus only 30% of controls. Sequencing of the FRAXE region showed no imperfections within the GCC repeat region, such as those commonly seen in FRAXA. The smaller size and limited range of repeats and the lack of imperfections suggests the molecular mechanisms underlying FRAXE triplet mutations may be different from those underlying FRAXA. 27 refs., 4 figs., 1 tab.

  15. Temperature-driven regime shifts in the dynamics of size-structured populations.

    PubMed

    Ohlberger, Jan; Edeline, Eric; Vøllestad, Leif Asbjørn; Stenseth, Nils C; Claessen, David

    2011-02-01

    Global warming impacts virtually all biota and ecosystems. Many of these impacts are mediated through direct effects of temperature on individual vital rates. Yet how this translates from the individual to the population level is still poorly understood, hampering the assessment of global warming impacts on population structure and dynamics. Here, we study the effects of temperature on intraspecific competition and cannibalism and the population dynamical consequences in a size-structured fish population. We use a physiologically structured consumer-resource model in which we explicitly model the temperature dependencies of the consumer vital rates and the resource population growth rate. Our model predicts that increased temperature decreases resource density despite higher resource growth rates, reflecting stronger intraspecific competition among consumers. At a critical temperature, the consumer population dynamics destabilize and shift from a stable equilibrium to competition-driven generation cycles that are dominated by recruits. As a consequence, maximum age decreases and the proportion of younger and smaller-sized fish increases. These model predictions support the hypothesis of decreasing mean body sizes due to increased temperatures. We conclude that in size-structured fish populations, global warming may increase competition, favor smaller size classes, and induce regime shifts that destabilize population and community dynamics.

  16. Spatially-explicit estimation of Wright's neighborhood size in continuous populations

    Treesearch

    Andrew J. Shirk; Samuel A. Cushman

    2014-01-01

    Effective population size (Ne) is an important parameter in conservation genetics because it quantifies a population's capacity to resist loss of genetic diversity due to inbreeding and drift. The classical approach to estimate Ne from genetic data involves grouping sampled individuals into discretely defined subpopulations assumed to be panmictic. Importantly,...

  17. Matrimonial distance, inbreeding coefficient and population size: Dhangar data.

    PubMed

    Majumder, P P; Malhotra, K C

    1979-01-01

    Data on the distance between the birthplaces of spouses (matrimonial distance) were collected from 2,260 married individuals belonging to 21 endogamous castes of the Dhangar (shepherd) cast-cluster of Maharashtra, India. The general form of the distribution of matrimonial distances is one which is extremely positively skewed and leptokurtic. The percentage of intra-village marriages generally decreases from the southern areas of Maharashtra to the northern areas of the state, as does the inbreeding coefficient. This situation is in conformity with the socio-cultural norms regulating matrimonial choice in south and north India. An attempt has been made to relate the degree of inbreeding to the mean matrimonial distance and population size. The mean matrimonial distance is more useful in predicting the degree of inbreeding than population size.

  18. Utility of Microcosm Studies for Predicting Phylloplane Bacterium Population Sizes in the Field

    PubMed Central

    Kinkel, L. L.; Wilson, M.; Lindow, S. E.

    1996-01-01

    Population sizes of two ice nucleation-active strains of Pseudomonas syringae were compared on leaves in controlled environments and in the field to determine the ability of microcosm studies to predict plant habitat preferences in the field. The P. syringae strains investigated were the parental strains of recombinant deletion mutant strains deficient in ice nucleation activity that had been field tested for their ability to control plant frost injury. The population size of the P. syringae strains was measured after inoculation at three field locations on up to 40 of the same plant species that were studied in the growth chamber. There was seldom a significant relationship between the mean population size of a given P. syringae strain incubated under either wet or dry conditions in microcosms and the mean population size which could be recovered from the same species when inoculated in the field. Specifically, on some plant species, the population size recovered from leaves in the field was substantially greater than from that species in a controlled environment, while for other plant species field populations were significantly smaller than those observed under controlled conditions. Population sizes of inoculated P. syringae strains, however, were frequently highly positively correlated with the indigenous bacterial population size on the same plant species in the field, suggesting that the ability of a particular plant species to support introduced bacterial strains is correlated with its ability to support large bacterial populations or that indigenous bacteria enhance the survival of introduced strains. Microcosm studies therefore seem most effective at assessing possible differences between parental and recombinant strains under a given environmental regime but are limited in their ability to predict the specific population sizes or plant habitat preferences of bacteria on leaves under field conditions. PMID:16535405

  19. Founding population size of an aquatic invasive species

    USGS Publications Warehouse

    Kalinowski, Steven T.; Muhlfeld, Clint C.; Guy, Christopher S.; Benjamin Cox,

    2010-01-01

    Non-native species of fish threaten native fishes throughout North America, and in the Rocky Mountains, introduced populations of lake trout threaten native populations of bull trout. Effective management of lake trout and other exotic species require understanding the dynamics of invasion in order to either suppress non-native populations or to prevent their spread. In this study, we used microsatellite genetic data to estimate the number of lake trout that invaded a population of bull trout in Swan Lake, MT. Examination of genetic diversity and allele frequencies within the Swan Lake populations showed that most of the genes in the lake trout population are descended from two founders. This emphasizes the importance of preventing even a few lake trout from colonizing new territory.

  20. Host-parasite coevolution: why changing population size matters.

    PubMed

    Papkou, Andrei; Gokhale, Chaitanya S; Traulsen, Arne; Schulenburg, Hinrich

    2016-08-01

    Host-parasite coevolution is widely assumed to have a major influence on biological evolution, especially as these interactions impose high selective pressure on the reciprocally interacting antagonists. The exact nature of the underlying dynamics is yet under debate and may be determined by recurrent selective sweeps (i.e., arms race dynamics), negative frequency-dependent selection (i.e., Red Queen dynamics), or a combination thereof. These interactions are often associated with reciprocally induced changes in population size, which, in turn, should have a strong impact on co-adaptation processes, yet are neglected in most current work on the topic. Here, we discuss potential consequences of temporal variations in population size on host-parasite coevolution. The limited empirical data available and the current theoretical literature in this field highlight that the consideration of such interaction-dependent population size changes is likely key for the full understanding of the coevolutionary dynamics, and, thus, a more realistic view on the complex nature of species interactions. Copyright © 2016 The Authors. Published by Elsevier GmbH.. All rights reserved.

  1. Determining population size of territorial red-winged blackbirds

    USGS Publications Warehouse

    Albers, P.H.

    1976-01-01

    Population sizes of territorial male red-winged blackbirds (Agelaius phoeniceus) were determined with counts of territorial males (area count) and a Petersen-Lincoln Index method for roadsides (roadside estimate). Weather conditions and time of day did not influence either method. Combined roadside estimates had smaller error bounds than the individual transect estimates and were not hindered by the problem of zero recaptures. Roadside estimates were usually one-half as large as the area counts, presumably due to an observer bias for marked birds. The roadside estimate provides only an index of major changes in populations of territorial male redwings. When the roadside estimate is employed, the area count should be used to determine the amount and nature of observer bias. For small population surveys, the area count is probably more reliable and accurate than the roadside estimate.

  2. A Primer on Basic Effect Size Concepts.

    ERIC Educational Resources Information Center

    Elmore, Patricia B.; Rotou, Ourania

    The increased interest in reporting effect sizes means that it is necessary to consider what should be included in a primer on effect sizes. A review of papers on effect sizes and commonly repeated statistical analyses suggests that it is important to discuss effect sizes relative to bivariate correlation, t-tests, analysis of variance/covariance,…

  3. Antarctic krill population genomics: apparent panmixia, but genome complexity and large population size muddy the water.

    PubMed

    Deagle, Bruce E; Faux, Cassandra; Kawaguchi, So; Meyer, Bettina; Jarman, Simon N

    2015-10-01

    Antarctic krill (Euphausia superba; hereafter krill) are an incredibly abundant pelagic crustacean which has a wide, but patchy, distribution in the Southern Ocean. Several studies have examined the potential for population genetic structuring in krill, but DNA-based analyses have focused on a limited number of markers and have covered only part of their circum-Antarctic range. We used mitochondrial DNA and restriction site-associated DNA sequencing (RAD-seq) to investigate genetic differences between krill from five sites, including two from East Antarctica. Our mtDNA results show no discernible genetic structuring between sites separated by thousands of kilometres, which is consistent with previous studies. Using standard RAD-seq methodology, we obtained over a billion sequences from >140 krill, and thousands of variable nucleotides were identified at hundreds of loci. However, downstream analysis found that markers with sufficient coverage were primarily from multicopy genomic regions. Careful examination of these data highlights the complexity of the RAD-seq approach in organisms with very large genomes. To characterize the multicopy markers, we recorded sequence counts from variable nucleotide sites rather than the derived genotypes; we also examined a small number of manually curated genotypes. Although these analyses effectively fingerprinted individuals, and uncovered a minor laboratory batch effect, no population structuring was observed. Overall, our results are consistent with panmixia of krill throughout their distribution. This result may indicate ongoing gene flow. However, krill's enormous population size creates substantial panmictic inertia, so genetic differentiation may not occur on an ecologically relevant timescale even if demographically separate populations exist. © 2015 John Wiley & Sons Ltd.

  4. Faltering lemming cycles reduce productivity and population size of a migratory Arctic goose species.

    PubMed

    Nolet, Bart A; Bauer, Silke; Feige, Nicole; Kokorev, Yakov I; Popov, Igor Yu; Ebbinge, Barwolt S

    2013-07-01

    The huge changes in population sizes of Arctic-nesting geese offer a great opportunity to study population limitation in migratory animals. In geese, population limitation seems to have shifted from wintering to summering grounds. There, in the Arctic, climate is rapidly changing, and this may impact reproductive performance, and perhaps population size of geese, both directly (e.g. by changes in snow melt) or indirectly (e.g. by changes in trophic interactions). Dark-bellied brent geese (Branta bernicla bernicla L.) increased 20-fold since the 1950s. Its reproduction fluctuates strongly in concert with the 3-year lemming cycle. An earlier analysis, covering the growth period until 1988, did not find evidence for density dependence, but thereafter the population levelled off and even decreased. The question is whether this is caused by changes in lemming cycles, population density or other factors like carry-over effects. Breeding success was derived from proportions of juveniles. We used an information-theoretical approach to investigate which environmental factors best explained the variation in breeding success over nearly 50 years (1960-2008). We subsequently combined GLM predictions of breeding success with published survival estimates to project the population trajectory since 1991 (year of maximum population size). In this way, we separated the effects of lemming abundance and population density on population development. Breeding success was mainly dependent on lemming abundance, the onset of spring at the breeding grounds, and the population size of brent goose. No evidence was found for carry-over effects (i.e. effects of conditions at main spring staging site). Negative density dependence was operating at a population size above c. 200 000 individuals, but the levelling off of the population could be explained by faltering lemming cycles alone. Lemmings have long been known to affect population productivity of Arctic-nesting migratory birds and, more

  5. Faltering lemming cycles reduce productivity and population size of a migratory Arctic goose species

    PubMed Central

    Nolet, Bart A; Bauer, Silke; Feige, Nicole; Kokorev, Yakov I; Popov, Igor Yu; Ebbinge, Barwolt S

    2013-01-01

    1. The huge changes in population sizes of Arctic-nesting geese offer a great opportunity to study population limitation in migratory animals. In geese, population limitation seems to have shifted from wintering to summering grounds. There, in the Arctic, climate is rapidly changing, and this may impact reproductive performance, and perhaps population size of geese, both directly (e.g. by changes in snow melt) or indirectly (e.g. by changes in trophic interactions). 2. Dark-bellied brent geese (Branta bernicla bernicla L.) increased 20-fold since the 1950s. Its reproduction fluctuates strongly in concert with the 3-year lemming cycle. An earlier analysis, covering the growth period until 1988, did not find evidence for density dependence, but thereafter the population levelled off and even decreased. The question is whether this is caused by changes in lemming cycles, population density or other factors like carry-over effects. 3. Breeding success was derived from proportions of juveniles. We used an information-theoretical approach to investigate which environmental factors best explained the variation in breeding success over nearly 50 years (1960–2008). We subsequently combined GLM predictions of breeding success with published survival estimates to project the population trajectory since 1991 (year of maximum population size). In this way, we separated the effects of lemming abundance and population density on population development. 4. Breeding success was mainly dependent on lemming abundance, the onset of spring at the breeding grounds, and the population size of brent goose. No evidence was found for carry-over effects (i.e. effects of conditions at main spring staging site). Negative density dependence was operating at a population size above c. 200 000 individuals, but the levelling off of the population could be explained by faltering lemming cycles alone. 5. Lemmings have long been known to affect population productivity of Arctic-nesting migratory

  6. Size of radial and ulnar artery in local population.

    PubMed

    Ashraf, Tariq; Panhwar, Ziauddin; Habib, Sultana; Memon, Muhammad Anis; Shamsi, Fahad; Arif, Javed

    2010-10-01

    To evaluate radial and ulnar artery diameter in patients undergoing diagnostic coronary angiography. This was a cross-sectional study in which we measured the inner diameter of radial and ulnar artery by using two dimensional ultrasound and Doppler examination in 251 patients visiting our hospital for diagnostic coronary angiography between February to September 2008. The mean diameter of right and left radial artery was 2.3 +/- 0.4 mm and 2.2 +/- 0.4 mm respectively. The mean diameter of right and left ulnar artery was 2.4 +/- 0.4 mm and 2.3 +/- 0.3 mm respectively. The factors found to positively influence the size of radial artery included male sex, diabetes mellitus and smoking. There was no relationship of the size of the radial and ulnar artery with body size parameters (height, weight, Body Surface Area (BSA) & Body Mass Index (BMI). We conclude that ulnar artery diameter is larger than the radial artery in our population. Knowing the size will guide the interventional cardiologist in using appropriate size sheaths and guide catheters. Cardiac surgeons can utilize ulnar artery for bypass grafting when it is deemed unsafe to harvest the radial artery.

  7. Size matters: How population size influences genotype–phenotype association studies in anonymized data

    PubMed Central

    Denny, Joshua C.; Haines, Jonathan L.; Roden, Dan M.; Malin, Bradley A.

    2014-01-01

    Objective Electronic medical records (EMRs) data is increasingly incorporated into genome-phenome association studies. Investigators hope to share data, but there are concerns it may be “re-identified” through the exploitation of various features, such as combinations of standardized clinical codes. Formal anonymization algorithms (e.g., k-anonymization) can prevent such violations, but prior studies suggest that the size of the population available for anonymization may influence the utility of the resulting data. We systematically investigate this issue using a large-scale biorepository and EMR system through which we evaluate the ability of researchers to learn from anonymized data for genome- phenome association studies under various conditions. Methods We use a k-anonymization strategy to simulate a data protection process (on data sets containing clinical codes) for resources of similar size to those found at nine academic medical institutions within the United States. Following the protection process, we replicate an existing genome-phenome association study and compare the discoveries using the protected data and the original data through the correlation (r2) of the p-values of association significance. Results Our investigation shows that anonymizing an entire dataset with respect to the population from which it is derived yields significantly more utility than small study-specific datasets anonymized unto themselves. When evaluated using the correlation of genome-phenome association strengths on anonymized data versus original data, all nine simulated sites, results from largest-scale anonymizations (population ∼ 100;000) retained better utility to those on smaller sizes (population ∼ 6000—75;000). We observed a general trend of increasing r2 for larger data set sizes: r2 = 0.9481 for small-sized datasets, r2 = 0.9493 for moderately-sized datasets, r2 = 0.9934 for large-sized datasets. Conclusions This research implies that regardless of the

  8. Effect of size on cracking of materials

    NASA Technical Reports Server (NTRS)

    Glucklick, J.

    1971-01-01

    Brittle behavior of large mild steel elements, glass plasticity, and fatigue specimen size sensitivity are manifestations of strain-energy size effect. Specimens physical size effect on material cracking initiation occurs according to flaw distribution statistics. Fracture size effect depends on stability or instability of crack propagation.

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

    USGS Publications Warehouse

    Link, W.A.

    2003-01-01

    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.

  10. Reconstructing the Phylogenetic History of Long-Term Effective Population Size and Life-History Traits Using Patterns of Amino Acid Replacement in Mitochondrial Genomes of Mammals and Birds

    PubMed Central

    Nabholz, Benoit; Lartillot, Nicolas

    2013-01-01

    The nearly neutral theory, which proposes that most mutations are deleterious or close to neutral, predicts that the ratio of nonsynonymous over synonymous substitution rates (dN/dS), and potentially also the ratio of radical over conservative amino acid replacement rates (Kr/Kc), are negatively correlated with effective population size. Previous empirical tests, using life-history traits (LHT) such as body-size or generation-time as proxies for population size, have been consistent with these predictions. This suggests that large-scale phylogenetic reconstructions of dN/dS or Kr/Kc might reveal interesting macroevolutionary patterns in the variation in effective population size among lineages. In this work, we further develop an integrative probabilistic framework for phylogenetic covariance analysis introduced previously, so as to estimate the correlation patterns between dN/dS, Kr/Kc, and three LHT, in mitochondrial genomes of birds and mammals. Kr/Kc displays stronger and more stable correlations with LHT than does dN/dS, which we interpret as a greater robustness of Kr/Kc, compared with dN/dS, the latter being confounded by the high saturation of the synonymous substitution rate in mitochondrial genomes. The correlation of Kr/Kc with LHT was robust when controlling for the potentially confounding effects of nucleotide compositional variation between taxa. The positive correlation of the mitochondrial Kr/Kc with LHT is compatible with previous reports, and with a nearly neutral interpretation, although alternative explanations are also possible. The Kr/Kc model was finally used for reconstructing life-history evolution in birds and mammals. This analysis suggests a fairly large-bodied ancestor in both groups. In birds, life-history evolution seems to have occurred mainly through size reduction in Neoavian birds, whereas in placental mammals, body mass evolution shows disparate trends across subclades. Altogether, our work represents a further step toward a more

  11. Reconstructing the phylogenetic history of long-term effective population size and life-history traits using patterns of amino acid replacement in mitochondrial genomes of mammals and birds.

    PubMed

    Nabholz, Benoit; Uwimana, Nicole; Lartillot, Nicolas

    2013-01-01

    The nearly neutral theory, which proposes that most mutations are deleterious or close to neutral, predicts that the ratio of nonsynonymous over synonymous substitution rates (dN/dS), and potentially also the ratio of radical over conservative amino acid replacement rates (Kr/Kc), are negatively correlated with effective population size. Previous empirical tests, using life-history traits (LHT) such as body-size or generation-time as proxies for population size, have been consistent with these predictions. This suggests that large-scale phylogenetic reconstructions of dN/dS or Kr/Kc might reveal interesting macroevolutionary patterns in the variation in effective population size among lineages. In this work, we further develop an integrative probabilistic framework for phylogenetic covariance analysis introduced previously, so as to estimate the correlation patterns between dN/dS, Kr/Kc, and three LHT, in mitochondrial genomes of birds and mammals. Kr/Kc displays stronger and more stable correlations with LHT than does dN/dS, which we interpret as a greater robustness of Kr/Kc, compared with dN/dS, the latter being confounded by the high saturation of the synonymous substitution rate in mitochondrial genomes. The correlation of Kr/Kc with LHT was robust when controlling for the potentially confounding effects of nucleotide compositional variation between taxa. The positive correlation of the mitochondrial Kr/Kc with LHT is compatible with previous reports, and with a nearly neutral interpretation, although alternative explanations are also possible. The Kr/Kc model was finally used for reconstructing life-history evolution in birds and mammals. This analysis suggests a fairly large-bodied ancestor in both groups. In birds, life-history evolution seems to have occurred mainly through size reduction in Neoavian birds, whereas in placental mammals, body mass evolution shows disparate trends across subclades. Altogether, our work represents a further step toward a more

  12. Increased Selection Response in Larger Populations. I. Selection for Wing-Tip Height in Drosophila Melanogaster at Three Population Sizes

    PubMed Central

    Weber, K. E.

    1990-01-01

    The effect of population size on selection response was investigated with replicated selection lines of 40, 200 and 1000 selected parents, using Drosophila melanogaster homozygous for the mutant raised. Selection for increased wing-tip height was carried out for 55 generations, with an average selection intensity of 0.6 standard deviation. The rank order of responses in the seven individual lines was significantly in order of population size, and the variance of response among lines showed a significant effect of population size. The final mean responses (selected - controls, +/- standard errors) in the three treatments, in order of increasing population size, were 8.6 +/- 1.8 mils (three small lines), 15.1 +/- 1.3 mils (two medium lines), and 19.8 +/- 1.5 mils (two large lines). The differences between treatments seem to have emerged too rapidly to be the result of mutations, and are probably due mainly to the utilization of existing variation with greater efficiency by selection in larger populations. PMID:2116358

  13. Interpreting surveys to estimate the size of the monarch butterfly population: Pitfalls and prospects

    USGS Publications Warehouse

    Pleasants, John M.; Zalucki, Myron P.; Oberhauser, Karen S.; Brower, Lincoln P.; Taylor, Orley R.; Thogmartin, Wayne E.

    2017-01-01

    To assess the change in the size of the eastern North American monarch butterfly summer population, studies have used long-term data sets of counts of adult butterflies or eggs per milkweed stem. Despite the observed decline in the monarch population as measured at overwintering sites in Mexico, these studies found no decline in summer counts in the Midwest, the core of the summer breeding range, leading to a suggestion that the cause of the monarch population decline is not the loss of Midwest agricultural milkweeds but increased mortality during the fall migration. Using these counts to estimate population size, however, does not account for the shift of monarch activity from agricultural fields to non-agricultural sites over the past 20 years, as a result of the loss of agricultural milkweeds due to the near-ubiquitous use of glyphosate herbicides. We present the counter-hypotheses that the proportion of the monarch population present in non-agricultural habitats, where counts are made, has increased and that counts reflect both population size and the proportion of the population observed. We use data on the historical change in the proportion of milkweeds, and thus monarch activity, in agricultural fields and non-agricultural habitats to show why using counts can produce misleading conclusions about population size. We then separate out the shifting proportion effect from the counts to estimate the population size and show that these corrected summer monarch counts show a decline over time and are correlated with the size of the overwintering population. In addition, we present evidence against the hypothesis of increased mortality during migration. The milkweed limitation hypothesis for monarch decline remains supported and conservation efforts focusing on adding milkweeds to the landscape in the summer breeding region have a sound scientific basis.

  14. Interpreting surveys to estimate the size of the monarch butterfly population: Pitfalls and prospects

    PubMed Central

    Zalucki, Myron P.; Oberhauser, Karen S.; Brower, Lincoln P.; Taylor, Orley R.; Thogmartin, Wayne E.

    2017-01-01

    To assess the change in the size of the eastern North American monarch butterfly summer population, studies have used long-term data sets of counts of adult butterflies or eggs per milkweed stem. Despite the observed decline in the monarch population as measured at overwintering sites in Mexico, these studies found no decline in summer counts in the Midwest, the core of the summer breeding range, leading to a suggestion that the cause of the monarch population decline is not the loss of Midwest agricultural milkweeds but increased mortality during the fall migration. Using these counts to estimate population size, however, does not account for the shift of monarch activity from agricultural fields to non-agricultural sites over the past 20 years, as a result of the loss of agricultural milkweeds due to the near-ubiquitous use of glyphosate herbicides. We present the counter-hypotheses that the proportion of the monarch population present in non-agricultural habitats, where counts are made, has increased and that counts reflect both population size and the proportion of the population observed. We use data on the historical change in the proportion of milkweeds, and thus monarch activity, in agricultural fields and non-agricultural habitats to show why using counts can produce misleading conclusions about population size. We then separate out the shifting proportion effect from the counts to estimate the population size and show that these corrected summer monarch counts show a decline over time and are correlated with the size of the overwintering population. In addition, we present evidence against the hypothesis of increased mortality during migration. The milkweed limitation hypothesis for monarch decline remains supported and conservation efforts focusing on adding milkweeds to the landscape in the summer breeding region have a sound scientific basis. PMID:28708851

  15. Interpreting surveys to estimate the size of the monarch butterfly population: Pitfalls and prospects.

    PubMed

    Pleasants, John M; Zalucki, Myron P; Oberhauser, Karen S; Brower, Lincoln P; Taylor, Orley R; Thogmartin, Wayne E

    2017-01-01

    To assess the change in the size of the eastern North American monarch butterfly summer population, studies have used long-term data sets of counts of adult butterflies or eggs per milkweed stem. Despite the observed decline in the monarch population as measured at overwintering sites in Mexico, these studies found no decline in summer counts in the Midwest, the core of the summer breeding range, leading to a suggestion that the cause of the monarch population decline is not the loss of Midwest agricultural milkweeds but increased mortality during the fall migration. Using these counts to estimate population size, however, does not account for the shift of monarch activity from agricultural fields to non-agricultural sites over the past 20 years, as a result of the loss of agricultural milkweeds due to the near-ubiquitous use of glyphosate herbicides. We present the counter-hypotheses that the proportion of the monarch population present in non-agricultural habitats, where counts are made, has increased and that counts reflect both population size and the proportion of the population observed. We use data on the historical change in the proportion of milkweeds, and thus monarch activity, in agricultural fields and non-agricultural habitats to show why using counts can produce misleading conclusions about population size. We then separate out the shifting proportion effect from the counts to estimate the population size and show that these corrected summer monarch counts show a decline over time and are correlated with the size of the overwintering population. In addition, we present evidence against the hypothesis of increased mortality during migration. The milkweed limitation hypothesis for monarch decline remains supported and conservation efforts focusing on adding milkweeds to the landscape in the summer breeding region have a sound scientific basis.

  16. Population size does not explain past changes in cultural complexity

    PubMed Central

    Vaesen, Krist; Collard, Mark; Cosgrove, Richard; Roebroeks, Wil

    2016-01-01

    Demography is increasingly being invoked to account for features of the archaeological record, such as the technological conservatism of the Lower and Middle Pleistocene, the Middle to Upper Paleolithic transition, and cultural loss in Holocene Tasmania. Such explanations are commonly justified in relation to population dynamic models developed by Henrich [Henrich J (2004) Am Antiq 69:197–214] and Powell et al. [Powell A, et al. (2009) Science 324(5932):1298–1301], which appear to demonstrate that population size is the crucial determinant of cultural complexity. Here, we show that these models fail in two important respects. First, they only support a relationship between demography and culture in implausible conditions. Second, their predictions conflict with the available archaeological and ethnographic evidence. We conclude that new theoretical and empirical research is required to identify the factors that drove the changes in cultural complexity that are documented by the archaeological record. PMID:27044082

  17. Population reference range for developmental lumbar spinal canal size

    PubMed Central

    Huang, Junbin; Law, Sheung-Wai; Xiao, Fan; Leung, Jason Chi Shun; Wang, Defeng; Shi, Lin

    2016-01-01

    Background Considerable variability exists in normal developmental lumbar spinal canal size. This impacts the likelihood of neural compromise. Spinal canal development is complete by 17 years. As diseases incurred thereafter do not knowingly affect the developmental size of the spinal canal, it is reasonable to use a selected population undergoing abdominopelvic computed tomography (CT) examination to determine developmental lumbar spinal canal size. Methods Study approval was granted by the Clinical Research Ethics Committee. Between Feb 2014 and Jan 2015, mid-vertebral spinal canal cross-sectional area (CSA), depth, width, and vertebral body CSA at each level from L1–L5 was measured, using a semi-automated computerized method in 1,080 ambulatory patients (540 males, 540 females, mean age, 50.5±17 years). Patient height and weight was measured. Results A reference range for developmental lumbar spinal canal dimensions was developed at each lumbar level for each sex. There was a 34% variation in spinal canal CSA between smallest and largest quartiles. Developmental spinal canal CSA and depth were consistently smallest at L3, enlarging cranially and caudally. Taller people had slightly larger lumbar spinal canals (P<0.0001). Males had larger spinal canal CSAs than females though relative to vertebral body CSA, spinal canal CSA was larger in females. There was no change in spinal canal CSA with age, weight or BMI (P<0.05). Conclusions A population reference range for developmental lumbar spinal canal size was developed. This allows one to objectively determine the degree of developmental spinal canal stenosis present on an individual patient basis. PMID:28090445

  18. When bigger is not better: intraspecific competition for pollination increases with population size in invasive milkweeds.

    PubMed

    Ward, Megan; Johnson, Steven D; Zalucki, Myron P

    2013-04-01

    One of the essential requirements for an introduced plant species to become invasive is an ability to reproduce outside the native range, particularly when initial populations are small. If a reproductive Allee effect is operating, plants in small populations will have reduced reproductive success relative to plants in larger populations. Alternatively, if plants in small populations experience less competition for pollination than those in large populations, they may actually have higher levels of reproductive success than plants in large populations. To resolve this uncertainty, we investigated how the per capita fecundity of plants was affected by population size in three invasive milkweed species. Field surveys of seed production in natural populations of different sizes but similar densities were conducted for three pollinator-dependent invasive species, namely Asclepias curassavica, Gomphocarpus fruticosus and G. physocarpus. Additionally, supplemental hand-pollinations were performed in small and large populations in order to determine whether reproductive output was limited by pollinator activity in these populations. Reproductive Allee effects were not detected in any of the study species. Instead, plants in small populations exhibited remarkably high levels of reproductive output compared to those in large populations. Increased fruit production following supplemental hand-pollinations suggested that the lower reproductive output of naturally pollinated plants in large populations is a consequence of pollen limitation rather than limitation due to abiotic resources. This is consistent with increased intraspecific competition for pollination amongst plants in large populations. It is likely that the invasion of these milkweed species in Australia has been enhanced because plants in small founding populations experience less intraspecific competition for pollinators than those in large populations, and thus have the ability to produce copious amounts of

  19. Class-Size Effects in Secondary School

    ERIC Educational Resources Information Center

    Krassel, Karl Fritjof; Heinesen, Eskil

    2014-01-01

    We analyze class-size effects on academic achievement in secondary school in Denmark exploiting an institutional setting where pupils cannot predict class size prior to enrollment, and where post-enrollment responses aimed at affecting realized class size are unlikely. We identify class-size effects combining a regression discontinuity design with…

  20. Class-Size Effects in Secondary School

    ERIC Educational Resources Information Center

    Krassel, Karl Fritjof; Heinesen, Eskil

    2014-01-01

    We analyze class-size effects on academic achievement in secondary school in Denmark exploiting an institutional setting where pupils cannot predict class size prior to enrollment, and where post-enrollment responses aimed at affecting realized class size are unlikely. We identify class-size effects combining a regression discontinuity design with…

  1. Cohort Size and Migration in a West Indian Population.

    ERIC Educational Resources Information Center

    Brittain, Ann W.

    1990-01-01

    Data from St. Barthelemy (French West Indies) show that, for people born from 1878 to 1967, neither cohort size nor fluctuations in external demands for labor had a lasting effect on the probability of eventual migration. Emigration slowed only after development of local tourism brought prosperity to the island. (AF)

  2. Cohort Size and Migration in a West Indian Population.

    ERIC Educational Resources Information Center

    Brittain, Ann W.

    1990-01-01

    Data from St. Barthelemy (French West Indies) show that, for people born from 1878 to 1967, neither cohort size nor fluctuations in external demands for labor had a lasting effect on the probability of eventual migration. Emigration slowed only after development of local tourism brought prosperity to the island. (AF)

  3. Towards a theory of cortical columns: From spiking neurons to interacting neural populations of finite size

    PubMed Central

    Gerstner, Wulfram

    2017-01-01

    Neural population equations such as neural mass or field models are widely used to study brain activity on a large scale. However, the relation of these models to the properties of single neurons is unclear. Here we derive an equation for several interacting populations at the mesoscopic scale starting from a microscopic model of randomly connected generalized integrate-and-fire neuron models. Each population consists of 50–2000 neurons of the same type but different populations account for different neuron types. The stochastic population equations that we find reveal how spike-history effects in single-neuron dynamics such as refractoriness and adaptation interact with finite-size fluctuations on the population level. Efficient integration of the stochastic mesoscopic equations reproduces the statistical behavior of the population activities obtained from microscopic simulations of a full spiking neural network model. The theory describes nonlinear emergent dynamics such as finite-size-induced stochastic transitions in multistable networks and synchronization in balanced networks of excitatory and inhibitory neurons. The mesoscopic equations are employed to rapidly integrate a model of a cortical microcircuit consisting of eight neuron types, which allows us to predict spontaneous population activities as well as evoked responses to thalamic input. Our theory establishes a general framework for modeling finite-size neural population dynamics based on single cell and synapse parameters and offers an efficient approach to analyzing cortical circuits and computations. PMID:28422957

  4. Towards a theory of cortical columns: From spiking neurons to interacting neural populations of finite size.

    PubMed

    Schwalger, Tilo; Deger, Moritz; Gerstner, Wulfram

    2017-04-01

    Neural population equations such as neural mass or field models are widely used to study brain activity on a large scale. However, the relation of these models to the properties of single neurons is unclear. Here we derive an equation for several interacting populations at the mesoscopic scale starting from a microscopic model of randomly connected generalized integrate-and-fire neuron models. Each population consists of 50-2000 neurons of the same type but different populations account for different neuron types. The stochastic population equations that we find reveal how spike-history effects in single-neuron dynamics such as refractoriness and adaptation interact with finite-size fluctuations on the population level. Efficient integration of the stochastic mesoscopic equations reproduces the statistical behavior of the population activities obtained from microscopic simulations of a full spiking neural network model. The theory describes nonlinear emergent dynamics such as finite-size-induced stochastic transitions in multistable networks and synchronization in balanced networks of excitatory and inhibitory neurons. The mesoscopic equations are employed to rapidly integrate a model of a cortical microcircuit consisting of eight neuron types, which allows us to predict spontaneous population activities as well as evoked responses to thalamic input. Our theory establishes a general framework for modeling finite-size neural population dynamics based on single cell and synapse parameters and offers an efficient approach to analyzing cortical circuits and computations.

  5. Geographical variation of skull size and shape in various populations in the black giant squirrel.

    PubMed

    Endo, Hideki; Kimura, Junpei; Oshida, Tatsuo; Stafford, Brian J; Rerkamnuaychoke, Worawut; Nishida, Takao; Sasaki, Motoki; Hayashida, Akiko; Hayashi, Yoshihiro

    2004-10-01

    We osteometrically examined the skulls of the black giant squirrel (Ratufa bicolor) from three mainland populations (M. Malayan Peninsula, V. South Vietnam, and B. Burma, India and North Thailand) and from two island populations (T. Tioman, and S. Sumatra Islands). The skull in the Malayan peninsula population was significantly smaller than that of the two other mainland populations. It is consistent with Bergmann's rule as shown in the gray-bellied squirrel. The two island populations did not show obvious differences in comparison with the Malayan population in many measurements. In the proportion analysis eliminating the size factor, the differences among populations were not easily confirmed and we concluded that the osteological characters peculiar to each population could not be shown in this species. The first and second principal component scores of M, S, and T populations were intermingled, whereas the V and B populations of V and B were not separated in the chart. We pointed out that the morphological differences were demonstrated between northern and southern groups of the Isthmus of Kra in the mainland populations, and that the two island populations did not show the island-isolation effect in comparison with the M population. The adaptational variation related to feeding and locomotion could not be confirmed among populations of the black giant squirrel as shown in the proportion analysis.

  6. Demographic population model for American shad: will access to additional habitat upstream of dams increase population sizes?

    USGS Publications Warehouse

    Harris, Julianne E.; Hightower, Joseph E.

    2012-01-01

    American shad Alosa sapidissima are in decline in their native range, and modeling possible management scenarios could help guide their restoration. We developed a density-dependent, deterministic, stage-based matrix model to predict the population-level results of transporting American shad to suitable spawning habitat upstream of dams on the Roanoke River, North Carolina and Virginia. We used data on sonic-tagged adult American shad and oxytetracycline-marked American shad fry both above and below dams on the Roanoke River with information from other systems to estimate a starting population size and vital rates. We modeled the adult female population over 30 years under plausible scenarios of adult transport, effective fecundity (egg production), and survival of adults (i.e., to return to spawn the next year) and juveniles (from spawned egg to age 1). We also evaluated the potential effects of increased survival for adults and juveniles. The adult female population size in the Roanoke River was estimated to be 5,224. With no transport, the model predicted a slow population increase over the next 30 years. Predicted population increases were highest when survival was improved during the first year of life. Transport was predicted to benefit the population only if high rates of effective fecundity and juvenile survival could be achieved. Currently, transported adults and young are less likely to successfully out-migrate than individuals below the dams, and the estimated adult population size is much smaller than either of two assumed values of carrying capacity for the lower river; therefore, transport is not predicted to help restore the stock under present conditions. Research on survival rates, density-dependent processes, and the impacts of structures to increase out-migration success would improve evaluation of the potential benefits of access to additional spawning habitat for American shad.

  7. Influence of habitat quality, population size, patch size, and connectivity on patch-occupancy dynamics of the middle spotted woodpecker.

    PubMed

    Robles, Hugo; Ciudad, Carlos

    2012-04-01

    Despite extensive research on the effects of habitat fragmentation, the ecological mechanisms underlying colonization and extinction processes are poorly known, but knowledge of these mechanisms is essential to understanding the distribution and persistence of populations in fragmented habitats. We examined these mechanisms through multiseason occupancy models that elucidated patch-occupancy dynamics of Middle Spotted Woodpeckers (Dendrocopos medius) in northwestern Spain. The number of occupied patches was relatively stable from 2000 to 2010 (15-24% of 101 patches occupied every year) because extinction was balanced by recolonization. Larger and higher quality patches (i.e., higher density of oaks >37 cm dbh [diameter at breast height]) were more likely to be occupied. Habitat quality (i.e., density of large oaks) explained more variation in patch colonization and extinction than did patch size and connectivity, which were both weakly associated with probabilities of turnover. Patches of higher quality were more likely to be colonized than patches of lower quality. Populations in high-quality patches were less likely to become extinct. In addition, extinction in a patch was strongly associated with local population size but not with patch size, which means the latter may not be a good surrogate of population size in assessments of extinction probability. Our results suggest that habitat quality may be a primary driver of patch-occupancy dynamics and may increase the accuracy of models of population survival. We encourage comparisons of competing models that assess occupancy, colonization, and extinction probabilities in a single analytical framework (e.g., dynamic occupancy models) so as to shed light on the association of habitat quality and patch geometry with colonization and extinction processes in different settings and species.

  8. Population size and cultural evolution in nonindustrial food-producing societies.

    PubMed

    Collard, Mark; Ruttle, April; Buchanan, Briggs; O'Brien, Michael J

    2013-01-01

    Modeling work suggests that population size affects cultural evolution such that larger populations can be expected to have richer and more complex cultural repertoires than smaller populations. Empirical tests of this hypothesis, however, have yielded conflicting results. Here, we report a study in which we investigated whether the subsistence toolkits of small-scale food-producers are influenced by population size in the manner the hypothesis predicts. We applied simple linear and standard multiple regression analysis to data from 40 nonindustrial farming and pastoralist groups to test the hypothesis. Results were consistent with predictions of the hypothesis: both the richness and the complexity of the toolkits of the food-producers were positively and significantly influenced by population size in the simple linear regression analyses. The multiple regression analyses demonstrated that these relationships are independent of the effects of risk of resource failure, which is the other main factor that has been found to influence toolkit richness and complexity in nonindustrial groups. Thus, our study strongly suggests that population size influences cultural evolution in nonindustrial food-producing populations.

  9. Cavitation erosion size scale effects

    NASA Technical Reports Server (NTRS)

    Rao, P. V.; Buckley, D. H.

    1984-01-01

    Size scaling in cavitation erosion is a major problem confronting the design engineers of modern high speed machinery. An overview and erosion data analysis presented in this paper indicate that the size scale exponent n in the erosion rate relationship as a function of the size or diameter can vary from 1.7 to 4.9 depending on the type of device used. There is, however, a general agreement as to the values of n if the correlations are made with constant cavitation number.

  10. Causality in Statistical Power: Isomorphic Properties of Measurement, Research Design, Effect Size, and Sample Size

    PubMed Central

    Heidel, R. Eric

    2016-01-01

    Statistical power is the ability to detect a significant effect, given that the effect actually exists in a population. Like most statistical concepts, statistical power tends to induce cognitive dissonance in hepatology researchers. However, planning for statistical power by an a priori sample size calculation is of paramount importance when designing a research study. There are five specific empirical components that make up an a priori sample size calculation: the scale of measurement of the outcome, the research design, the magnitude of the effect size, the variance of the effect size, and the sample size. A framework grounded in the phenomenon of isomorphism, or interdependencies amongst different constructs with similar forms, will be presented to understand the isomorphic effects of decisions made on each of the five aforementioned components of statistical power. PMID:27073717

  11. Causality in Statistical Power: Isomorphic Properties of Measurement, Research Design, Effect Size, and Sample Size.

    PubMed

    Heidel, R Eric

    2016-01-01

    Statistical power is the ability to detect a significant effect, given that the effect actually exists in a population. Like most statistical concepts, statistical power tends to induce cognitive dissonance in hepatology researchers. However, planning for statistical power by an a priori sample size calculation is of paramount importance when designing a research study. There are five specific empirical components that make up an a priori sample size calculation: the scale of measurement of the outcome, the research design, the magnitude of the effect size, the variance of the effect size, and the sample size. A framework grounded in the phenomenon of isomorphism, or interdependencies amongst different constructs with similar forms, will be presented to understand the isomorphic effects of decisions made on each of the five aforementioned components of statistical power.

  12. Effect Sizes in Gifted Education Research

    ERIC Educational Resources Information Center

    Gentry, Marcia; Peters, Scott J.

    2009-01-01

    Recent calls for reporting and interpreting effect sizes have been numerous, with the 5th edition of the "Publication Manual of the American Psychological Association" (2001) calling for the inclusion of effect sizes to interpret quantitative findings. Many top journals have required that effect sizes accompany claims of statistical significance.…

  13. Effect Sizes in Gifted Education Research

    ERIC Educational Resources Information Center

    Gentry, Marcia; Peters, Scott J.

    2009-01-01

    Recent calls for reporting and interpreting effect sizes have been numerous, with the 5th edition of the "Publication Manual of the American Psychological Association" (2001) calling for the inclusion of effect sizes to interpret quantitative findings. Many top journals have required that effect sizes accompany claims of statistical significance.…

  14. Population size and winter distribution of eastern American oystercatchers

    USGS Publications Warehouse

    Brown, S.C.; Schulte, Shiloh A.; Harrington, B.; Winn, Brad; Bart, J.; Howe, M.

    2005-01-01

    Conservation of the eastern subspecies of the American oystercatcher (Haematopus palliatus palliatus) is a high priority in the U.S. Shorebird Conservation Plan, but previous population estimates were unreliable, information on distribution and habitat associations during winter was incomplete, and methods for long-term monitoring had not been developed prior to this survey. We completed the aerial survey proposed in the U.S. Shorebird Conservation Plan to determine population size, winter distribution, and habitat associations. We conducted coastal aerial surveys from New Jersey to Texas during November 2002 to February 2003. This area comprised the entire wintering range of the eastern American oystercatcher within the United States. Surveys covered all suitable habitat in the United States for the subspecies, partitioned into 3 survey strata: known roost sites, high-use habitat, and inter-coastal tidal habitat. We determined known roost sites from extensive consultation with biologists and local experts in each state. High-use habitat included sand islands, sand spits at inlets, shell rakes, and oyster reefs. Partner organizations conducted ground counts in most states. We used high resolution still photography to determine detection rates for estimates of the number of birds in particular flocks, and we used ground counts to determine detection rates of flocks. Using a combination of ground and aerial counts, we estimated the population of eastern American oystercatchers to be 10,971 +/- 298. Aerial surveys can serve an important management function for shorebirds and possibly other coastal waterbirds by providing population status and trend information across a wide geographic scale.

  15. When phenology matters: age-size truncation alters population response to trophic mismatch.

    PubMed

    Ohlberger, Jan; Thackeray, Stephen J; Winfield, Ian J; Maberly, Stephen C; Vøllestad, L Asbjørn

    2014-10-22

    Climate-induced shifts in the timing of life-history events are a worldwide phenomenon, and these shifts can de-synchronize species interactions such as predator-prey relationships. In order to understand the ecological implications of altered seasonality, we need to consider how shifts in phenology interact with other agents of environmental change such as exploitation and disease spread, which commonly act to erode the demographic structure of wild populations. Using long-term observational data on the phenology and dynamics of a model predator-prey system (fish and zooplankton in Windermere, UK), we show that age-size truncation of the predator population alters the consequences of phenological mismatch for offspring survival and population abundance. Specifically, age-size truncation reduces intraspecific density regulation due to competition and cannibalism, and thereby amplifies the population sensitivity to climate-induced predator-prey asynchrony, which increases variability in predator abundance. High population variability poses major ecological and economic challenges as it can diminish sustainable harvest rates and increase the risk of population collapse. Our results stress the importance of maintaining within-population age-size diversity in order to buffer populations against phenological asynchrony, and highlight the need to consider interactive effects of environmental impacts if we are to understand and project complex ecological outcomes.

  16. THE MASSIVE SATELLITE POPULATION OF MILKY-WAY-SIZED GALAXIES

    SciTech Connect

    Rodriguez-Puebla, Aldo; Avila-Reese, Vladimir; Drory, Niv

    2013-08-20

    subhalos should agree with the abundance of massive satellites in all MW-sized hosts, i.e., there is not a missing (massive) satellite problem for the {Lambda}CDM cosmology. However, we confirm that the maximum circular velocity, v{sub max}, of the subhalos of satellites smaller than m{sub *} {approx} 10{sup 8} M{sub Sun} is systematically larger than the v{sub max} inferred from current observational studies of the MW bright dwarf satellites; different from previous works, this conclusion is based on an analysis of the overall population of MW-sized galaxies. Some pieces of evidence suggest that the issue could refer only to satellite dwarfs but not to central dwarfs, then environmental processes associated with dwarfs inside host halos combined with supernova-driven core expansion should be on the basis of the lowering of v{sub max}.

  17. The Massive Satellite Population of Milky-Way-sized Galaxies

    NASA Astrophysics Data System (ADS)

    Rodríguez-Puebla, Aldo; Avila-Reese, Vladimir; Drory, Niv

    2013-08-01

    CDM cosmology. However, we confirm that the maximum circular velocity, v max, of the subhalos of satellites smaller than m * ~ 108 M ⊙ is systematically larger than the v max inferred from current observational studies of the MW bright dwarf satellites; different from previous works, this conclusion is based on an analysis of the overall population of MW-sized galaxies. Some pieces of evidence suggest that the issue could refer only to satellite dwarfs but not to central dwarfs, then environmental processes associated with dwarfs inside host halos combined with supernova-driven core expansion should be on the basis of the lowering of v max.

  18. Dynamics of stochastic SEIS epidemic model with varying population size

    NASA Astrophysics Data System (ADS)

    Liu, Jiamin; Wei, Fengying

    2016-12-01

    We introduce the stochasticity into a deterministic model which has state variables susceptible-exposed-infected with varying population size in this paper. The infected individuals could return into susceptible compartment after recovering. We show that the stochastic model possesses a unique global solution under building up a suitable Lyapunov function and using generalized Itô's formula. The densities of the exposed and infected tend to extinction when some conditions are being valid. Moreover, the conditions of persistence to a global solution are derived when the parameters are subject to some simple criteria. The stochastic model admits a stationary distribution around the endemic equilibrium, which means that the disease will prevail. To check the validity of the main results, numerical simulations are demonstrated as end of this contribution.

  19. Natural selection on body size is mediated by multiple interacting factors: a comparison of beetle populations varying naturally and experimentally in body size