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Sample records for effective population sizes

  1. 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.

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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.

  8. 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.

  9. 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

  10. 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

  11. 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.

  12. 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.

  13. 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.

  14. 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

  15. 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.

  16. 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.

  17. 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

  18. 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.

  19. 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.

  20. 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.

  1. 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

  2. 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

  3. 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

  4. 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.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  6. 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

  7. 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

  8. 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.

  9. 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

  10. 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

  11. 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.

  12. 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.

  13. 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

  14. 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

  15. 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.

  16. 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

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  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. 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.

  5. 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

  6. 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.

  7. 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.

  8. 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

  9. 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

  10. 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.

  11. 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

  12. 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

  13. 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.

  14. 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

  15. 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

  16. 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.

  17. 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

  18. 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

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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

  4. 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

  5. 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

  6. 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.

  7. 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.

  8. 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.

  9. 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

  10. 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

  11. 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.

  12. 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

  13. 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.

  14. 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

  15. 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

  16. 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.

  17. 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.

  18. 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

  19. 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.

  20. 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

  1. 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

  2. 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

  3. 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.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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

  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

    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.

  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. 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.

  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. 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

  16. 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.

  17. 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.

  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. 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.

  20. 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.

  1. 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

  2. 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

  3. 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

    2017-01-30

    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.

  4. 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.

  5. 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

  6. 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.

  7. 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

  8. 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

  9. 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.

  10. 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

  11. 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.

  12. 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.

  13. 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

  14. 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.

  15. 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

  16. 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.

  17. 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

  18. 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

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  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 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.

  8. 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.

  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. 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.

  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. 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.

  14. 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.

  15. 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

  16. 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

  17. 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.

  18. 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

  19. 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.

  20. 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.

  1. 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.

  2. 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

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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

  11. 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.

  12. 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.

  13. 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

  14. 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.

  15. 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.

  16. 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

  17. 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.

  18. 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.

  19. 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''.

  20. 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…

  1. 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,…

  2. 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

  3. 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

  4. 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

  5. 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.

  6. 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)

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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

  13. 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

  14. 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

  15. 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.

  16. 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.

  17. 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

  18. 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. ?? 2009 by The American Ornithologists' Union. All rights reserved.

  19. 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

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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

  8. 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.

  9. 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.

  10. 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.

  11. 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...

  12. 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

  13. 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

  14. 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

  15. 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.

  16. 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

  17. 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.

  18. 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.

  19. 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

  20. 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.

  1. 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

  2. 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.

  3. 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.

  4. 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...

  5. 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...

  6. 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...

  7. 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...

  8. 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...

  9. 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.

  10. 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…

  11. 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

  12. 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.

  13. 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…

  14. 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

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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

  4. 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…

  5. 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.

  6. 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

  7. 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.

  8. 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

  9. 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

  10. 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.

  11. 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.

  12. 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

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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

  18. 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

  19. 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

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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

  10. 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

  11. 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.

  12. 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.

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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.

  20. 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)

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. Host Plant Determines the Population Size of an Obligate Symbiont (Buchnera aphidicola) in Aphids

    PubMed Central

    Zhang, Yuan-Chen; Cao, Wen-Jie; Zhong, Le-Rong; Godfray, H. Charles J.

    2016-01-01

    Buchnera aphidicola is an obligate endosymbiont that provides aphids with several essential nutrients. Though much is known about aphid-Buchnera interactions, the effect of the host plant on Buchnera population size remains unclear. Here we used quantitative PCR (qPCR) techniques to explore the effects of the host plant on Buchnera densities in the cotton-melon aphid, Aphis gossypii. Buchnera titers were significantly higher in populations that had been reared on cucumber for over 10 years than in populations maintained on cotton for a similar length of time. Aphids collected in the wild from hibiscus and zucchini harbored more Buchnera symbionts than those collected from cucumber and cotton. The effect of aphid genotype on the population size of Buchnera depended on the host plant upon which they fed. When aphids from populations maintained on cucumber or cotton were transferred to novel host plants, host survival and Buchnera population size fluctuated markedly for the first two generations before becoming relatively stable in the third and later generations. Host plant extracts from cucumber, pumpkin, zucchini, and cowpea added to artificial diets led to a significant increase in Buchnera titers in the aphids from the population reared on cotton, while plant extracts from cotton and zucchini led to a decrease in Buchnera titers in the aphids reared on cucumber. Gossypol, a secondary metabolite from cotton, suppressed Buchnera populations in populations from both cotton and cucumber, while cucurbitacin from cucurbit plants led to higher densities. Together, the results suggest that host plants influence Buchnera population processes and that this may provide phenotypic plasticity in host plant use for clonal aphids. PMID:26850304

  7. Host Plant Determines the Population Size of an Obligate Symbiont (Buchnera aphidicola) in Aphids.

    PubMed

    Zhang, Yuan-Chen; Cao, Wen-Jie; Zhong, Le-Rong; Godfray, H Charles J; Liu, Xiang-Dong

    2016-04-01

    Buchnera aphidicolais an obligate endosymbiont that provides aphids with several essential nutrients. Though much is known about aphid-Buchnera interactions, the effect of the host plant on Buchnera population size remains unclear. Here we used quantitative PCR (qPCR) techniques to explore the effects of the host plant on Buchnera densities in the cotton-melon aphid, Aphis gossypii Buchneratiters were significantly higher in populations that had been reared on cucumber for over 10 years than in populations maintained on cotton for a similar length of time. Aphids collected in the wild from hibiscus and zucchini harbored more Buchnera symbionts than those collected from cucumber and cotton. The effect of aphid genotype on the population size of Buchnera depended on the host plant upon which they fed. When aphids from populations maintained on cucumber or cotton were transferred to novel host plants, host survival and Buchnera population size fluctuated markedly for the first two generations before becoming relatively stable in the third and later generations. Host plant extracts from cucumber, pumpkin, zucchini, and cowpea added to artificial diets led to a significant increase in Buchnera titers in the aphids from the population reared on cotton, while plant extracts from cotton and zucchini led to a decrease in Buchnera titers in the aphids reared on cucumber. Gossypol, a secondary metabolite from cotton, suppressed Buchnera populations in populations from both cotton and cucumber, while cucurbitacin from cucurbit plants led to higher densities. Together, the results suggest that host plants influence Buchnera population processes and that this may provide phenotypic plasticity in host plant use for clonal aphids.

  8. 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…

  9. 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.

  10. 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}.

  11. Population size vs. social connectedness - A gene-culture coevolutionary approach to cumulative cultural evolution.

    PubMed

    Kobayashi, Yutaka; Ohtsuki, Hisashi; Wakano, Joe Y

    2016-10-01

    It has long been debated if population size is a crucial determinant of the level of culture. While empirical results are mixed, recent theoretical studies suggest that social connectedness between people may be a more important factor than the size of the entire population. These models, however, do not take into account evolutionary responses of learning strategies determining the mode of transmission and innovation and are hence not suitable for predicting the long-term implications of parameters of interest. In the present paper, to address this issue, we provide a gene-culture coevolution model, in which the microscopic learning process of each individual is explicitly described as a continuous-time stochastic process and time allocation to social and individual learning is allowed to evolve. We have found that social connectedness has a larger impact on the equilibrium level of culture than population size especially when connectedness is weak and population size is large. This result, combined with those of previous culture-only models, points to the importance of studying separate effects of population size and internal social structure to better understand spatiotemporal variation in the level of culture.

  12. Population regulation in Magellanic penguins: what determines changes in colony size?

    PubMed

    Pozzi, Luciana M; García Borboroglu, Pablo; Boersma, P Dee; Pascual, Miguel A

    2015-01-01

    Seabirds are often studied at individual colonies, but the confounding effects of emigration and mortality processes in open populations may lead to inappropriate conclusions on the mechanisms underlying population changes. Magellanic penguin (Spheniscus magellanicus) colonies of variable population sizes are distributed along the Argentine coastline. In recent decades, several population and distributional changes have occurred, with some colonies declining and others newly established or increasing. We integrated data of eight colonies scattered along ∼600 km in Northern Patagonia (from 41°26´S, 65°01´W to 45°11´S, 66°30´W, Rio Negro and Chubut provinces) and conducted analysis in terms of their growth rates, production of young and of the dependence of those vital rates on colony age, size, and location. We contrasted population trends estimated from abundance data with those derived from population modeling to understand if observed growth rates were attainable under closed population scenarios. Population trends were inversely related to colony size, suggesting a density dependent growth pattern. All colonies located in the north--which were established during the last decades--increased at high rates, with the smallest, recently established colonies growing at the fastest rate. In central-southern Chubut, where colonies are the oldest, the largest breeding aggregations declined, but smaller colonies remained relatively stable. Results provided strong evidence that dispersal played a major role in driving local trends. Breeding success was higher in northern colonies, likely mediated by favorable oceanographic conditions. However, mean foraging distance and body condition of chicks at fledging were influenced by colony size. Recruitment of penguins in the northern area may have been triggered by a combination of density dependence, likely exacerbated by less favorable oceanographic conditions in the southern sector. Our results reaffirm the idea that

  13. Population Regulation in Magellanic Penguins: What Determines Changes in Colony Size?

    PubMed Central

    Pozzi, Luciana M.; Borboroglu, Pablo García; Boersma, P. Dee; Pascual, Miguel A.

    2015-01-01

    Seabirds are often studied at individual colonies, but the confounding effects of emigration and mortality processes in open populations may lead to inappropriate conclusions on the mechanisms underlying population changes. Magellanic penguin (Spheniscus magellanicus) colonies of variable population sizes are distributed along the Argentine coastline. In recent decades, several population and distributional changes have occurred, with some colonies declining and others newly established or increasing. We integrated data of eight colonies scattered along ∼ 600 km in Northern Patagonia (from 41°26´S, 65°01´W to 45°11´S, 66°30´W, Rio Negro and Chubut provinces) and conducted analysis in terms of their growth rates, production of young and of the dependence of those vital rates on colony age, size, and location. We contrasted population trends estimated from abundance data with those derived from population modeling to understand if observed growth rates were attainable under closed population scenarios. Population trends were inversely related to colony size, suggesting a density dependent growth pattern. All colonies located in the north—which were established during the last decades—increased at high rates, with the smallest, recently established colonies growing at the fastest rate. In central-southern Chubut, where colonies are the oldest, the largest breeding aggregations declined, but smaller colonies remained relatively stable. Results provided strong evidence that dispersal played a major role in driving local trends. Breeding success was higher in northern colonies, likely mediated by favorable oceanographic conditions. However, mean foraging distance and body condition of chicks at fledging were influenced by colony size. Recruitment of penguins in the northern area may have been triggered by a combination of density dependence, likely exacerbated by less favorable oceanographic conditions in the southern sector. Our results reaffirm the idea

  14. Transgender Population Size in the United States: a Meta-Regression of Population-Based Probability Samples

    PubMed Central

    Sevelius, Jae M.

    2017-01-01

    Background. Transgender individuals have a gender identity that differs from the sex they were assigned at birth. The population size of transgender individuals in the United States is not well-known, in part because official records, including the US Census, do not include data on gender identity. Population surveys today more often collect transgender-inclusive gender-identity data, and secular trends in culture and the media have created a somewhat more favorable environment for transgender people. Objectives. To estimate the current population size of transgender individuals in the United States and evaluate any trend over time. Search methods. In June and July 2016, we searched PubMed, Cumulative Index to Nursing and Allied Health Literature, and Web of Science for national surveys, as well as “gray” literature, through an Internet search. We limited the search to 2006 through 2016. Selection criteria. We selected population-based surveys that used probability sampling and included self-reported transgender-identity data. Data collection and analysis. We used random-effects meta-analysis to pool eligible surveys and used meta-regression to address our hypothesis that the transgender population size estimate would increase over time. We used subsample and leave-one-out analysis to assess for bias. Main results. Our meta-regression model, based on 12 surveys covering 2007 to 2015, explained 62.5% of model heterogeneity, with a significant effect for each unit increase in survey year (F = 17.122; df = 1,10; b = 0.026%; P = .002). Extrapolating these results to 2016 suggested a current US population size of 390 adults per 100 000, or almost 1 million adults nationally. This estimate may be more indicative for younger adults, who represented more than 50% of the respondents in our analysis. Authors’ conclusions. Future national surveys are likely to observe higher numbers of transgender people. The large variety in questions used to ask

  15. Population size and incidence of virus infection in free-living populations of Cucurbita pepo.

    PubMed

    Quemada, Hector; Strehlow, Laura; Decker-Walters, Deena S; Staub, Jack E

    2008-01-01

    Impact assessments of virus resistance transgene introgression into wild, free-living populations are important for determining whether these transgenes present a risk to agriculture or the environment. Transgenic virus-resistant Cucurbita pepo ssp. ovifera var. ovifera L. (squash) cultivars have been commercialized, and may be cultivated in close proximity to cross-compatible wild, free-living relatives (C. pepo subsp. pepo vars. ozarkana and texana). Therefore, the potential impact of these virus resistance transgenes was studied by surveying the incidence and fluctuations of virus infection (as assayed by ELISA), virus symptoms (which may not be seen in an infected plant) and population size in forty-three free-living C. pepo populations in Illinois, Missouri, Arkansas, Mississippi, Louisiana, and Texas. Ten of these populations were studied over three consecutive seasons. Depending on the year, 61% to 78% percent of the populations had at least one individual infected by at CMV, ZYMV or WMV2, but the median incidence of infection within populations was 13%. The observed infection level in free-living populations was consistent with levels defined as "low" in field plot experiments conducted by others, leading to the conclusion that transgenic virus resistance should not provide a significant fitness advantage to the free-living populations examined. Viral symptoms were detected in only 2% of plants observed, indicating that severity of viral infection was low. CMV, ZYMV, and WMV2 were not the only viruses infecting these populations, further reducing the likelihood that resistance to these viruses would release populations from constraints imposed by virus diseases.

  16. Retrotransposon populations of Vicia species with varying genome size.

    PubMed

    Hill, Pamela; Burford, Debbie; Martin, David M A; Flavell, Andrew J

    2005-06-01

    The (non-LTR) LINE and Ty3-gypsy-type LTR retrotransposon populations of three Vicia species that differ in genome size (Vicia faba, Vicia melanops and Vicia sativa) have been characterised. In each species the LINE retrotransposons comprise a complex, very heterogeneous set of sequences, while the Ty3-gypsy elements are much more homogeneous. Copy numbers of all three retrotransposon groups (Ty1-copia, Ty3-gypsy and LINE) in these species have been estimated by random genomic sequencing and Southern hybridisation analysis. The Ty3-gypsy elements are extremely numerous in all species, accounting for 18-35% of their genomes. The Ty1-copia group elements are somewhat less abundant and LINE elements are present in still lower amounts. Collectively, 20-45% of the genomes of these three Vicia species are comprised of retrotransposons. These data show that the three retrotransposon groups have proliferated to different extents in members of the Vicia genus and high proliferation has been associated with homogenisation of the retrotransposon population.

  17. Population size of snowy plovers breeding in North America

    USGS Publications Warehouse

    Thomas, Susan M.; Lyons, James E.; Andres, Brad A.; T-Smith, Elise Elliot; Palacios, Eduardo; Cavitt, John F.; Royle, J. Andrew; Fellows, Suzanne D.; Maty, Kendra; Howe, William H.; Mellink, Eric; Melvin, Stefani; Zimmerman, Tara

    2012-01-01

    Snowy Plovers (Charadrius nivosus) may be one of the rarest shorebirds in North America yet a comprehensive assessment of their abundance and distribution has not been completed. During 2007 and 2008, 557 discrete wetlands were surveyed and nine additional large wetland complexes sampled in México and the USA. From these surveys, a population of 23,555 (95% CI = 17,299 – 29,859) breeding Snowy Plovers was estimated. Combining the estimate with information from areas not surveyed, the total North American population was assessed at 25,869 (95% CI = 18,917 – 32,173). Approximately 42% of all breeding Snowy Plovers in North America resided at two sites (Great Salt Lake, Utah, and Salt Plains National Wildlife Refuge, Oklahoma), and 33% of all these were on wetlands in the Great Basin (including Great Salt Lake). Also, coastal habitats in central and southern Texas supported large numbers of breeding plovers. New breeding sites were discovered in interior deserts and highlands and along the Pacific coast of México; approximately 9% of the North American breeding population occurred in México. Because of uncertainties about effects of climate change and current stresses to breeding habitats, the species should be a management and conservation priority. Periodic monitoring should be undertaken at important sites to ensure high quality habitat is available to support the Snowy Plover population.

  18. 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

  19. 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.

  20. Extinction-effective population index: incorporating life-history variations in population viability analysis.

    PubMed

    Fujiwara, Masami

    2007-09-01

    Viability status of populations is a commonly used measure for decision-making in the management of populations. One of the challenges faced by managers is the need to consistently allocate management effort among populations. This allocation should in part be based on comparison of extinction risks among populations. Unfortunately, common criteria that use minimum viable population size or count-based population viability analysis (PVA) often do not provide results that are comparable among populations, primarily because they lack consistency in determining population size measures and threshold levels of population size (e.g., minimum viable population size and quasi-extinction threshold). Here I introduce a new index called the "extinction-effective population index," which accounts for differential effects of demographic stochasticity among organisms with different life-history strategies and among individuals in different life stages. This index is expected to become a new way of determining minimum viable population size criteria and also complement the count-based PVA. The index accounts for the difference in life-history strategies of organisms, which are modeled using matrix population models. The extinction-effective population index, sensitivity, and elasticity are demonstrated in three species of Pacific salmonids. The interpretation of the index is also provided by comparing them with existing demographic indices. Finally, a measure of life-history-specific effect of demographic stochasticity is derived.

  1. Using maximum likelihood to estimate population size from temporal changes in allele frequencies.

    PubMed Central

    Williamson, E G; Slatkin, M

    1999-01-01

    We develop a maximum-likelihood framework for using temporal changes in allele frequencies to estimate the number of breeding individuals in a population. We use simulations to compare the performance of this estimator to an F-statistic estimator of variance effective population size. The maximum-likelihood estimator had a lower variance and smaller bias. Taking advantage of the likelihood framework, we extend the model to include exponential growth and show that temporal allele frequency data from three or more sampling events can be used to test for population growth. PMID:10353915

  2. 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.…

  3. Making It Count: Improving Estimates of the Size of Transgender and Gender Nonconforming Populations.

    PubMed

    Deutsch, Madeline B

    2016-06-01

    An accurate estimate of the number of transgender and gender nonconforming people is essential to inform policy and funding priorities and decisions. Historical reports of population sizes of 1 in 4000 to 1 in 50,000 have been based on clinical populations and likely underestimate the size of the transgender population. More recent population-based studies have found a 10- to 100-fold increase in population size. Studies that estimate population size should be population based, employ the two-step method to allow for collection of both gender identity and sex assigned at birth, and include measures to capture the range of transgender people with nonbinary gender identities.

  4. Genetic evidence for larger African population size during recent human evolution.

    PubMed

    Relethford, J H; Jorde, L B

    1999-03-01

    Genetic evidence suggests that the long-term average effective size of sub-Saharan Africa is larger than other geographic regions. A method is described that allows estimation of relative long-term regional population sizes. This method is applied to 60 microsatellite DNA loci from a sample of 72 sub-Saharan Africans, 63 East Asians, and 120 Europeans. Average heterozygosity is significantly higher in the sub-Saharan African sample. Expected heterozygosity was computed for each region and locus using a population genetic model based on the null hypothesis of equal long-term population sizes. Average residual heterozygosity is significantly higher in the sub-Saharan African sample, indicating that African population size was larger than other regions during recent human evolution. The best fit of the model is with relative population weights of 0.73 for sub-Saharan Africa, 0.09 for East Asia, and 0.18 for Europe. These results are similar to those obtained using craniometric variation for these three geographic regions. These results, combined with inferences from other genetic studies, support a major role of Africa in the origin of modern humans. It is less clear, however, whether complete African replacement is the most appropriate model. An alternative is an African origin with non-African gene flow. While Africa is an important region in recent human evolution, it is not clear whether the gene pool of our species is completely out of Africa or predominately out of Africa.

  5. Interference versus exploitative competition in the regulation of size-structured populations.

    PubMed

    Le Bourlot, Vincent; Tully, Thomas; Claessen, David

    2014-11-01

    Competition is a major regulatory factor in population and community dynamics. Its effects can be either direct in interference competition or indirect in exploitative competition. The impact of exploitative competition on population dynamics has been extensively studied from empirical and theoretical points of view, but the consequences of interference competition remain poorly understood. Here we study the effect of different levels of intraspecific interference competition on the dynamics of a size-structured population. We study a physiologically structured population model accounting for direct individual interactions, allowing for a gradient from exploitative competition to interference competition. We parameterize our model with data on experimental populations of the collembolan Folsomia candida. Our model predicts contrasting dynamics, depending on the level of interference competition. With low interference, our model predicts juvenile-driven generation cycles, but interference competition tends to dampen these cycles. With intermediate interference, giant individuals emerge and start dominating the population. Finally, strong interference competition causes a novel kind of adult-driven generation cycles referred to as interference-induced cycles. Our results shed new light on the interpretation of the size-structured dynamics of natural and experimental populations.

  6. Diminishing Returns of Population Size in the Rate of RNA Virus Adaptation

    PubMed Central

    Miralles, Rosario; Moya, Andrés; Elena, Santiago F.

    2000-01-01

    Whenever an asexual viral population evolves by adapting to new environmental conditions, beneficial mutations, the ultimate cause of adaptation, are randomly produced and then fixed in the population. The larger the population size and the higher the mutation rate, the more beneficial mutations can be produced per unit time. With the usually high mutation rate of RNA viruses and in a large enough population, several beneficial mutations could arise at the same time but in different genetic backgrounds, and if the virus is asexual, they will never be brought together through recombination. Thus, the best of these genotypes must outcompete each other on their way to fixation. This competition among beneficial mutations has the effect of slowing the overall rate of adaptation. This phenomenon is known as clonal interference. Clonal interference predicts a speed limit for adaptation as the population size increases. In the present report, by varying the size of evolving vesicular stomatitis virus populations, we found evidence clearly demonstrating this speed limit and thus indicating that clonal interference might be an important factor modulating the rate of adaptation to an in vitro cell system. Several evolutionary and epidemiological implications of the clonal interference model applied to RNA viruses are discussed. PMID:10729131

  7. Surprising migration and population size dynamics in ancient Iberian brown bears (Ursus arctos)

    PubMed Central

    Valdiosera, Cristina E.; García-Garitagoitia, José Luis; Garcia, Nuria; Doadrio, Ignacio; Thomas, Mark G.; Hänni, Catherine; Arsuaga, Juan-Luis; Barnes, Ian; Hofreiter, Michael; Orlando, Ludovic; Götherström, Anders

    2008-01-01

    The endangered brown bear populations (Ursus arctos) in Iberia have been suggested to be the last fragments of the brown bear population that served as recolonization stock for large parts of Europe during the Pleistocene. Conservation efforts are intense, and results are closely monitored. However, the efforts are based on the assumption that the Iberian bears are a unique unit that has evolved locally for an extended period. We have sequenced mitochondrial DNA (mtDNA) from ancient Iberian bear remains and analyzed them as a serial dataset, monitoring changes in diversity and occurrence of European haplogroups over time. Using these data, we show that the Iberian bear population has experienced a dynamic, recent evolutionary history. Not only has the population undergone mitochondrial gene flow from other European brown bears, but the effective population size also has fluctuated substantially. We conclude that the Iberian bear population has been a fluid evolutionary unit, developed by gene flow from other populations and population bottlenecks, far from being in genetic equilibrium or isolated from other brown bear populations. Thus, the current situation is highly unusual and the population may in fact be isolated for the first time in its history. PMID:18347332

  8. Pollinator population size and pollination ecosystem service responses to enhancing floral and nesting resources.

    PubMed

    Häussler, Johanna; Sahlin, Ullrika; Baey, Charlotte; Smith, Henrik G; Clough, Yann

    2017-03-01

    Modeling pollination ecosystem services requires a spatially explicit, process-based approach because they depend on both the behavioral responses of pollinators to the amount and spatial arrangement of habitat and on the within- and between-season dynamics of pollinator populations in response to land use. We describe a novel pollinator model predicting flower visitation rates by wild central-place foragers (e.g., nesting bees) in spatially explicit landscapes. The model goes beyond existing approaches by: (1) integrating preferential use of more rewarding floral and nesting resources; (2) considering population growth over time; (3) allowing different dispersal distances for workers and reproductives; (4) providing visitation rates for use in crop pollination models. We use the model to estimate the effect of establishing grassy field margins offering nesting resources and a low quantity of flower resources, and/or late-flowering flower strips offering no nesting resources but abundant flowers, on bumble bee populations and visitation rates to flowers in landscapes that differ in amounts of linear seminatural habitats and early mass-flowering crops. Flower strips were three times more effective in increasing pollinator populations and visitation rates than field margins, and this effect increased over time. Late-blooming flower strips increased early-season visitation rates, but decreased visitation rates in other late-season flowers. Increases in population size over time in response to flower strips and amounts of linear seminatural habitats reduced this apparent competition for pollinators. Our spatially explicit, process-based model generates emergent patterns reflecting empirical observations, such that adding flower resources may have contrasting short- and long-term effects due to apparent competition for pollinators and pollinator population size increase. It allows exploring these effects and comparing effect sizes in ways not possible with other

  9. Population size and trend of Yellow-billed Loons in northern Alaska

    USGS Publications Warehouse

    Earnst, Susan L.; Stehn, R.A.; Platte, Robert; Larned, W.W.; Mallek, E.J.

    2005-01-01

    The Yellow-billed Loon (Gavia adamsii) is of conservation concern due to its restricted range, small population size, specific habitat requirements, and perceived threats to its breeding and wintering habitat. Within the U.S., this species breeds almost entirely within the National Petroleum Reserve-Alaska, nearly all of which is open, or proposed to be opened, for oil development. Rigorous estimates of Yellow-billed Loon population size and trend are lacking but essential for informed conservation. We used two annual aerial waterfowl surveys, conducted 1986a??2003 and 1992a??2003, to estimate population size and trend on northern Alaskan breeding grounds. In estimating population trend, we used mixed-effects regression models to reduce bias and sampling error associated with improvement in observer skill and annual effects of spring phenology. The estimated population trend on Alaskan breeding grounds since 1986 was near 0 with an estimated annual change of a??0.9% (95% CI of a??3.6% to +1.8%). The estimated population size, averaged over the past 12 years and adjusted by a correction factor based on an intensive, lake-circling, aerial survey method, was 2221 individuals (95% CI of 1206a??3235) in early June and 3369 individuals (95% CI of 1910a??4828) in late June. Based on estimates from other studies of the proportion of loons nesting in a given year, it is likely that <1000 nesting pairs inhabit northern Alaska in most years. The highest concentration of Yellow-billed Loons occurred between the Meade and Ikpikpuk Rivers; and across all of northern Alaska, 53% of recorded sightings occurred within 12% of the area.

  10. Individual size variation and population stability in a seasonal environment: a discrete-time model and its calibration using grasshoppers.

    PubMed

    Filin, Ido; Ovadia, Ofer

    2007-11-01

    Much recent literature is concerned with how variation among individuals (e.g., variability in their traits and fates) translates into higher-level (i.e., population and community) dynamics. Although several theoretical frameworks have been devised to deal with the effects of individual variation on population dynamics, there are very few reports of empirically based estimates of the sign and magnitude of these effects. Here we describe an analytical model for size-dependent, seasonal life cycles and evaluate the effect of individual size variation on population dynamics and stability. We demonstrate that the effect of size variation on the population net reproductive rate varies in both magnitude and sign, depending on season length. We calibrate our model with field data on size- and density-dependent growth and survival of the generalist grasshopper Melanoplus femurrubrum. Under deterministic dynamics (fixed season length), size variation impairs population stability, given naturally occurring densities. However, in the stochastic case, where season length exhibits yearly fluctuations, size variation reduces the variance in population growth rates, thus enhancing stability. This occurs because the effect of size variation on net reproductive rate is dependent on season length. We discuss several limitations of the current model and outline possible routes for future model development.

  11. Epidemiological effects of group size variation in social species

    PubMed Central

    Caillaud, Damien; Craft, Meggan E.; Meyers, Lauren Ancel

    2013-01-01

    Contact patterns in group-structured populations determine the course of infectious disease outbreaks. Network-based models have revealed important connections between group-level contact patterns and the dynamics of epidemics, but these models typically ignore heterogeneities in within-group composition. Here, we analyse a flexible mathematical model of disease transmission in a hierarchically structured wildlife population, and find that increased variation in group size reduces the epidemic threshold, making social animal populations susceptible to a broader range of pathogens. Variation in group size also increases the likelihood of an epidemic for mildly transmissible diseases, but can reduce the likelihood and expected size of an epidemic for highly transmissible diseases. Further, we introduce the concept of epidemiological effective group size, which we define to be the group size of a hypothetical population containing groups of identical size that has the same epidemic threshold as an observed population. Using data from the Serengeti Lion Project, we find that pride-living Serengeti lions are epidemiologically comparable to a homogeneous population with up to 20 per cent larger prides. PMID:23576784

  12. Genetic factors associated with population size may increase extinction risks and decrease colonization potential in a keystone tropical pine

    PubMed Central

    del Castillo, Rafael F; Trujillo-Argueta, Sonia; Sánchez-Vargas, Nahúm; Newton, Adrian C

    2011-01-01

    Pioneer species are essential for forest regeneration and ecosystem resilience. Pinus chiapensis is an endangered pioneer key species for tropical montane cloud forest regeneration in Mesoamerica. Human activities have severely reduced some P. chiapensis populations, which exhibited a small or null colonization potential suggesting the involvement of genetic factors associated with small populations. We explored the relationships between (i) population genetic diversity (allozymes) and population size, including sampling size effects, (ii) fitness estimates associated with colonization potential (seed viability and seedling performance) in a common environment and population size, and (iii) fitness estimates and observed heterozygosity in populations with sizes spanning five orders of magnitude. All the estimates of genetic diversity and fitness increased significantly with population size. Low fitness was detected in progenies of small populations of disturbed and undisturbed habitats. Progenies with the lowest observed heterozygosity displayed the lowest fitness estimates, which, in turn, increased with heterozygosity, but seed viability peaked at intermediate heterozygosity values suggesting inbreeding and outbreeding depression. Inbreeding depression appears to be the most immediate genetic factor in population decline. Conservation efforts should try to maintain large and genetically diverse populations, enhance gene flow by restoring connectivity between adjacent populations, and avoid genetically distant individuals. PMID:25568006

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

    PubMed

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

    2013-03-01

    We estimated local and metapopulation effective sizes ([Formula: see text] and meta-[Formula: see text]) for three coexisting salmonid species (Salmo salar, Salvelinus fontinalis, Salvelinus alpinus) inhabiting a freshwater system comprising seven interconnected lakes. First, we hypothesized that [Formula: see text] 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 [Formula: see text] ([Formula: see text]) between species, consistent with a hierarchy of adult population sizes ([Formula: see text]). Using another method based on a measure of linkage disequilibrium (LDNE: [Formula: see text]), we found more finite [Formula: see text] values for S. salar than for the other two salmonids, in line with the results above that indicate that S. salar exhibits the lowest [Formula: see text] among the three species. Considering subpopulations as open to migration (i.e., removing putative immigrants) led to only marginal and non-significant changes in [Formula: see text], suggesting that migration may be at equilibrium between genetically similar sources. Second, we hypothesized that meta-[Formula: see text] might be significantly smaller than the sum of local [Formula: see text]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-[Formula: see text] 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

  14. Small population size and extremely low levels of genetic diversity in island populations of the platypus, Ornithorhynchus anatinus

    PubMed Central

    Furlan, Elise; Stoklosa, J; Griffiths, J; Gust, N; Ellis, R; Huggins, R M; Weeks, A R

    2012-01-01

    Genetic diversity generally underpins population resilience and persistence. Reductions in population size and absence of gene flow can lead to reductions in genetic diversity, reproductive fitness, and a limited ability to adapt to environmental change increasing the risk of extinction. Island populations are typically small and isolated, and as a result, inbreeding and reduced genetic diversity elevate their extinction risk. Two island populations of the platypus, Ornithorhynchus anatinus, exist; a naturally occurring population on King Island in Bass Strait and a recently introduced population on Kangaroo Island off the coast of South Australia. Here we assessed the genetic diversity within these two island populations and contrasted these patterns with genetic diversity estimates in areas from which the populations are likely to have been founded. On Kangaroo Island, we also modeled live capture data to determine estimates of population size. Levels of genetic diversity in King Island platypuses are perilously low, with eight of 13 microsatellite loci fixed, likely reflecting their small population size and prolonged isolation. Estimates of heterozygosity detected by microsatellites (HE= 0.032) are among the lowest level of genetic diversity recorded by this method in a naturally outbreeding vertebrate population. In contrast, estimates of genetic diversity on Kangaroo Island are somewhat higher. However, estimates of small population size and the limited founders combined with genetic isolation are likely to lead to further losses of genetic diversity through time for the Kangaroo Island platypus population. Implications for the future of these and similarly isolated or genetically depauperate populations are discussed. PMID:22837830

  15. Do Class Size Effects Differ across Grades?

    ERIC Educational Resources Information Center

    Nandrup, Anne Brink

    2016-01-01

    This paper contributes to the class size literature by analysing whether short-run class size effects are constant across grade levels in compulsory school. Results are based on administrative data on all pupils enrolled in Danish public schools. Identification is based on a government-imposed class size cap that creates exogenous variation in…

  16. Climate change influenced female population sizes through time across the Indonesian archipelago.

    PubMed

    Guillot, Elsa G; Tumonggor, Meryanne K; Lansing, J Stephen; Sudoyo, Herawati; Cox, Murray P

    2013-01-01

    Lying at the crossroads of Asia and the Pacific world, the Indonesian archipelago hosts one of the world's richest accumulations of cultural, linguistic, and genetic variation. While the role of human migration into and around the archipelago is now known in some detail, other aspects of Indonesia's complex history are less understood. Here, we focus on population size changes from the first settlement of Indonesia nearly 50 kya up to the historic era. We reconstructed the past effective population sizes of Indonesian women using mitochondrial DNA sequences from 2,104 individuals in 55 village communities on four islands spanning the Indonesian archipelago (Bali, Flores, Sumba, and Timor). We found little evidence for large fluctuations in effective population size. Most communities grew slowly during the late Pleistocene, peaked 15-20 kya, and subsequently declined slowly into the Holocene. This unexpected pattern may reflect population declines caused by the flooding of lowland hunter/gatherer habitat during sea-level rises following the last glacial maximum.

  17. How to control chaotic behaviour and population size with proportional feedback

    NASA Astrophysics Data System (ADS)

    Liz, Eduardo

    2010-01-01

    We study the control of chaos in one-dimensional discrete maps as they often occur in modelling population dynamics. For managing the population, we seek to suppress any possible chaotic behavior, leading the system to a stable equilibrium. In this Letter, we make a rigorous analysis of the proportional feedback method under certain conditions fulfilled by a wide family of maps. We show that it is possible to stabilize the chaotic dynamics towards a globally stable positive equilibrium, that can be chosen among a broad range of possible values. In particular, the size of the population can be enhanced by control in form of population reduction. This paradoxical phenomenon is known as the hydra effect, and it has important implications in the design of strategies in such areas as fishing, pest management, and conservation biology.

  18. Population Size and Decadal Trends of Three Penguin Species Nesting at Signy Island, South Orkney Islands.

    PubMed

    Dunn, Michael J; Jackson, Jennifer A; Adlard, Stacey; Lynnes, Amanda S; Briggs, Dirk R; Fox, Derren; Waluda, Claire M

    2016-01-01

    We report long-term changes in population size of three species of sympatrically breeding pygoscelid penguins: Adélie (Pygoscelis adeliae), chinstrap (Pygoscelis antarctica) and gentoo (Pygoscelis papua ellsworthii) over a 38 year period at Signy Island, South Orkney Islands, based on annual counts from selected colonies and decadal all-island systematic counts of occupied nests. Comparing total numbers of breeding pairs over the whole island from 1978/79 to 2015/16 revealed varying fortunes: gentoo penguin pairs increased by 255%, (3.5% per annum), chinstrap penguins declined by 68% (-3.6% per annum) and Adélie penguins declined by 42% (-1.5% per annum). The chinstrap population has declined steadily over the last four decades. In contrast, Adélie and gentoo penguins have experienced phases of population increase and decline. Annual surveys of selected chinstrap and Adélie colonies produced similar trends from those revealed by island-wide surveys, allowing total island population trends to be inferred relatively well. However, while the annual colony counts of chinstrap and Adélie penguins showed a trend consistent in direction with the results from all-island surveys, the magnitude of estimated population change was markedly different between colony wide and all island counts. Annual population patterns suggest that pair numbers in the study areas partly reflect immigration and emigration of nesting birds between different parts of the island. Breeding success for all three species remained broadly stable over time in the annually monitored colonies. Breeding success rates in gentoo and chinstrap penguins were strongly correlated, despite the differing trends in population size. This study shows the importance of effective, standardised monitoring to accurately determine long-term population trajectories. Our results indicate significant declines in the Adélie and chinstrap penguin populations at Signy Island over the last five decades, and a gradual

  19. Population Size and Decadal Trends of Three Penguin Species Nesting at Signy Island, South Orkney Islands

    PubMed Central

    Dunn, Michael J.; Jackson, Jennifer A.; Adlard, Stacey; Lynnes, Amanda S.; Briggs, Dirk R.; Fox, Derren; Waluda, Claire M.

    2016-01-01

    We report long-term changes in population size of three species of sympatrically breeding pygoscelid penguins: Adélie (Pygoscelis adeliae), chinstrap (Pygoscelis antarctica) and gentoo (Pygoscelis papua ellsworthii) over a 38 year period at Signy Island, South Orkney Islands, based on annual counts from selected colonies and decadal all-island systematic counts of occupied nests. Comparing total numbers of breeding pairs over the whole island from 1978/79 to 2015/16 revealed varying fortunes: gentoo penguin pairs increased by 255%, (3.5% per annum), chinstrap penguins declined by 68% (-3.6% per annum) and Adélie penguins declined by 42% (-1.5% per annum). The chinstrap population has declined steadily over the last four decades. In contrast, Adélie and gentoo penguins have experienced phases of population increase and decline. Annual surveys of selected chinstrap and Adélie colonies produced similar trends from those revealed by island-wide surveys, allowing total island population trends to be inferred relatively well. However, while the annual colony counts of chinstrap and Adélie penguins showed a trend consistent in direction with the results from all-island surveys, the magnitude of estimated population change was markedly different between colony wide and all island counts. Annual population patterns suggest that pair numbers in the study areas partly reflect immigration and emigration of nesting birds between different parts of the island. Breeding success for all three species remained broadly stable over time in the annually monitored colonies. Breeding success rates in gentoo and chinstrap penguins were strongly correlated, despite the differing trends in population size. This study shows the importance of effective, standardised monitoring to accurately determine long-term population trajectories. Our results indicate significant declines in the Adélie and chinstrap penguin populations at Signy Island over the last five decades, and a gradual

  20. Influence of Population Density on Offspring Number and Size in Burying Beetles

    ERIC Educational Resources Information Center

    Rauter, Claudia M.

    2010-01-01

    This laboratory exercise investigates the influence of population density on offspring number and size in burying beetles. Students test the theoretical predictions that brood size declines and offspring size increases when competition over resources becomes stronger with increasing population density. Students design the experiment, collect and…

  1. Hazards of explosives dusts: Particle size effects

    SciTech Connect

    Cashdollar, K L; Hertzberg, M; Green, G M

    1992-02-01

    At the request of the Department of Energy, the Bureau of Mines has investigated the hazards of military explosives dispersed as dust clouds in a 20-L test chamber. In this report, the effect of particle size for HMX, HNS, RDX, TATB, and TNT explosives dusts is studied in detail. The explosibility data for these dusts are also compared to those for pure fuel dusts. The data show that all of the sizes of the explosives dusts that were studied were capable of sustaining explosions as dust clouds dispersed in air. The finest sizes (<10 [mu]m) of explosives dusts were less reactive than the intermediate sizes (20 to 60 [mu]m); this is opposite to the particle size effect observed previously for the pure fuel dusts. At the largest sizes studied, the explosives dusts become somewhat less reactive as dispersed dust clouds. The six sizes of the HMX dust were also studied as dust clouds dispersed in nitrogen.

  2. Evidence that the rate of strong selective sweeps increases with population size in the great apes

    PubMed Central

    Nam, Kiwoong; Munch, Kasper; Mailund, Thomas; Nater, Alexander; Greminger, Maja Patricia; Krützen, Michael; Marquès-Bonet, Tomàs; Schierup, Mikkel Heide

    2017-01-01

    Quantifying the number of selective sweeps and their combined effects on genomic diversity in humans and other great apes is notoriously difficult. Here we address the question using a comparative approach to contrast diversity patterns according to the distance from genes in all great ape taxa. The extent of diversity reduction near genes compared with the rest of intergenic sequences is greater in a species with larger effective population size. Also, the maximum distance from genes at which the diversity reduction is observed is larger in species with large effective population size. In Sumatran orangutans, the overall genomic diversity is ∼30% smaller than diversity levels far from genes, whereas this reduction is only 9% in humans. We show by simulation that selection against deleterious mutations in the form of background selection is not expected to cause these differences in diversity among species. Instead, selective sweeps caused by positive selection can reduce diversity level more severely in a large population if there is a higher number of selective sweeps per unit time. We discuss what can cause such a correlation, including the possibility that more frequent sweeps in larger populations are due to a shorter waiting time for the right mutations to arise. PMID:28137852

  3. Evidence that the rate of strong selective sweeps increases with population size in the great apes.

    PubMed

    Nam, Kiwoong; Munch, Kasper; Mailund, Thomas; Nater, Alexander; Greminger, Maja Patricia; Krützen, Michael; Marquès-Bonet, Tomàs; Schierup, Mikkel Heide

    2017-02-14

    Quantifying the number of selective sweeps and their combined effects on genomic diversity in humans and other great apes is notoriously difficult. Here we address the question using a comparative approach to contrast diversity patterns according to the distance from genes in all great ape taxa. The extent of diversity reduction near genes compared with the rest of intergenic sequences is greater in a species with larger effective population size. Also, the maximum distance from genes at which the diversity reduction is observed is larger in species with large effective population size. In Sumatran orangutans, the overall genomic diversity is ∼30% smaller than diversity levels far from genes, whereas this reduction is only 9% in humans. We show by simulation that selection against deleterious mutations in the form of background selection is not expected to cause these differences in diversity among species. Instead, selective sweeps caused by positive selection can reduce diversity level more severely in a large population if there is a higher number of selective sweeps per unit time. We discuss what can cause such a correlation, including the possibility that more frequent sweeps in larger populations are due to a shorter waiting time for the right mutations to arise.

  4. Computing & Interpreting Effect Sizes in Educational Research

    ERIC Educational Resources Information Center

    Thompson, Bruce

    2009-01-01

    The present article provides a primer on using effect sizes in research. A small heuristic data set is used in order to make the discussion concrete. Additionally, various admonitions for best practice in reporting and interpreting effect sizes are presented. Among these is the admonition to not use Cohen's benchmarks for "small," "medium," and…

  5. Reduction of egg size in natural populations of threespine stickleback infected with a cestode macroparasite.

    PubMed

    Heins, David C; Baker, John A

    2003-02-01

    Manifestations of infectious disease may represent host adaptations to avoid or reduce the effects of infection on host fitness, parasite manipulations that benefit the pathogen's fitness, or nonadaptive side effects of parasitism. Threespine stickleback fish (Gasterosteus aculeatus) from Alaska and the cestode macroparasite Schistocephalus solidus provide an excellent system for study of the effects of parasitism on host egg size because females in populations there are capable of producing clutches of eggs in the face of substantial infection, contrary to the inhibition of reproduction that has been observed in other stickleback populations or other species of fish. A side effect resulting in reduction of mean ovummass among infected females was predicted based on the egg production process in female stickleback, the considerable energy and resource demands of S. solidus, and the chronic and progressive nature of the effects the macroparasite should have on the host fish. In each of 9 populations of G. aculeatus representing replicate natural experiments in lakes scattered across the Matanuska-Susitna Valley and the Kenai Peninsula of south-central Alaska and among all populations combined, the mean ovum mass of infected female fish is significantly reduced in comparison with that of uninfected females taken from the same population at the same time. Reduction in mean female egg mass ranged from 8 to 32% across all populations. To examine whether reduction in mean female ovum mass was a nonadaptive side effect or an adaptation, relatively large data sets from 2 of the populations were used. Mean ovum mass of infected females was predicted to decrease directly in relation to parasite index (PI) if the diminution in mean egg mass were the result of a nonadaptive side effect resulting from host nutrient loss. Alternatively, the absence of a relationship between PI and reduction in ovum mass is predicted if decreases in mean female ovum mass result from host or

  6. Whitebark pine, population density, and home-range size of grizzly bears in the greater yellowstone ecosystem.

    PubMed

    Bjornlie, Daniel D; Van Manen, Frank T; Ebinger, Michael R; Haroldson, Mark A; Thompson, Daniel J; Costello, Cecily M

    2014-01-01

    Changes in life history traits of species can be an important indicator of potential factors influencing populations. For grizzly bears (Ursus arctos) in the Greater Yellowstone Ecosystem (GYE), recent decline of whitebark pine (WBP; Pinus albicaulis), an important fall food resource, has been paired with a slowing of population growth following two decades of robust population increase. These observations have raised questions whether resource decline or density-dependent processes may be associated with changes in population growth. Distinguishing these effects based on changes in demographic rates can be difficult. However, unlike the parallel demographic responses expected from both decreasing food availability and increasing population density, we hypothesized opposing behavioral responses of grizzly bears with regard to changes in home-range size. We used the dynamic changes in food resources and population density of grizzly bears as a natural experiment to examine hypotheses regarding these potentially competing influences on grizzly bear home-range size. We found that home-range size did not increase during the period of whitebark pine decline and was not related to proportion of whitebark pine in home ranges. However, female home-range size was negatively associated with an index of population density. Our data indicate that home-range size of grizzly bears in the GYE is not associated with availability of WBP, and, for female grizzly bears, increasing population density may constrain home-range size.

  7. Whitebark pine, population density, and home-range size of grizzly bears in the greater Yellowstone ecosystem

    USGS Publications Warehouse

    Daniel D, Bjornlie; van Manen, Frank T.; Michael R, Ebinger; Haroldson, Mark A.; Daniel J, Thompson; Cecily M, Costello

    2014-01-01

    Changes in life history traits of species can be an important indicator of potential factors influencing populations. For grizzly bears (Ursus arctos) in the Greater Yellowstone Ecosystem (GYE), recent decline of whitebark pine (WBP; Pinus albicaulis), an important fall food resource, has been paired with a slowing of population growth following two decades of robust population increase. These observations have raised questions whether resource decline or density-dependent processes may be associated with changes in population growth. Distinguishing these effects based on changes in demographic rates can be difficult. However, unlike the parallel demographic responses expected from both decreasing food availability and increasing population density, we hypothesized opposing behavioral responses of grizzly bears with regard to changes in home-range size. We used the dynamic changes in food resources and population density of grizzly bears as a natural experiment to examine hypotheses regarding these potentially competing influences on grizzly bear home-range size. We found that home-range size did not increase during the period of whitebark pine decline and was not related to proportion of whitebark pine in home ranges. However, female home-range size was negatively associated with an index of population density. Our data indicate that home-range size of grizzly bears in the GYE is not associated with availability of WBP, and, for female grizzly bears, increasing population density may constrain home-range size.

  8. Population size, survival, growth, and movements of Rana sierrae

    USGS Publications Warehouse

    Fellers, Gary M.; Kleeman, Patrick M.; Miller, David A. W.; Halstead, Brian J.; Link, William

    2013-01-01

    Based on 2431 captures of 757 individual frogs over a 9-yr period, we found that the population of R. sierrae in one meadow–stream complex in Yosemite National Park ranged from an estimated 45 to 115 adult frogs. Rana sierrae at our relatively low elevation site (2200 m) grew at a fast rate (K = 0.73–0.78), had high overwintering survival rates (44.6–95%), lived a long time (up to 16 yr), and tended to be fairly sedentary during the summer (100% minimum convex polygon annual home ranges of 139 m2) but had low year-to-year site fidelity. Even though the amphibian chytrid fungus (Batrachochytrium dendrobatidis, Bd) has been present in the population for at least 13 yr, there was no clear downward trend as might be expected from reports of R. sierrae population declines associated with Bd or from reports of widespread population decline of R. sierrae throughout its range.

  9. Structural effect of size on interracial friendship.

    PubMed

    Cheng, Siwei; Xie, Yu

    2013-04-30

    Social contexts exert structural effects on individuals' social relationships, including interracial friendships. In this study, we posit that, net of group composition, total context size has a distinct effect on interracial friendship. Under the assumptions of (i) maximization of preference in choosing a friend, (ii) multidimensionality of preference, and (iii) preference for same-race friends, we conducted analyses using microsimulation that yielded three main findings. First, increased context size decreases the likelihood of forming an interracial friendship. Second, the size effect increases with the number of preference dimensions. Third, the size effect is diluted by noise, i.e., the random component affecting friendship formation. Analysis of actual friendship data among 4,745 American high school students yielded results consistent with the main conclusion that increased context size promotes racial segregation and discourages interracial friendship.

  10. An aerial sightability model for estimating ferruginous hawk population size

    USGS Publications Warehouse

    Ayers, L.W.; Anderson, S.H.

    1999-01-01

    Most raptor aerial survey projects have focused on numeric description of visibility bias without identifying the contributing factors or developing predictive models to account for imperfect detection rates. Our goal was to develop a sightability model for nesting ferruginous hawks (Buteo regalis) that could account for nests missed during aerial surveys and provide more accurate population estimates. Eighteen observers, all unfamiliar with nest locations in a known population, searched for nests within 300 m of flight transects via a Maule fixed-wing aircraft. Flight variables tested for their influence on nest-detection rates included aircraft speed, height, direction of travel, time of day, light condition, distance to nest, and observer experience level. Nest variables included status (active vs. inactive), condition (i.e., excellent, good, fair, poor, bad), substrate type, topography, and tree density. A multiple logistic regression model identified nest substrate type, distance to nest, and observer experience level as significant predictors of detection rates (P < 0.05). The overall model was significant (??26 = 124.4, P < 0.001, n = 255 nest observations), and the correct classification rate was 78.4%. During 2 validation surveys, observers saw 23.7% (14/59) and 36.5% (23/63) of the actual population. Sightability model predictions, with 90% confidence intervals, captured the true population in both tests. Our results indicate standardized aerial surveys, when used in conjunction with the predictive sightability model, can provide unbiased population estimates for nesting ferruginous hawks.

  11. Estimating population size of Pygoscelid Penguins from TM data

    NASA Technical Reports Server (NTRS)

    Olson, Charles E., Jr.; Schwaller, Mathew R.; Dahmer, Paul A.

    1987-01-01

    An estimate was made toward a continent wide population of penguins. The results indicate that Thematic Mapper data can be used to identify penguin rookeries due to the unique reflectance properties of guano. Strong correlations exist between nesting populations and rookery area occupied by the birds. These correlations allow estimation of the number of nesting pairs in colonies. The success of remote sensing and biometric analyses leads one to believe that a continent wide estimate of penguin populations is possible based on a timely sample employing ground based and remote sensing techniques. Satellite remote sensing along the coastline may well locate previously undiscovered penguin nesting sites, or locate rookeries which have been assumed to exist for over a half century, but never located. Observations which found that penguins are one of the most sensitive elements in the complex of Southern Ocean ecosystems motivated this study.

  12. Reporting Confidence Intervals and Effect Sizes: Collecting the Evidence

    ERIC Educational Resources Information Center

    Zientek, Linda Reichwein; Ozel, Z. Ebrar Yetkiner; Ozel, Serkan; Allen, Jeff

    2012-01-01

    Confidence intervals (CIs) and effect sizes are essential to encourage meta-analytic thinking and to accumulate research findings. CIs provide a range of plausible values for population parameters with a degree of confidence that the parameter is in that particular interval. CIs also give information about how precise the estimates are. Comparison…

  13. Small Class Size and Its Effects.

    ERIC Educational Resources Information Center

    Biddle, Bruce J.; Berliner, David C.

    2002-01-01

    Describes several prominent early grades small-class-size projects and their effects on student achievement: Indiana's Project Prime Time, Tennessee's Project STAR (Student/Teacher Achievement Ratio), Wisconsin's SAGE (Student Achievement Guarantee in Education) Program, and the California class-size-reduction program. Lists several conclusions,…

  14. The Abundance and Pollen Foraging Behaviour of Bumble Bees in Relation to Population Size of Whortleberry (Vaccinium uliginosum)

    PubMed Central

    Mayer, Carolin; Michez, Denis; Chyzy, Alban; Brédat, Elise; Jacquemart, Anne-Laure

    2012-01-01

    Habitat fragmentation can have severe effects on plant pollinator interactions, for example changing the foraging behaviour of pollinators. To date, the impact of plant population size on pollen collection by pollinators has not yet been investigated. From 2008 to 2010, we monitored nine bumble bee species (Bombus campestris, Bombus hortorum s.l., Bombus hypnorum, Bombus lapidarius, Bombus pascuorum, Bombus pratorum, Bombus soroensis, Bombus terrestris s.l., Bombus vestalis s.l.) on Vaccinium uliginosum (Ericaceae) in up to nine populations in Belgium ranging in size from 80 m2 to over 3.1 ha. Bumble bee abundance declined with decreasing plant population size, and especially the proportion of individuals of large bumble bee species diminished in smaller populations. The most remarkable and novel observation was that bumble bees seemed to switch foraging behaviour according to population size: while they collected both pollen and nectar in large populations, they largely neglected pollen collection in small populations. This pattern was due to large bumble bee species, which seem thus to be more likely to suffer from pollen shortages in smaller habitat fragments. Comparing pollen loads of bumble bees we found that fidelity to V. uliginosum pollen did not depend on plant population size but rather on the extent shrub cover and/or openness of the site. Bumble bees collected pollen only from three plant species (V. uliginosum, Sorbus aucuparia and Cytisus scoparius). We also did not discover any pollination limitation of V. uliginosum in small populations. We conclude that habitat fragmentation might not immediately threaten the pollination of V. uliginosum, nevertheless, it provides important nectar and pollen resources for bumble bees and declining populations of this plant could have negative effects for its pollinators. The finding that large bumble bee species abandon pollen collection when plant populations become small is of interest when considering plant and

  15. The abundance and pollen foraging behaviour of bumble bees in relation to population size of whortleberry (Vaccinium uliginosum).

    PubMed

    Mayer, Carolin; Michez, Denis; Chyzy, Alban; Brédat, Elise; Jacquemart, Anne-Laure

    2012-01-01

    Habitat fragmentation can have severe effects on plant pollinator interactions, for example changing the foraging behaviour of pollinators. To date, the impact of plant population size on pollen collection by pollinators has not yet been investigated. From 2008 to 2010, we monitored nine bumble bee species (Bombus campestris, Bombus hortorum s.l., Bombus hypnorum, Bombus lapidarius, Bombus pascuorum, Bombus pratorum, Bombus soroensis, Bombus terrestris s.l., Bombus vestalis s.l.) on Vaccinium uliginosum (Ericaceae) in up to nine populations in Belgium ranging in size from 80 m(2) to over 3.1 ha. Bumble bee abundance declined with decreasing plant population size, and especially the proportion of individuals of large bumble bee species diminished in smaller populations. The most remarkable and novel observation was that bumble bees seemed to switch foraging behaviour according to population size: while they collected both pollen and nectar in large populations, they largely neglected pollen collection in small populations. This pattern was due to large bumble bee species, which seem thus to be more likely to suffer from pollen shortages in smaller habitat fragments. Comparing pollen loads of bumble bees we found that fidelity to V. uliginosum pollen did not depend on plant population size but rather on the extent shrub cover and/or openness of the site. Bumble bees collected pollen only from three plant species (V.uliginosum, Sorbus aucuparia and Cytisus scoparius). We also did not discover any pollination limitation of V. uliginosum in small populations. We conclude that habitat fragmentation might not immediately threaten the pollination of V. uliginosum, nevertheless, it provides important nectar and pollen resources for bumble bees and declining populations of this plant could have negative effects for its pollinators. The finding that large bumble bee species abandon pollen collection when plant populations become small is of interest when considering plant and

  16. Individual increase in inbreeding allows estimating effective sizes from pedigrees

    PubMed Central

    Gutiérrez, Juan Pablo; Cervantes, Isabel; Molina, Antonio; Valera, Mercedes; Goyache, Félix

    2008-01-01

    We present here a simple approach to obtain reliable estimates of the effective population size in real world populations via the computation of the increase in inbreeding for each individual (delta Fi) in a given population. The values of delta Fi are computed as t-root of 1 - (1 - Fi) where Fi is the inbreeding coefficient and t is the equivalent complete generations for each individual. The values of delta F computed for a pre-defined reference subset can be averaged and used to estimate effective size. A standard error of this estimate of Ne can be further computed from the standard deviation of the individual increase in inbreeding. The methodology is demonstrated by applying it to several simulated examples and to a real pedigree in which other methodologies fail when considering reference subpopulations. The main characteristics of the approach and its possible use are discussed both for predictive purposes and for analyzing genealogies. PMID:18558071

  17. A computer program for estimating fish population sizes and annual production rates

    SciTech Connect

    Railsback, S.F.; Holcomb, B.D.; Ryon, M.G.

    1989-10-01

    This report documents a program that estimates fish population sizes and annual production rates in small streams from multiple-pass sampling data. A maximum weighted likelihood method is used to estimate population sizes (Carle and Strub, 1978), and a size-frequency method is used to estimate production (Garman and Waters, 1983). The program performs the following steps: (1) reads in the data and performs error checking; (2) where required, uses length-weight regression to fill in missing weights; (3) assigns length classes to the fish; (4) for each date, species, and length class, estimates the population size and its variance; (5) for each date and species, estimates the total population size and its variance; and (6) for each species, estimates the annual production rate and its variance between sampling dates selected by the user. If data from only date are used, only populations are estimated. 9 refs.

  18. Breeding durations as estimators of adult sex ratios and population size.

    PubMed

    Payne, Nicholas Leslie; Gillanders, Bronwyn May; Semmens, Jayson

    2011-02-01

    Adult sex ratios (ASRs) and population size are two of the most fundamental parameters in population biology, as they are the main determinants of genetic and demographic viability, and vulnerability of a population to stochastic events. Underpinning the application of population viability analysis for predicting the extinction risk of populations is the need to accurately estimate parameters that determine the viability of populations (i.e. the ASR and population size). Here we demonstrate that a lack of temporal information can confound estimation of both parameters. Using acoustic telemetry, we compared differences in breeding durations of both sexes for a giant Australian cuttlefish Sepia apama breeding aggregation to the strongly male-biased operational sex ratio (4:1), in order to estimate the population ASR. The ratio of breeding durations between sexes was equal to the operational sex ratio, suggesting that the ASR is not strongly male-biased, but balanced. Furthermore, the short residence times of individuals at the breeding aggregation suggests that previous density-based abundance estimates have significantly underestimated population size. With the current wide application of population viability analysis for predicting the extinction risk of populations, tools to improve the accuracy of such predictions are vital. Here we provide a new approach to estimating the fundamental ASR parameter, and call for temporal considerations when estimating population size.

  19. Using Wolbachia Releases to Estimate Aedes aegypti (Diptera: Culicidae) Population Size and Survival

    PubMed Central

    Garcia, Gabriela de Azambuja; dos Santos, Lilha Maria Barbosa; Villela, Daniel Antunes Maciel; Maciel-de-Freitas, Rafael

    2016-01-01

    Mosquitoes carrying the endosymbiont bacterium Wolbachia have been deployed in field trials as a biological control intervention due to Wolbachia effects on reducing transmission of arboviruses. We performed mark, release and recapture (MRR) experiments using Wolbachia as an internal marker with daily collections with BG-Traps during the first two weeks of releases in Rio de Janeiro, Brazil. The MRR design allowed us to investigate two critical parameters that determine whether Wolbachia would successful invade a field population: the probability of daily survival (PDS) of Wolbachia-infected Aedes aegypti females, and the wild population density during releases. Released females had a PDS of 0.82 and 0.89 in the first and second weeks, respectively, immediately after releases, which is well within the range of previous estimates of survivorship of wild mosquitoes in Rio de Janeiro. Abundance estimation of wild population varied up to 10-fold higher depending on the estimation method used (634–3565 females on the average-difference model to 6365–16188 females according to Lincoln-Petersen). Wolbachia-released mosquitoes were lower than the density estimation of their wild counterparts, irrespectively of the model used. Individually screening mosquitoes for the presence of Wolbachia reduced uncertainty on abundance estimations due to fluctuation in capturing per week. A successful invasion into local population requires Ae. aegypti fitness is unaffected by Wolbachia presence, but also reliable estimates on the population size of wild mosquitoes. PMID:27479050

  20. From intracellular signaling to population oscillations: bridging size- and time-scales in collective behavior

    PubMed Central

    Sgro, Allyson E; Schwab, David J; Noorbakhsh, Javad; Mestler, Troy; Mehta, Pankaj; Gregor, Thomas

    2015-01-01

    Collective behavior in cellular populations is coordinated by biochemical signaling networks within individual cells. Connecting the dynamics of these intracellular networks to the population phenomena they control poses a considerable challenge because of network complexity and our limited knowledge of kinetic parameters. However, from physical systems, we know that behavioral changes in the individual constituents of a collectively behaving system occur in a limited number of well-defined classes, and these can be described using simple models. Here, we apply such an approach to the emergence of collective oscillations in cellular populations of the social amoeba Dictyostelium discoideum. Through direct tests of our model with quantitative in vivo measurements of single-cell and population signaling dynamics, we show how a simple model can effectively describe a complex molecular signaling network at multiple size and temporal scales. The model predicts novel noise-driven single-cell and population-level signaling phenomena that we then experimentally observe. Our results suggest that like physical systems, collective behavior in biology may be universal and described using simple mathematical models. PMID:25617347

  1. Genetic rescue in interconnected populations of small and large size of the self-incompatible Ranunculus reptans.

    PubMed

    Willi, Y; Fischer, M

    2005-12-01

    Small populations of our study species Ranunculus reptans have reduced fitness because of inbreeding, genetic load, and reduced mate availability; that is, they suffer from a three-fold genetic Allee effect. Here, we investigate how the effect of interpopulation outbreeding on offspring fitness depends on population size. We performed within- and between-population crosses with plants originating from 15 populations, and measured offspring performance in a common environment. Interpopulation outbreeding led to an increase in population means of clonal performance, which was defined as the number of rooted offspring rosettes produced per maternal ovule. This fitness gain mainly occurred at the life stage of seed set. It was especially pronounced for populations with a long-term history of small size inferred from their low genetic diversity, estimated from eight allozyme loci. We conclude that in a self-incompatible plant such as R. reptans, interpopulation outbreeding can lead to an immediate genetic rescue effect due to increased cross-compatibility and heterosis, and that this rescue effect is increased as population size decreases.

  2. Statistical Aspects of Effect Size Estimation.

    ERIC Educational Resources Information Center

    Hedges, Larry V.

    When the results of a series of independent studies are combined, it is useful to quantitatively estimate the magnitude of the effects. Several methods for estimating effect size are compared in this paper. Glass' estimator and the uniformly minimum variance unbiased estimator are based on the ratio of the sample mean difference and the pooled…

  3. Size scale effect in cavitation erosion

    NASA Technical Reports Server (NTRS)

    Rao, P. V.; Rao, B. C.; Buckley, D. H.

    1982-01-01

    An overview and data analyses pertaining to cavitation erosion size scale effects are presented. The exponents n in the power law relationship are found to vary from 1.7 to 4.9 for venturi and rotating disk devices supporting the values reported in the literature. Suggestions for future studies were made to arrive at further true scale effects.

  4. Effects of population outcrossing on rotifer fitness

    PubMed Central

    2010-01-01

    Background Outcrossing between populations can exert either positive or negative effects on offspring fitness. Cyclically parthenogenetic rotifers, like other continental zooplankters, show high genetic differentiation despite their high potential for passive dispersal. Within this context, the effects of outcrossing may be relevant in modulating gene flow between populations through selection for or against interpopulation hybrids. Nevertheless, these effects remain practically unexplored in rotifers. Here, the consequences of outcrossing on the rotifer Brachionus plicatilis were investigated. Cross-mating experiments were performed between a reference population and three alternative populations that differed in their genetic distance with regard to the former. Two offspring generations were obtained: F1 and BC ('backcross'). Fitness of the outcrossed offspring was compared with fitness of the offspring of the reference population for both generations and for three different between-population combinations. Four fitness components were measured throughout the rotifer life cycle: the diapausing egg-hatching proportion, clone viability (for the clones originating from diapausing eggs), initial net growth rate R for each viable clone, and the proportion of male-producing clones. Additionally, both the parental fertilisation proportion and a compound fitness measure, integrating the complete life cycle, were estimated. Results In the F1 generation, hybrid vigour was detected for the diapausing egg-hatching proportion, while R was lower in the outcrossed offspring than in the offspring of the reference population. Despite these contrasting results, hybrid vigour was globally observed for the compound measure of fitness. Moreover, there was evidence that this vigour could increase with the genetic differentiation of the outcrossed populations. In the BC generation, the hybrid vigour detected for the egg-hatching proportion in the F1 generation reverted to outbreeding

  5. Population Size Estimates for Men who Have Sex with Men and Persons who Inject Drugs.

    PubMed

    Oster, Alexandra M; Sternberg, Maya; Lansky, Amy; Broz, Dita; Wejnert, Cyprian; Paz-Bailey, Gabriela

    2015-08-01

    Understanding geographic variation in the numbers of men who have sex with men (MSM) and persons who inject drugs (PWID) is critical to targeting and scaling up HIV prevention programs, but population size estimates are not available at generalizable sub-national levels. We analyzed 1999-2010 National Health and Nutrition Examination Survey data on persons aged 18-59 years. We estimated weighted prevalence of recent (past 12 month) male-male sex and injection drug use by urbanicity (the degree to which a geographic area is urban) and US census region and calculated population sizes. Large metro areas (population ≥1,000,000) had higher prevalence of male-male sex (central areas, 4.4% of men; fringe areas, 2.5%) compared with medium/small metro areas (1.4%) and nonmetro areas (1.1%). Injection drug use did not vary by urbanicity and neither varied by census region. Three-quarters of MSM, but only half of PWID, resided in large metro areas. Two-thirds of MSM and two-thirds of PWID resided in the South and West. Efforts to reach MSM would benefit from being focused in large metro areas, while efforts to reach PWID should be delivered more broadly. These data allow for more effective allocation of funds for prevention programs.

  6. Size-frequency distribution of different secondary crater populations: 1. Equilibrium caused by secondary impacts

    NASA Astrophysics Data System (ADS)

    Xiao, Zhiyong

    2016-12-01

    Accumulation of impact craters is the major reason causing equilibrium of crater populations on airless planetary surfaces. Besides primary craters, the effect of widespread secondaries on the equilibrium of local crater populations is little studied. Here the different secondary crater populations formed by the Hokusai crater on Mercury are systematically studied, and they are compared with those on the Moon to investigate their contribution to the evolution of local crater populations. Self-secondaries cause equilibrium on continuous ejecta deposits in a short time, and the equilibrium crater population has a differential size-frequency distribution (SFD) slope of about -3. Background secondaries are abundant on Mercury, and equilibrium caused by a combination of primaries and potential background secondaries follows the same pattern on the Moon and Mercury. The spatial dispersion of fragments that form both near-field and distant secondaries is the major factor affecting the degree of mutual destruction and thus the final crater SFD. Some clustered distant secondaries on Mercury are likely formed by individual fragments considering their large spatial dispersion and identical morphology with same-sized primaries, and the SFD rollovers of these secondaries possibly reflect the inherent SFD rollovers of the impact fragments. Near-field secondaries and many other distant secondaries have morphology and spatial distribution that are consistent with being formed by clustered fragments, and mutual destruction of secondaries may be the major reason causing the observed SFD rollovers. Heterogeneous secondary impacts are a potential explanation for both different crater densities within the equilibrium diameter range and different regolith thicknesses on coeval surfaces.

  7. Genome size differentiates co-occurring populations of the planktonic diatom Ditylum brightwellii (Bacillariophyta)

    PubMed Central

    2010-01-01

    Background Diatoms are one of the most species-rich groups of eukaryotic microbes known. Diatoms are also the only group of eukaryotic micro-algae with a diplontic life history, suggesting that the ancestral diatom switched to a life history dominated by a duplicated genome. A key mechanism of speciation among diatoms could be a propensity for additional stable genome duplications. Across eukaryotic taxa, genome size is directly correlated to cell size and inversely correlated to physiological rates. Differences in relative genome size, cell size, and acclimated growth rates were analyzed in isolates of the diatom Ditylum brightwellii. Ditylum brightwellii consists of two main populations with identical 18s rDNA sequences; one population is distributed globally at temperate latitudes and the second appears to be localized to the Pacific Northwest coast of the USA. These two populations co-occur within the Puget Sound estuary of WA, USA, although their peak abundances differ depending on local conditions. Results All isolates from the more regionally-localized population (population 2) possessed 1.94 ± 0.74 times the amount of DNA, grew more slowly, and were generally larger than isolates from the more globally distributed population (population 1). The ITS1 sequences, cell sizes, and genome sizes of isolates from New Zealand were the same as population 1 isolates from Puget Sound, but their growth rates were within the range of the slower-growing population 2 isolates. Importantly, the observed genome size difference between isolates from the two populations was stable regardless of time in culture or the changes in cell size that accompany the diatom life history. Conclusions The observed two-fold difference in genome size between the D. brightwellii populations suggests that whole genome duplication occurred within cells of population 1 ultimately giving rise to population 2 cells. The apparent regional localization of population 2 is consistent with a recent

  8. The adaptive significance of population differentiation in offspring size of the least killifish, Heterandria formosa

    PubMed Central

    Leips, Jeff; Helen Rodd, F; Travis, Joseph

    2013-01-01

    We tested the hypothesis that density-dependent competition influences the evolution of offspring size. We studied two populations of the least killifish (Heterandria formosa) that differ dramatically in population density; these populations are genetically differentiated for offspring size, and females from both populations produce larger offspring when they experience higher social densities. To look at the influences of population of origin and relative body size on competitive ability, we held females from the high-density population at two different densities to create large and small offspring with the same genetic background. We measured the competitive ability of those offspring in mesocosms that contained either pure or mixed population treatments at either high or low density. High density increased competition, which was most evident in greatly reduced individual growth rates. Larger offspring from the high-density population significantly delayed the onset of maturity of fish from the low-density population. From our results, we infer that competitive conditions in nature have contributed to the evolution of genetically based interpopulation differences in offspring size as well as plasticity in offspring size in response to conspecific density. PMID:23610636

  9. Understanding the effect size and its measures

    PubMed Central

    Ialongo, Cristiano

    2016-01-01

    The evidence based medicine paradigm demands scientific reliability, but modern research seems to overlook it sometimes. The power analysis represents a way to show the meaningfulness of findings, regardless to the emphasized aspect of statistical significance. Within this statistical framework, the estimation of the effect size represents a means to show the relevance of the evidences produced through research. In this regard, this paper presents and discusses the main procedures to estimate the size of an effect with respect to the specific statistical test used for hypothesis testing. Thus, this work can be seen as an introduction and a guide for the reader interested in the use of effect size estimation for its scientific endeavour. PMID:27346958

  10. Population variation and individual maximum size in two leech populations: energy extraction from cannibalism or niche widening?

    PubMed

    Persson, Lennart; Elliott, J Malcolm

    2013-05-01

    The theory of cannibal dynamics predicts a link between population dynamics and individual life history. In particular, increased individual growth has, in both modeling and empirical studies, been shown to result from a destabilization of population dynamics. We used data from a long-term study of the dynamics of two leech (Erpobdella octoculata) populations to test the hypothesis that maximum size should be higher in a cycling population; one of the study populations exhibited a delayed feedback cycle while the other population showed no sign of cyclicity. A hump-shaped relationship between individual mass of 1-year-old leeches and offspring density the previous year was present in both populations. As predicted from the theory, the maximum mass of individuals was much larger in the fluctuating population. In contrast to predictions, the higher growth rate was not related to energy extraction from cannibalism. Instead, the higher individual mass is suggested to be due to increased availability of resources due to a niche widening with increased individual body mass. The larger individual mass in the fluctuating population was related to a stronger correlation between the densities of 1-year-old individuals and 2-year-old individuals the following year in this population. Although cannibalism was the major mechanism regulating population dynamics, its importance was negligible in terms of providing cannibalizing individuals with energy subsequently increasing their fecundity. Instead, the study identifies a need for theoretical and empirical studies on the largely unstudied interplay between ontogenetic niche shifts and cannibalistic population dynamics.

  11. Gaussian process-based Bayesian nonparametric inference of population size trajectories from gene genealogies.

    PubMed

    Palacios, Julia A; Minin, Vladimir N

    2013-03-01

    Changes in population size influence genetic diversity of the population and, as a result, leave a signature of these changes in individual genomes in the population. We are interested in the inverse problem of reconstructing past population dynamics from genomic data. We start with a standard framework based on the coalescent, a stochastic process that generates genealogies connecting randomly sampled individuals from the population of interest. These genealogies serve as a glue between the population demographic history and genomic sequences. It turns out that only the times of genealogical lineage coalescences contain information about population size dynamics. Viewing these coalescent times as a point process, estimating population size trajectories is equivalent to estimating a conditional intensity of this point process. Therefore, our inverse problem is similar to estimating an inhomogeneous Poisson process intensity function. We demonstrate how recent advances in Gaussian process-based nonparametric inference for Poisson processes can be extended to Bayesian nonparametric estimation of population size dynamics under the coalescent. We compare our Gaussian process (GP) approach to one of the state-of-the-art Gaussian Markov random field (GMRF) methods for estimating population trajectories. Using simulated data, we demonstrate that our method has better accuracy and precision. Next, we analyze two genealogies reconstructed from real sequences of hepatitis C and human Influenza A viruses. In both cases, we recover more believed aspects of the viral demographic histories than the GMRF approach. We also find that our GP method produces more reasonable uncertainty estimates than the GMRF method.

  12. The evolutionary legacy of size-selective harvesting extends from genes to populations

    PubMed Central

    Uusi-Heikkilä, Silva; Whiteley, Andrew R; Kuparinen, Anna; Matsumura, Shuichi; Venturelli, Paul A; Wolter, Christian; Slate, Jon; Primmer, Craig R; Meinelt, Thomas; Killen, Shaun S; Bierbach, David; Polverino, Giovanni; Ludwig, Arne; Arlinghaus, Robert

    2015-01-01

    Size-selective harvesting is assumed to alter life histories of exploited fish populations, thereby negatively affecting population productivity, recovery, and yield. However, demonstrating that fisheries-induced phenotypic changes in the wild are at least partly genetically determined has proved notoriously difficult. Moreover, the population-level consequences of fisheries-induced evolution are still being controversially discussed. Using an experimental approach, we found that five generations of size-selective harvesting altered the life histories and behavior, but not the metabolic rate, of wild-origin zebrafish (Danio rerio). Fish adapted to high positively size selective fishing pressure invested more in reproduction, reached a smaller adult body size, and were less explorative and bold. Phenotypic changes seemed subtle but were accompanied by genetic changes in functional loci. Thus, our results provided unambiguous evidence for rapid, harvest-induced phenotypic and evolutionary change when harvesting is intensive and size selective. According to a life-history model, the observed life-history changes elevated population growth rate in harvested conditions, but slowed population recovery under a simulated moratorium. Hence, the evolutionary legacy of size-selective harvesting includes populations that are productive under exploited conditions, but selectively disadvantaged to cope with natural selection pressures that often favor large body size. PMID:26136825

  13. Long Term Population, City Size and Climate Trends in the Fertile Crescent: A First Approximation

    PubMed Central

    Lawrence, Dan; Philip, Graham; Hunt, Hannah; Snape-Kennedy, Lisa; Wilkinson, T. J.

    2016-01-01

    Over the last 8000 years the Fertile Crescent of the Near East has seen the emergence of urban agglomerations, small scale polities and large territorial empires, all of which had profound effects on settlement patterns. Computational approaches, including the use of remote sensing data, allow us to analyse these changes at unprecedented geographical and temporal scales. Here we employ these techniques to examine and compare long term trends in urbanisation, population and climate records. Maximum city size is used as a proxy for the intensity of urbanisation, whilst population trends are modelled from settlement densities in nine archaeological surveys conducted over the last 30 years across the region. These two measures are then compared with atmospheric moisture levels derived from multiple proxy analyses from two locations close to the study area, Soreq Cave in Israel and Lake Van in south-eastern Turkey, as well as wider literature. The earliest urban sites emerged during a period of relatively high atmospheric moisture levels and conform to a series of size thresholds. However, after the Early Bronze Age maximum urban size and population levels increase rapidly whilst atmospheric moisture declines. We argue that although the initial phase of urbanization may have been linked to climate conditions, we can see a definitive decoupling of climate and settlement patterns after 2000 BC. We relate this phenomenon to changes in socio-economic organisation and integration in large territorial empires. The complex relationships sustaining urban growth during this later period resulted in an increase in system fragility and ultimately impacted on the sustainability of cities in the long term. PMID:27018998

  14. Estimation of the size of the female sex worker population in Rwanda using three different methods.

    PubMed

    Mutagoma, Mwumvaneza; Kayitesi, Catherine; Gwiza, Aimé; Ruton, Hinda; Koleros, Andrew; Gupta, Neil; Balisanga, Helene; Riedel, David J; Nsanzimana, Sabin

    2015-10-01

    HIV prevalence is disproportionately high among female sex workers compared to the general population. Many African countries lack useful data on the size of female sex worker populations to inform national HIV programmes. A female sex worker size estimation exercise using three different venue-based methodologies was conducted among female sex workers in all provinces of Rwanda in August 2010. The female sex worker national population size was estimated using capture-recapture and enumeration methods, and the multiplier method was used to estimate the size of the female sex worker population in Kigali. A structured questionnaire was also used to supplement the data. The estimated number of female sex workers by the capture-recapture method was 3205 (95% confidence interval: 2998-3412). The female sex worker size was estimated at 3348 using the enumeration method. In Kigali, the female sex worker size was estimated at 2253 (95% confidence interval: 1916-2524) using the multiplier method. Nearly 80% of all female sex workers in Rwanda were found to be based in the capital, Kigali. This study provided a first-time estimate of the female sex worker population size in Rwanda using capture-recapture, enumeration, and multiplier methods. The capture-recapture and enumeration methods provided similar estimates of female sex worker in Rwanda. Combination of such size estimation methods is feasible and productive in low-resource settings and should be considered vital to inform national HIV programmes.

  15. Population size influences amphibian detection probability: implications for biodiversity monitoring programs.

    PubMed

    Tanadini, Lorenzo G; Schmidt, Benedikt R

    2011-01-01

    Monitoring is an integral part of species conservation. Monitoring programs must take imperfect detection of species into account in order to be reliable. Theory suggests that detection probability may be determined by population size but this relationship has not yet been assessed empirically. Population size is particularly important because it may induce heterogeneity in detection probability and thereby cause bias in estimates of biodiversity. We used a site occupancy model to analyse data from a volunteer-based amphibian monitoring program to assess how well different variables explain variation in detection probability. An index to population size best explained detection probabilities for four out of six species (to avoid circular reasoning, we used the count of individuals at a previous site visit as an index to current population size). The relationship between the population index and detection probability was positive. Commonly used weather variables best explained detection probabilities for two out of six species. Estimates of site occupancy probabilities differed depending on whether the population index was or was not used to model detection probability. The relationship between the population index and detectability has implications for the design of monitoring and species conservation. Most importantly, because many small populations are likely to be overlooked, monitoring programs should be designed in such a way that small populations are not overlooked. The results also imply that methods cannot be standardized in such a way that detection probabilities are constant. As we have shown here, one can easily account for variation in population size in the analysis of data from long-term monitoring programs by using counts of individuals from surveys at the same site in previous years. Accounting for variation in population size is important because it can affect the results of long-term monitoring programs and ultimately the conservation of

  16. Inferring Population Size History from Large Samples of Genome-Wide Molecular Data - An Approximate Bayesian Computation Approach

    PubMed Central

    Boitard, Simon; Rodríguez, Willy; Jay, Flora; Mona, Stefano; Austerlitz, Frédéric

    2016-01-01

    Inferring the ancestral dynamics of effective population size is a long-standing question in population genetics, which can now be tackled much more accurately thanks to the massive genomic data available in many species. Several promising methods that take advantage of whole-genome sequences have been recently developed in this context. However, they can only be applied to rather small samples, which limits their ability to estimate recent population size history. Besides, they can be very sensitive to sequencing or phasing errors. Here we introduce a new approximate Bayesian computation approach named PopSizeABC that allows estimating the evolution of the effective population size through time, using a large sample of complete genomes. This sample is summarized using the folded allele frequency spectrum and the average zygotic linkage disequilibrium at different bins of physical distance, two classes of statistics that are widely used in population genetics and can be easily computed from unphased and unpolarized SNP data. Our approach provides accurate estimations of past population sizes, from the very first generations before present back to the expected time to the most recent common ancestor of the sample, as shown by simulations under a wide range of demographic scenarios. When applied to samples of 15 or 25 complete genomes in four cattle breeds (Angus, Fleckvieh, Holstein and Jersey), PopSizeABC revealed a series of population declines, related to historical events such as domestication or modern breed creation. We further highlight that our approach is robust to sequencing errors, provided summary statistics are computed from SNPs with common alleles. PMID:26943927

  17. Introducing the Mean Absolute Deviation "Effect" Size

    ERIC Educational Resources Information Center

    Gorard, Stephen

    2015-01-01

    This paper revisits the use of effect sizes in the analysis of experimental and similar results, and reminds readers of the relative advantages of the mean absolute deviation as a measure of variation, as opposed to the more complex standard deviation. The mean absolute deviation is easier to use and understand, and more tolerant of extreme…

  18. Effect Sizes in Cluster-Randomized Designs

    ERIC Educational Resources Information Center

    Hedges, Larry V.

    2007-01-01

    Multisite research designs involving cluster randomization are becoming increasingly important in educational and behavioral research. Researchers would like to compute effect size indexes based on the standardized mean difference to compare the results of cluster-randomized studies (and corresponding quasi-experiments) with other studies and to…

  19. Disruption effects on the beam size measurement

    SciTech Connect

    Raimondi, P.; Decker, F.J.; Chen, P.

    1995-06-01

    At the SLC Final Focus with higher currents and smaller beam sizes, the disruption parameter D{sub y} is close to one and so the pinch effect should produce a luminosity enhancement. Since a flat beam-beam function is fit to deflection scan data to measure the beam size, disruption can affect the measurement. Here the authors discuss the quantitative effects of disruption for typical SLC beam parameters. With 3.5 10{sup 10} particles per pulse, bunch length of 0.8 mm and beam sizes of 2.1 {mu}m horizontally and 0.55 {mu}m vertically, the measured vertical size can be as much as 25% bigger than the real one. Furthermore during the collision the spot size actually decrease, producing an enhancement factor H{sub D} of about 1.25. This would yield to a true luminosity which is 1.6 times that which is estimated from the beam-beam deflection fit.

  20. Investigations of initiation spot size effects

    SciTech Connect

    Clarke, Steven A; Akinci, Adrian A; Leichty, Gary; Schaffer, Timothy; Murphy, Michael J; Munger, Alan; Thomas, Keith A

    2010-01-01

    As explosive components become smaller, a greater understanding of the effect of initiation spot size on detonation becomes increasingly critical. A series of tests of the effect of initiation spot size will be described. A series of DOI (direct optical initiation) detonators with initiation spots sizes from {approx}50 um to 1000um have been tested to determine laser parameters for threshold firing of low density PETN pressings. Results will be compared with theoretical predictions. Outputs of the initiation source (DOI ablation) have been characterized by a suite of diagnostics including PDV and schlieren imaging. Outputs of complete detonators have been characterized using PDV, streak, and/or schlieren imaging. At present, we have not found the expected change in the threshold energy to spot size relationship for DOI type detonators found in similar earlier for projectiles, slappers and EBWs. New detonators designs (Type C) are currently being tested that will allow the determination of the threshold for spot sizes from 250 um to 105um, where we hope to see change in the threshold vs. spot size relationship. Also, one test of an extremely small diameter spot size (50um) has resulted in preliminary NoGo only results even at energy densities as much as 8 times the energy density of the threshold results presented here. This gives preliminary evidence that 50um spot may be beyond the critical initiation diameter. The constant threshold energy to spot size relationship in the data to date does however still give some insight into the initiation mechanism of DOI detonators. If the DOI initiation mechanism were a 1D mechanism similar to a slapper or a flyer impact, the expected inflection point in the graph would have been between 300um and 500um diameter spot size, within the range of the data presented here. The lack of that inflection point indicates that the DOI initiation mechanism is more likely a 2D mechanism similar to a sphere or rod projectile. We expect to

  1. Size-assortative mating and effect of maternal body size on the reproductive output of the nassariid Buccinanops globulosus

    NASA Astrophysics Data System (ADS)

    Avaca, María Soledad; Narvarte, Maite; Martín, Pablo

    2012-04-01

    Size- assortative mating is usually present in populations where there is a positive relationship between female size and reproductive output. In this study, we tested for the presence of sexual size dimorphism, size-assortative mating and the effects of female size on reproductive output in a wild population of Buccinanops globulosus, an endemic nassariid of the Southwestern Atlantic Ocean with direct development. The results showed that: 1) females were larger than males, indicating sexual size dimorphism; 2) mate sizes were significantly correlated, indicating a component of size-assortative mating; 3) males of medium and large size classes were paired with larger females than small-sized males; 4) larger females were paired with large males; 5) maternal body size was positively related to some proxies of reproductive success (number of nurse eggs per egg capsule, egg capsular area and total length at hatching). Our results suggest that larger females may be favored as mates over smaller ones owing to their higher investment per offspring and consequently a larger initial juvenile size as juvenile.

  2. First molar size and wear within and among modern hunter-gatherers and agricultural populations.

    PubMed

    Górka, Katarzyna; Romero, Alejandro; Pérez-Pérez, Alejandro

    2015-08-01

    Apart from reflecting modern human dental variation, differences in dental size among populations provide a means for studying continuous evolutionary processes and their mechanisms. Dental wear, on the other hand, has been widely used to infer dietary adaptations and variability among or within diverse ancient human populations. Few such studies have focused on modern foragers and farmers, however, and diverse methods have been used. This research aimed to apply a single, standardized, and systematic quantitative procedure to measure dental size and dentin exposure in order to analyze differences among several hunter-gatherer and agricultural populations from various environments and geographic origins. In particular, we focused on sexual dimorphism and intergroup differences in the upper and lower first molars. Results indicated no sexual dimorphism in molar size and wear within the studied populations. Despite the great ethnographic variation in subsistence strategies among these populations, our findings suggest that differences in sexual division of labor do not affect dietary wear patterns.

  3. Modeling of LEO Orbital Debris Populations in Centimeter and Millimeter Size Regimes

    NASA Technical Reports Server (NTRS)

    Xu, Y.-L.; Hill, . M.; Horstman, M.; Krisko, P. H.; Liou, J.-C.; Matney, M.; Stansbery, E. G.

    2010-01-01

    The building of the NASA Orbital Debris Engineering Model, whether ORDEM2000 or its recently updated version ORDEM2010, uses as its foundation a number of model debris populations, each truncated at a minimum object-size ranging from 10 micron to 1 m. This paper discusses the development of the ORDEM2010 model debris populations in LEO (low Earth orbit), focusing on centimeter (smaller than 10 cm) and millimeter size regimes. Primary data sets used in the statistical derivation of the cm- and mm-size model populations are from the Haystack radar operated in a staring mode. Unlike cataloged objects of sizes greater than approximately 10 cm, ground-based radars monitor smaller-size debris only in a statistical manner instead of tracking every piece. The mono-static Haystack radar can detect debris as small as approximately 5 mm at moderate LEO altitudes. Estimation of millimeter debris populations (for objects smaller than approximately 6 mm) rests largely on Goldstone radar measurements. The bi-static Goldstone radar can detect 2- to 3-mm objects. The modeling of the cm- and mm-debris populations follows the general approach to developing other ORDEM2010-required model populations for various components and types of debris. It relies on appropriate reference populations to provide necessary prior information on the orbital structures and other important characteristics of the debris objects. NASA's LEO-to-GEO Environment Debris (LEGEND) model is capable of furnishing such reference populations in the desired size range. A Bayesian statistical inference process, commonly adopted in ORDEM2010 model-population derivations, changes a priori distribution into a posteriori distribution and thus refines the reference populations in terms of data. This paper describes key elements and major steps in the statistical derivations of the cm- and mm-size debris populations and presents results. Due to lack of data for near 1-mm sizes, the model populations of 1- to 3.16-mm

  4. (Finite) statistical size effects on compressive strength

    PubMed Central

    Weiss, Jérôme; Girard, Lucas; Gimbert, Florent; Amitrano, David; Vandembroucq, Damien

    2014-01-01

    The larger structures are, the lower their mechanical strength. Already discussed by Leonardo da Vinci and Edmé Mariotte several centuries ago, size effects on strength remain of crucial importance in modern engineering for the elaboration of safety regulations in structural design or the extrapolation of laboratory results to geophysical field scales. Under tensile loading, statistical size effects are traditionally modeled with a weakest-link approach. One of its prominent results is a prediction of vanishing strength at large scales that can be quantified in the framework of extreme value statistics. Despite a frequent use outside its range of validity, this approach remains the dominant tool in the field of statistical size effects. Here we focus on compressive failure, which concerns a wide range of geophysical and geotechnical situations. We show on historical and recent experimental data that weakest-link predictions are not obeyed. In particular, the mechanical strength saturates at a nonzero value toward large scales. Accounting explicitly for the elastic interactions between defects during the damage process, we build a formal analogy of compressive failure with the depinning transition of an elastic manifold. This critical transition interpretation naturally entails finite-size scaling laws for the mean strength and its associated variability. Theoretical predictions are in remarkable agreement with measurements reported for various materials such as rocks, ice, coal, or concrete. This formalism, which can also be extended to the flowing instability of granular media under multiaxial compression, has important practical consequences for future design rules. PMID:24733930

  5. Statistical Estimation of Orbital Debris Populations with a Spectrum of Object Size

    NASA Technical Reports Server (NTRS)

    Xu, Y. -l; Horstman, M.; Krisko, P. H.; Liou, J. -C; Matney, M.; Stansbery, E. G.; Stokely, C. L.; Whitlock, D.

    2008-01-01

    Orbital debris is a real concern for the safe operations of satellites. In general, the hazard of debris impact is a function of the size and spatial distributions of the debris populations. To describe and characterize the debris environment as reliably as possible, the current NASA Orbital Debris Engineering Model (ORDEM2000) is being upgraded to a new version based on new and better quality data. The data-driven ORDEM model covers a wide range of object sizes from 10 microns to greater than 1 meter. This paper reviews the statistical process for the estimation of the debris populations in the new ORDEM upgrade, and discusses the representation of large-size (greater than or equal to 1 m and greater than or equal to 10 cm) populations by SSN catalog objects and the validation of the statistical approach. Also, it presents results for the populations with sizes of greater than or equal to 3.3 cm, greater than or equal to 1 cm, greater than or equal to 100 micrometers, and greater than or equal to 10 micrometers. The orbital debris populations used in the new version of ORDEM are inferred from data based upon appropriate reference (or benchmark) populations instead of the binning of the multi-dimensional orbital-element space. This paper describes all of the major steps used in the population-inference procedure for each size-range. Detailed discussions on data analysis, parameter definition, the correlation between parameters and data, and uncertainty assessment are included.

  6. Statistical Estimation of Orbital Debris Populations with a Spectrum of Object Size

    NASA Astrophysics Data System (ADS)

    Xu, Yu-Lin; Horstman, Matthew; Krisko, Paula; Liou, J.-C.; Matney, Mark; Stansbery, Eugene; Stokely, Christopher; Whitlock, David

    Orbital debris is a real concern for the safe operations of satellites. In general, the hazard of debris impact is a function of the size and spatial distributions of the debris populations. To describe and characterize the debris environment as reliably as possible, the current NASA Orbital Debris Engineering Model (ORDEM2000) is being upgraded to a new version based on new and better-quality data. The data-driven ORDEM model covers a wide range of object sizes from 10 microns to greater than 1 meter. This paper reviews the statistical process for the estimation of the debris populations in the new ORDEM upgrade, and discusses the representation of large-size (≥1 m and ≥10 cm) populations by SSN catalog objects and the validation of the statistical approach. Also, it presents results for the populations with sizes of ≥3.3 cm, ≥1 cm, ≥100 µm, and ≥10 µm. The orbital debris populations used in the new version of ORDEM are inferred from data based upon appropriate reference (or benchmark) populations instead of the binning of the multi-dimensional orbital-element space. This paper describes all of the major steps used in the population-inference procedure for each size-range. Detailed discussions on data analysis, parameter definition, the correlation between parameters and data, and uncertainty assessment are included.

  7. Measuring a hidden population: A novel technique to estimate the population size of women with sexual violence-related pregnancies in South Kivu Province, Democratic Republic of Congo.

    PubMed

    Johnston, Lisa G; McLaughlin, Katherine R; Rouhani, Shada A; Bartels, Susan A

    2017-03-01

    Successive sampling (SS)-population size estimation (PSE) is a technique used to estimate the sizes of hidden populations using data collected in respondent-driven sampling (RDS) surveys. We assess past estimations and use new data from an RDS survey to calculate a new PSE. In 2012, 852 adult women in South Kivu Province, Democratic Republic of Congo, who self-identified as survivors of sexual violence, resulting in a pregnancy, since the start of the war (in 1996) were sampled using RDS. We used imputed visibility, enrollment order, and prior estimates for PSE using SS-PSE in RDS Analyst. Prior estimates varied between Congolese local experts and researchers. We calculated the PSE of women with a sexual violence-related pregnancy in South Kivu using researchers' priors to be approximately 17,400. SS-PSE is an effective method for estimating the population sizes of hidden populations, useful for providing evidence for services and resource allocation. SS-PSE is beneficial because population sizes can be calculated after conducting the survey and do not rely on separate studies or additional data (as in network scale-up, multiplier, and capture-recapture methods).

  8. Family reintegration of children and adolescents in foster care in Brazilian municipalities with different population sizes.

    PubMed

    Iannelli, Andrea M; Assis, Simone Gonçalves; Pinto, Liana Wernersbach; Pinto, Liana Wenersbach

    2015-01-01

    The scope of this article is to present and analyze data from Brazilian foster care services for children / adolescents from the perspective of family reintegration. It also seeks to support the implementation of public policies in order to provide effective reintegration in accordance with the differing local contexts. It uses data from 1,157 municipalities that have foster care services. The methodology takes into account the data collection of 2,624 Brazilian centers and 36,929 children and adolescents in care. The growing number of children/adolescents in care is in line with the increase in population size: 8.4 per small city; 60 per large city and 602.4 per metropolis. With respect to care residence in a different municipality there are varying indices: 12.4% in metropolises and 33.6% in small cities, revealing the absence of centers close to family units in the smaller communities. Regarding the activities promoted together with families, it was seen that there are still units that do not perform any activities, which runs contrary to Brazilian law. It is clear that policies for the child/adolescent in foster care centers need to consider the capacity of the municipality in accordance with population size to implement support actions for families to assist in family reintegration.

  9. Epigenetic effects of nano-sized materials.

    PubMed

    Stoccoro, Andrea; Karlsson, Hanna L; Coppedè, Fabio; Migliore, Lucia

    2013-11-08

    The term epigenetics includes several phenomena such as DNA methylation, histone tail modifications, and microRNA mediated mechanisms, which are able to mold the chromatin structure and/or gene expression levels, without altering the primary DNA sequence. Environmental agents can exert epigenetic properties and there is increasing evidence of epigenetic deregulation of gene expression in several human diseases, including cancer, cardiovascular diseases, autism spectrum disorders, autoimmune diseases, and neurodegeneration, among others. Given the widespread use and dispersion in the environment of nano-sized materials, this article summarizes the studies performed so far to evaluate their potential epigenetic properties. Those studies highlight the ability of certain nano-sized compounds to induce an impaired expression of genes involved in DNA methylation reactions leading to global DNA methylation changes, as well as changes of gene specific methylation of tumor suppressor genes, inflammatory genes, and DNA repair genes, all potentially involved in cancer development. Moreover, some nano-sized compounds are able to induce changes in the acetylation and methylation of histone tails, as well as microRNA deregulated expression. We also provided a detailed description of currently available methodologies to evaluate epigenetic modifications. Standard protocols are currently available to evaluate cytotoxic and genotoxic effects of nano-sized materials. By contrast, there are at present no available standard protocols to evaluate the epigenetic potential of any given compound. The currently available methodologies offer different, but often complementary information to characterize potential epigenetic changes induced by exposure to nano-sized compounds. Given the widespread use and dispersion in the environment of nano-sized materials, at present and foreseeable in the near future, and in light of the indication of potential epigenetic properties here reviewed, more

  10. Population Size and Suicide in U.S. Cities: A Static and Dynamic Exploration

    ERIC Educational Resources Information Center

    McCall, Patricia L.; Tittle, Charles R.

    2007-01-01

    The relationship between city population size and suicide rates rarely has been examined directly, though scholars often assume such a relationship exists based on studies of the association between suicide rates and urbanization (percent of the population living in cities) in various social contexts. In an effort to determine the basic…

  11. People of New Mexico: Size, Growth and Hispanic Population from the 1980 Census. Research Report 482.

    ERIC Educational Resources Information Center

    Williams, James D.

    New Mexico, while small, is a state of great diversity in terms of size, growth, and Hispanic concentration of population. Data from the 1980 census indicate New Mexico is the 37th largest state with slightly more than 1.3 million persons and is ninth among the states in percentage of population growth. Growth comes from two demographic sources:…

  12. Changes in size and trends of North American sea duck populations associated with North Pacific oceanic regime shifts

    USGS Publications Warehouse

    Flint, Paul L.

    2013-01-01

    Broad-scale multi-species declines in populations of North American sea ducks for unknown reasons is cause for management concern. Oceanic regime shifts have been associated with rapid changes in ecosystem structure of the North Pacific and Bering Sea. However, relatively little is known about potential effects of these changes in oceanic conditions on marine bird populations at broad scales. I examined changes in North American breeding populations of sea ducks from 1957 to 2011 in relation to potential oceanic regime shifts in the North Pacific in 1977, 1989, and 1998. There was strong support for population-level effects of regime shifts in 1977 and 1989, but little support for an effect of the 1998 shift. The continental-level effects of these regime shifts differed across species groups and time. Based on patterns of sea duck population dynamics associated with regime shifts, it is unclear if the mechanism of change relates to survival or reproduction. Results of this analysis support the hypothesis that population size and trends of North American sea ducks are strongly influenced by oceanic conditions. The perceived population declines appear to have halted >20 years ago, and populations have been relatively stable or increasing since that time. Given these results, we should reasonably expect dramatic changes in sea duck population status and trends with future oceanic regime shifts.

  13. Isolation Distance, Inflorescence Sampling, and Population Size: Maintaining Genetic Diversity in the U.S. Temperate Grass Germplasm Collection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    During the regeneration of cross-pollinating accessions, genetic contamination from foreign pollen and reduction of the effective population size can be a hindrance to maintaining the genetic diversity in the temperate grass collection at the Western Regional Plant Introduction Station (WRPIS). The...

  14. Effects of macromolecular crowding on nuclear size.

    PubMed

    Rosania, G R; Swanson, J A

    1995-05-01

    The concentration of macromolecules inside cells is high, and the resultant crowding of cytoplasm can be expected to affect many interactions involving macromolecular assemblies. Here, we have examined the effect of solute size and concentration on nuclear volume in saponin-permeabilized macrophages. Nuclei swelled in the presence of small solutes and shrank reversibly in the presence of larger permeant solutes. Remarkably, the smallest solutes capable of shrinking the nucleus were not excluded by the pores in the nuclear envelope. Indeed, nuclei shrank in the presence of such solutes even after the nuclear envelope had been sheared mechanically or permeabilized with detergent. Nuclei extracted with 1% Triton X-100 shrank in the presence of very high concentrations of small solute molecules (30% w/v) as well as in lower concentrations of larger solutes. Consistent with a macromolecular crowding effect, changes in nuclear volume were dependent on solute size and not simply dependent on the colligative properties of solutes or the exclusion of solutes by the nuclear envelope. Solute size-dependent changes in nuclear volume were independent of the chemical nature of the solutes and of the activity of the ions in the buffer. Together, these observations indicate that high concentrations of macromolecules such as those found inside cells can influence the size of the nucleus by directly affecting nuclear structure.

  15. Slow-fast stochastic diffusion dynamics and quasi-stationarity for diploid populations with varying size.

    PubMed

    Coron, Camille

    2016-01-01

    We are interested in the long-time behavior of a diploid population with sexual reproduction and randomly varying population size, characterized by its genotype composition at one bi-allelic locus. The population is modeled by a 3-dimensional birth-and-death process with competition, weak cooperation and Mendelian reproduction. This stochastic process is indexed by a scaling parameter K that goes to infinity, following a large population assumption. When the individual birth and natural death rates are of order K, the sequence of stochastic processes indexed by K converges toward a new slow-fast dynamics with variable population size. We indeed prove the convergence toward 0 of a fast variable giving the deviation of the population from quasi Hardy-Weinberg equilibrium, while the sequence of slow variables giving the respective numbers of occurrences of each allele converges toward a 2-dimensional diffusion process that reaches (0,0) almost surely in finite time. The population size and the proportion of a given allele converge toward a Wright-Fisher diffusion with stochastically varying population size and diploid selection. We insist on differences between haploid and diploid populations due to population size stochastic variability. Using a non trivial change of variables, we study the absorption of this diffusion and its long time behavior conditioned on non-extinction. In particular we prove that this diffusion starting from any non-trivial state and conditioned on not hitting (0,0) admits a unique quasi-stationary distribution. We give numerical approximations of this quasi-stationary behavior in three biologically relevant cases: neutrality, overdominance, and separate niches.

  16. Factors influencing the effect size distribution of adaptive substitutions

    PubMed Central

    Oakley, Christopher G.; Gould, Billie A.; Schemske, Douglas W.

    2016-01-01

    The distribution of effect sizes of adaptive substitutions has been central to evolutionary biology since the modern synthesis. Early theory proposed that because large-effect mutations have negative pleiotropic consequences, only small-effect mutations contribute to adaptation. More recent theory suggested instead that large-effect mutations could be favoured when populations are far from their adaptive peak. Here we suggest that the distributions of effect sizes are expected to differ among study systems, reflecting the wide variation in evolutionary forces and ecological conditions experienced in nature. These include selection, mutation, genetic drift, gene flow, and other factors such as the degree of pleiotropy, the distance to the phenotypic optimum, whether the optimum is stable or moving, and whether new mutation or standing genetic variation provides the source of adaptive alleles. Our goal is to review how these factors might affect the distribution of effect sizes and to identify new research directions. Until more theory and empirical work is available, we feel that it is premature to make broad generalizations about the effect size distribution of adaptive substitutions important in nature. PMID:27053750

  17. Empirically Based Criteria for Determining Meaningful Effect Size.

    ERIC Educational Resources Information Center

    Barnette, J. Jackson; McLean, James E.

    The purpose of this study was to determine: (1) the extent to which effect sizes vary by chance; (2) the proportion of standardized effect sizes that achieve or exceed commonly used criteria for small, medium, and large effect sizes; (3) whether standardized effect sizes are random or systematic across numbers of groups and sample sizes; and (4)…

  18. Using pedigree reconstruction to estimate population size: genotypes are more than individually unique marks

    PubMed Central

    Creel, Scott; Rosenblatt, Elias

    2013-01-01

    Estimates of population size are critical for conservation and management, but accurate estimates are difficult to obtain for many species. Noninvasive genetic methods are increasingly used to estimate population size, particularly in elusive species such as large carnivores, which are difficult to count by most other methods. In most such studies, genotypes are treated simply as unique individual identifiers. Here, we develop a new estimator of population size based on pedigree reconstruction. The estimator accounts for individuals that were directly sampled, individuals that were not sampled but whose genotype could be inferred by pedigree reconstruction, and individuals that were not detected by either of these methods. Monte Carlo simulations show that the population estimate is unbiased and precise if sampling is of sufficient intensity and duration. Simulations also identified sampling conditions that can cause the method to overestimate or underestimate true population size; we present and discuss methods to correct these potential biases. The method detected 2–21% more individuals than were directly sampled across a broad range of simulated sampling schemes. Genotypes are more than unique identifiers, and the information about relationships in a set of genotypes can improve estimates of population size. PMID:23762516

  19. Factors determining the average body size of geographically separated Arctodiaptomus salinus (Daday, 1885) populations

    PubMed Central

    Anufriieva, Elena V.; Shadrin, Nickolai V.

    2014-01-01

    Arctodiaptomus salinus inhabits water bodies across Eurasia and North Africa. Based on our own data and that from the literature, we analyzed the influences of several factors on the intra- and inter-population variability of this species. A strong negative linear correlation between temperature and average body size in the Crimean and African populations was found, in which the parameters might be influenced by salinity. Meanwhile, asignificant negative correlation between female body size and the altitude of habitats was found by comparing body size in populations from different regions. Individuals from environments with highly varying abiotic parameters, e.g. temporary reservoirs, had a larger body size than individuals from permanent water bodies. The changes in average body mass in populations were at 11.4 times, whereas, those in individual metabolic activities were at 6.2 times. Moreover, two size groups of A. salinus in the Crimean and the Siberian lakes were observed. The ratio of female length to male length fluctuatedbetween 1.02 and 1.30. The average size of A. salinus in populations and its variations were determined by both genetic and environmental factors. However, the paritiesof these factors were unequal in either spatial or temporal scales. PMID:24668656

  20. Size segregation in the Brazil nut effect

    NASA Astrophysics Data System (ADS)

    Soterroni, Aline C.; Ramos, Fernando M.

    2013-10-01

    Granular materials are ubiquitous in nature and in our daily lives, and used in many industrial processes. Depending on the physical conditions that they are subjected, granular materials may present unusual behavior, combining properties of solids, liquids or gases, and displaying interesting and diversified phenomena. In this work we numerically simulated a granular system in order to investigate the phenomena of size segregation in the Brazil Nut Effect. Our simulations indicate that the phenomenon of size segregation results from the combined effect of two different mechanisms: buoyancy and convection. Increasing the vibration amplitude, the behavior of the system becomes less periodic and more turbulent, with evidence of deterministic chaos in the dynamics of the large particle.

  1. State-space modeling of population sizes and trends in Nihoa Finch and Millerbird

    USGS Publications Warehouse

    Gorresen, P. Marcos; Brinck, Kevin W.; Camp, Richard J.; Farmer, Chris; Plentovich, Sheldon M.; Banko, Paul C.

    2016-01-01

    Both of the 2 passerines endemic to Nihoa Island, Hawai‘i, USA—the Nihoa Millerbird (Acrocephalus familiaris kingi) and Nihoa Finch (Telespiza ultima)—are listed as endangered by federal and state agencies. Their abundances have been estimated by irregularly implemented fixed-width strip-transect sampling from 1967 to 2012, from which area-based extrapolation of the raw counts produced highly variable abundance estimates for both species. To evaluate an alternative survey method and improve abundance estimates, we conducted variable-distance point-transect sampling between 2010 and 2014. We compared our results to those obtained from strip-transect samples. In addition, we applied state-space models to derive improved estimates of population size and trends from the legacy time series of strip-transect counts. Both species were fairly evenly distributed across Nihoa and occurred in all or nearly all available habitat. Population trends for Nihoa Millerbird were inconclusive because of high within-year variance. Trends for Nihoa Finch were positive, particularly since the early 1990s. Distance-based analysis of point-transect counts produced mean estimates of abundance similar to those from strip-transects but was generally more precise. However, both survey methods produced biologically unrealistic variability between years. State-space modeling of the long-term time series of abundances obtained from strip-transect counts effectively reduced uncertainty in both within- and between-year estimates of population size, and allowed short-term changes in abundance trajectories to be smoothed into a long-term trend.

  2. Targeted agri-environment schemes significantly improve the population size of common farmland bumblebee species.

    PubMed

    Wood, Thomas J; Holland, John M; Hughes, William O H; Goulson, Dave

    2015-04-01

    Changes in agricultural practice across Europe and North America have been associated with range contractions and local extinction of bumblebees (Bombus spp.). A number of agri-environment schemes have been implemented to halt and reverse these declines, predominantly revolving around the provision of additional forage plants. Although it has been demonstrated that these schemes can attract substantial numbers of foraging bumblebees, it remains unclear to what extent they actually increase bumblebee populations. We used standardized transect walks and molecular techniques to compare the size of bumblebee populations between Higher Level Stewardship (HLS) farms implementing pollinator-friendly schemes and Entry Level Stewardship (ELS) control farms. Bumblebee abundance on the transect walks was significantly higher on HLS farms than ELS farms. Molecular analysis suggested maximum foraging ranges of 566 m for Bombus hortorum, 714 m for B. lapidarius, 363 m for B. pascuorum and 799 m for B. terrestris. Substantial differences in maximum foraging range were found within bumblebee species between farm types. Accounting for foraging range differences, B. hortorum (47 vs 13 nests/km(2) ) and B. lapidarius (45 vs 22 nests/km(2) ) were found to nest at significantly greater densities on HLS farms than ELS farms. There were no significant differences between farm type for B. terrestris (88 vs 38 nests/km(2) ) and B. pascuorum (32 vs 39 nests/km(2) ). Across all bumblebee species, HLS management had a significantly positive effect on bumblebee nest density. These results show that targeted agri-environment schemes that increase the availability of suitable forage can significantly increase the size of wild bumblebee populations.

  3. Estimating the size of key populations at higher risk of HIV infection: a summary of experiences and lessons presented during a technical meeting on size estimation among key populations in Asian countries

    PubMed Central

    Calleja, Jesus Maria Garcia; Zhao, Jinkou; Reddy, Amala; Seguy, Nicole

    2014-01-01

    Problem Size estimates of key populations at higher risk of HIV exposure are recognized as critical for understanding the trajectory of the HIV epidemic and planning and monitoring an effective response, especially for countries with concentrated and low epidemics such as those in Asia. Context To help countries estimate population sizes of key populations, global guidelines were updated in 2011 to reflect new technical developments and recent field experiences in applying these methods. Action In September 2013, a meeting of programme managers and experts experienced with population size estimates (PSE) for key populations was held for 13 Asian countries. This article summarizes the key results presented, shares practical lessons learnt and reviews the methodological approaches from implementing PSE in 13 countries. Lessons learnt It is important to build capacity to collect, analyse and use PSE data; establish a technical review group; and implement a transparent, well documented process. Countries should adapt global PSE guidelines and maintain operational definitions that are more relevant and useable for country programmes. Development of methods for non-venue-based key populations requires more investment and collaborative efforts between countries and among partners. PMID:25320676

  4. Simulation of Micron-Sized Debris Populations in Low Earth Orbit

    NASA Astrophysics Data System (ADS)

    Xu, Yu-Lin; Matney, Mark; Liou, J.-C.; Hyde, James; Prior, Thomas G.

    The update of ORDEM2000, the NASA Orbital Debris Engineering Model, to its new version -ORDEM2010, is nearly complete. As a part of the ORDEM upgrade, this paper addresses the simulation of micro-debris (greater than 10 µm and smaller than 1 mm in size) populations in low Earth orbit. The principal data used in the modeling of the micron-sized debris popu-lations are in-situ hypervelocity impact records, accumulated in post-flight damage surveys on the space-exposed surfaces of returned spacecrafts. The development of the micro-debris model populations follows the general approach to deriving other ORDEM2010-required input popu-lations for various components and types of debris. This paper describes the key elements and major steps in the statistical inference of the ORDEM2010 micro-debris populations. A crucial step is the construction of a degradation/ejecta source model to provide prior information on the micron-sized objects (such as orbital and object-size distributions). Another critical step is to link model populations with data, which is rather involved. It demands detailed information on area-time/directionality for all the space-exposed elements of a shuttle orbiter and damage laws, which relate impact damage with the physical properties of a projectile and impact con-ditions such as impact angle and velocity. Also needed are model-predicted debris fluxes as a function of object size and impact velocity from all possible directions. In spite of the very limited quantity of the available shuttle impact data, the population-derivation process is satis-factorily stable. Final modeling results obtained from shuttle window and radiator impact data are reasonably convergent and consistent, especially for the debris populations with object-size thresholds at 10 and 100 µm.

  5. Simulation of Micron-Sized Debris Populations in Low Earth Orbit

    NASA Technical Reports Server (NTRS)

    Xu, Y.-L.; Hyde, J. L.; Prior, T.; Matney, Mark

    2010-01-01

    The update of ORDEM2000, the NASA Orbital Debris Engineering Model, to its new version ORDEM2010, is nearly complete. As a part of the ORDEM upgrade, this paper addresses the simulation of micro-debris (greater than 10 m and smaller than 1 mm in size) populations in low Earth orbit. The principal data used in the modeling of the micron-sized debris populations are in-situ hypervelocity impact records, accumulated in post-flight damage surveys on the space-exposed surfaces of returned spacecrafts. The development of the micro-debris model populations follows the general approach to deriving other ORDEM2010-required input populations for various components and types of debris. This paper describes the key elements and major steps in the statistical inference of the ORDEM2010 micro-debris populations. A crucial step is the construction of a degradation/ejecta source model to provide prior information on the micron-sized objects (such as orbital and object-size distributions). Another critical step is to link model populations with data, which is rather involved. It demands detailed information on area-time/directionality for all the space-exposed elements of a shuttle orbiter and damage laws, which relate impact damage with the physical properties of a projectile and impact conditions such as impact angle and velocity. Also needed are model-predicted debris fluxes as a function of object size and impact velocity from all possible directions. In spite of the very limited quantity of the available shuttle impact data, the population-derivation process is satisfactorily stable. Final modeling results obtained from shuttle window and radiator impact data are reasonably convergent and consistent, especially for the debris populations with object-size thresholds at 10 and 100 m.

  6. Simulation of Micron-Sized Debris Populations in Low Earth Orbit

    NASA Technical Reports Server (NTRS)

    Xu, Y.-L.; Matney, M.; Liou, J.-C.; Hyde, J. L.; Prior, T. G.

    2010-01-01

    The update of ORDEM2000, the NASA Orbital Debris Engineering Model, to its new version . ORDEM2010, is nearly complete. As a part of the ORDEM upgrade, this paper addresses the simulation of micro-debris (greater than 10 micron and smaller than 1 mm in size) populations in low Earth orbit. The principal data used in the modeling of the micron-sized debris populations are in-situ hypervelocity impact records, accumulated in post-flight damage surveys on the space-exposed surfaces of returned spacecrafts. The development of the micro-debris model populations follows the general approach to deriving other ORDEM2010-required input populations for various components and types of debris. This paper describes the key elements and major steps in the statistical inference of the ORDEM2010 micro-debris populations. A crucial step is the construction of a degradation/ejecta source model to provide prior information on the micron-sized objects (such as orbital and object-size distributions). Another critical step is to link model populations with data, which is rather involved. It demands detailed information on area-time/directionality for all the space-exposed elements of a shuttle orbiter and damage laws, which relate impact damage with the physical properties of a projectile and impact conditions such as impact angle and velocity. Also needed are model-predicted debris fluxes as a function of object size and impact velocity from all possible directions. In spite of the very limited quantity of the available shuttle impact data, the population-derivation process is satisfactorily stable. Final modeling results obtained from shuttle window and radiator impact data are reasonably convergent and consistent, especially for the debris populations with object-size thresholds at 10 and 100 micron.

  7. Estimating Effects of Species Interactions on Populations of Endangered Species.

    PubMed

    Roth, Tobias; Bühler, Christoph; Amrhein, Valentin

    2016-04-01

    Global change causes community composition to change considerably through time, with ever-new combinations of interacting species. To study the consequences of newly established species interactions, one available source of data could be observational surveys from biodiversity monitoring. However, approaches using observational data would need to account for niche differences between species and for imperfect detection of individuals. To estimate population sizes of interacting species, we extended N-mixture models that were developed to estimate true population sizes in single species. Simulations revealed that our model is able to disentangle direct effects of dominant on subordinate species from indirect effects of dominant species on detection probability of subordinate species. For illustration, we applied our model to data from a Swiss amphibian monitoring program and showed that sizes of expanding water frog populations were negatively related to population sizes of endangered yellow-bellied toads and common midwife toads and partly of natterjack toads. Unlike other studies that analyzed presence and absence of species, our model suggests that the spread of water frogs in Central Europe is one of the reasons for the decline of endangered toad species. Thus, studying population impacts of dominant species on population sizes of endangered species using data from biodiversity monitoring programs should help to inform conservation policy and to decide whether competing species should be subject to population management.

  8. Socio-Economic Instability and the Scaling of Energy Use with Population Size.

    PubMed

    DeLong, John P; Burger, Oskar

    2015-01-01

    The size of the human population is relevant to the development of a sustainable world, yet the forces setting growth or declines in the human population are poorly understood. Generally, population growth rates depend on whether new individuals compete for the same energy (leading to Malthusian or density-dependent growth) or help to generate new energy (leading to exponential and super-exponential growth). It has been hypothesized that exponential and super-exponential growth in humans has resulted from carrying capacity, which is in part determined by energy availability, keeping pace with or exceeding the rate of population growth. We evaluated the relationship between energy use and population size for countries with long records of both and the world as a whole to assess whether energy yields are consistent with the idea of an increasing carrying capacity. We find that on average energy use has indeed kept pace with population size over long time periods. We also show, however, that the energy-population scaling exponent plummets during, and its temporal variability increases preceding, periods of social, political, technological, and environmental change. We suggest that efforts to increase the reliability of future energy yields may be essential for stabilizing both population growth and the global socio-economic system.

  9. Estimating the Size of Populations at High Risk for HIV Using Respondent-Driven Sampling Data

    PubMed Central

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

    2015-01-01

    Summary The study of hard-to-reach populations presents significant challenges. Typically, a sampling frame is not available, and population members are difficult to identify or recruit from broader sampling frames. This is especially true of populations at high risk for HIV/AIDS. Respondent-driven sampling (RDS) is often used in such settings with the primary goal of estimating the prevalence of infection. In such populations, the number of people at risk for infection and the number of people infected are of fundamental importance. This article presents a case-study of the estimation of the size of the hard-to-reach population based on data collected through RDS. We study two populations of female sex workers and men-who-have-sex-with-men in El Salvador. The approach is Bayesian and we consider different forms of prior information, including using the UNAIDS population size guidelines for this region. We show that the method is able to quantify the amount of information on population size available in RDS samples. As separate validation, we compare our results to those estimated by extrapolating from a capture–recapture study of El Salvadorian cities. The results of our case-study are largely comparable to those of the capture–recapture study when they differ from the UNAIDS guidelines. Our method is widely applicable to data from RDS studies and we provide a software package to facilitate this. PMID:25585794

  10. Socio-Economic Instability and the Scaling of Energy Use with Population Size

    PubMed Central

    DeLong, John P.; Burger, Oskar

    2015-01-01

    The size of the human population is relevant to the development of a sustainable world, yet the forces setting growth or declines in the human population are poorly understood. Generally, population growth rates depend on whether new individuals compete for the same energy (leading to Malthusian or density-dependent growth) or help to generate new energy (leading to exponential and super-exponential growth). It has been hypothesized that exponential and super-exponential growth in humans has resulted from carrying capacity, which is in part determined by energy availability, keeping pace with or exceeding the rate of population growth. We evaluated the relationship between energy use and population size for countries with long records of both and the world as a whole to assess whether energy yields are consistent with the idea of an increasing carrying capacity. We find that on average energy use has indeed kept pace with population size over long time periods. We also show, however, that the energy-population scaling exponent plummets during, and its temporal variability increases preceding, periods of social, political, technological, and environmental change. We suggest that efforts to increase the reliability of future energy yields may be essential for stabilizing both population growth and the global socio-economic system. PMID:26091499

  11. The Relationship between Sample Sizes and Effect Sizes in Systematic Reviews in Education

    ERIC Educational Resources Information Center

    Slavin, Robert; Smith, Dewi

    2009-01-01

    Research in fields other than education has found that studies with small sample sizes tend to have larger effect sizes than those with large samples. This article examines the relationship between sample size and effect size in education. It analyzes data from 185 studies of elementary and secondary mathematics programs that met the standards of…

  12. Predicting the size of the progeny mapping population required to positionally clone a gene.

    PubMed

    Dinka, Stephen J; Campbell, Matthew A; Demers, Tyler; Raizada, Manish N

    2007-08-01

    A key frustration during positional gene cloning (map-based cloning) is that the size of the progeny mapping population is difficult to predict, because the meiotic recombination frequency varies along chromosomes. We describe a detailed methodology to improve this prediction using rice (Oryza sativa L.) as a model system. We derived and/or validated, then fine-tuned, equations that estimate the mapping population size by comparing these theoretical estimates to 41 successful positional cloning attempts. We then used each validated equation to test whether neighborhood meiotic recombination frequencies extracted from a reference RFLP map can help researchers predict the mapping population size. We developed a meiotic recombination frequency map (MRFM) for approximately 1400 marker intervals in rice and anchored each published allele onto an interval on this map. We show that neighborhood recombination frequencies (R-map, >280-kb segments) extracted from the MRFM, in conjunction with the validated formulas, better predicted the mapping population size than the genome-wide average recombination frequency (R-avg), with improved results whether the recombination frequency was calculated as genes/cM or kb/cM. Our results offer a detailed road map for better predicting mapping population size in diverse eukaryotes, but useful predictions will require robust recombination frequency maps based on sampling more progeny.

  13. Embryonic IGF2 Expression Is Not Associated with Offspring Size among Populations of a Placental Fish

    PubMed Central

    Schrader, Matthew; Travis, Joseph

    2012-01-01

    In organisms that provision young between fertilization and birth, mothers and their developing embryos are expected to be in conflict over embryonic growth. In mammalian embryos, the expression of Insulin-like growth factor II (IGF2) plays a key role in maternal-fetal interactions and is thought to be a focus of maternal-fetal conflict. Recent studies have suggested that IGF2 is also a focus of maternal-fetal conflict in placental fish in the family Poeciliidae. However, whether the expression of IGF2 influences offspring size, the trait over which mothers and embryos are likely to be in conflict, has not been assessed in a poeciliid. We tested whether embryonic IGF2 expression varied among four populations of a placental poeciliid that display large and consistent differences in offspring size at birth. We found that IGF2 expression varied significantly among embryonic stages with expression being 50% higher in early stage embryos than late stage embryos. There were no significant differences among populations in IGF2 expression; small differences in expression between population pairs with different offspring sizes were comparable in magnitude to those between population pairs with the same offspring sizes. Our results indicate that variation in IGF2 transcript abundance does not contribute to differences in offspring size among H. formosa populations. PMID:23029026

  14. Novel estimates of Aedes aegypti (Diptera: Culicidae) population size and adult survival based on Wolbachia releases.

    PubMed

    Ritchie, Scott A; Montgomery, Brian L; Hoffmann, Ary A

    2013-05-01

    The size of Aedes aegypti (L.) mosquito populations and adult survival rates have proven difficult to estimate because of a lack of consistent quantitative measures to equate sampling methods, such as adult trapping, to actual population size. However, such estimates are critical for devising control methods and for modeling the transmission of dengue and other infectious agents carried by this species. Here we take advantage of recent releases of Wolbachia-infected Ae. aegypti coupled with the results of ongoing monitoring to estimate the size of adult Ae. aegypti populations around Cairns in far north Queensland, Australia. Based on the association between released adults infected with Wolbachia and data from Biogents Sentinel traps, we show that data from two locations are consistent with population estimates of approximately 5-10 females per house and daily survival rates of 0.7-0.9 for the released Wolbachia-infected females. Moreover, we estimate that networks of Biogents Sentinel traps at a density of one per 15 houses capture around 5-10% of the adult population per week, and provide a rapid estimate of the absolute population size of Ae. aegypti. These data are discussed with respect to release rates and monitoring in future Wolbachia releases and also the levels of suppression required to reduce dengue transmission.

  15. Population Variation Reveals Independent Selection toward Small Body Size in Chinese Debao Pony

    PubMed Central

    Kader, Adiljan; Li, Yan; Dong, Kunzhe; Irwin, David M.; Zhao, Qianjun; He, Xiaohong; Liu, Jianfeng; Pu, Yabin; Gorkhali, Neena Amatya; Liu, Xuexue; Jiang, Lin; Li, Xiangchen; Guan, Weijun; Zhang, Yaping; Wu, Dong-Dong; Ma, Yuehui

    2016-01-01

    Body size, one of the most important quantitative traits under evolutionary scrutiny, varies considerably among species and among populations within species. Revealing the genetic basis underlying this variation is very important, particularly in humans where there is a close relationship with diseases and in domestic animals as the selective patterns are associated with improvements in production traits. The Debao pony is a horse breed with small body size that is unique to China; however, it is unknown whether the size-related candidate genes identified in Western breeds also account for the small body size of the Debao pony. Here, we compared individual horses from the Debao population with other two Chinese horse populations using single nucleotide polymorphisms (SNPs) identified with the Equine SNP 65 Bead Chip. The previously reported size-related candidate gene HMGA2 showed a significant signature for selection, consistent with its role observed in human populations. More interestingly, we found a candidate gene TBX3, which had not been observed in previous studies on horse body size that displayed the highest differentiation and most significant association, and thus likely is the dominating factor for the small stature of the Debao pony. Further comparison between the Debao pony and other breeds of horses from around the world demonstrated that TBX3 was selected independently in the Debao pony, suggesting that there were multiple origins of small stature in the horse. PMID:26637467

  16. Floral display size, conspecific density and florivory affect fruit set in natural populations of Phlox hirsuta, an endangered species

    PubMed Central

    Ruane, Lauren G.; Rotzin, Andrew T.; Congleton, Philip H.

    2014-01-01

    Background and Aims Natural variation in fruit and seed set may be explained by factors that affect the composition of pollen grains on stigmas. Self-incompatible species require compatible outcross pollen grains to produce seeds. The siring success of outcross pollen grains, however, can be hindered if self (or other incompatible) pollen grains co-occur on stigmas. This study identifies factors that determine fruit set in Phlox hirsuta, a self-sterile endangered species that is prone to self-pollination, and its associated fitness costs. Methods Multiple linear regressions were used to identify factors that explain variation in percentage fruit set within three of the five known populations of this endangered species. Florivorous beetle density, petal colour, floral display size, local conspecific density and pre-dispersal seed predation were quantified and their effects on the ability of flowers to produce fruits were assessed. Key Results In all three populations, percentage fruit set decreased as florivorous beetle density increased and as floral display size increased. The effect of floral display size on fruit set, however, often depended on the density of nearby conspecific plants. High local conspecific densities offset – even reversed – the negative effects of floral display size on percentage fruit set. Seed predation by mammals decreased fruit set in one population. Conclusions The results indicate that seed production in P. hirsuta can be maximized by selectively augmenting populations in areas containing isolated large plants, by reducing the population sizes of florivorous beetles and by excluding mammals that consume unripe fruits. PMID:24557879

  17. Size effects in lithium ion batteries

    NASA Astrophysics Data System (ADS)

    Hu-Rong, Yao; Ya-Xia, Yin; Yu-Gao, Guo

    2016-01-01

    Size-related properties of novel lithium battery materials, arising from kinetics, thermodynamics, and newly discovered lithium storage mechanisms, are reviewed. Complementary experimental and computational investigations of the use of the size effects to modify electrodes and electrolytes for lithium ion batteries are enumerated and discussed together. Size differences in the materials in lithium ion batteries lead to a variety of exciting phenomena. Smaller-particle materials with highly connective interfaces and reduced diffusion paths exhibit higher rate performance than the corresponding bulk materials. The thermodynamics is also changed by the higher surface energy of smaller particles, affecting, for example, secondary surface reactions, lattice parameter, voltage, and the phase transformation mechanism. Newly discovered lithium storage mechanisms that result in superior storage capacity are also briefly highlighted. Project supported by the National Natural Science Foundation of China (Grant Nos. 51225204 and 21303222), the Shandong Taishan Scholarship, China, the Ministry of Science and Technology, China (Grant No. 2012CB932900), and the Strategic Priority Research Program of the Chinese Academy of Sciences (Grant No. XDA09010000).

  18. Population size estimation in Yellowstone wolves with error-prone noninvasive microsatellite genotypes.

    PubMed

    Creel, Scott; Spong, Goran; Sands, Jennifer L; Rotella, Jay; Zeigle, Janet; Joe, Lawrence; Murphy, Kerry M; Smith, Douglas

    2003-07-01

    Determining population sizes can be difficult, but is essential for conservation. By counting distinct microsatellite genotypes, DNA from noninvasive samples (hair, faeces) allows estimation of population size. Problems arise because genotypes from noninvasive samples are error-prone, but genotyping errors can be reduced by multiple polymerase chain reaction (PCR). For faecal genotypes from wolves in Yellowstone National Park, error rates varied substantially among samples, often above the 'worst-case threshold' suggested by simulation. Consequently, a substantial proportion of multilocus genotypes held one or more errors, despite multiple PCR. These genotyping errors created several genotypes per individual and caused overestimation (up to 5.5-fold) of population size. We propose a 'matching approach' to eliminate this overestimation bias.

  19. A fitness trade-off between seasons causes multigenerational cycles in phenotype and population size

    PubMed Central

    Betini, Gustavo S; McAdam, Andrew G; Griswold, Cortland K; Norris, D Ryan

    2017-01-01

    Although seasonality is widespread and can cause fluctuations in the intensity and direction of natural selection, we have little information about the consequences of seasonal fitness trade-offs for population dynamics. Here we exposed populations of Drosophila melanogaster to repeated seasonal changes in resources across 58 generations and used experimental and mathematical approaches to investigate how viability selection on body size in the non-breeding season could affect demography. We show that opposing seasonal episodes of natural selection on body size interacted with both direct and delayed density dependence to cause populations to undergo predictable multigenerational density cycles. Our results provide evidence that seasonality can set the conditions for life-history trade-offs and density dependence, which can, in turn, interact to cause multigenerational population cycles. DOI: http://dx.doi.org/10.7554/eLife.18770.001 PMID:28164780

  20. Nautilus at Risk – Estimating Population Size and Demography of Nautilus pompilius

    PubMed Central

    Dunstan, Andrew; Bradshaw, Corey J. A.; Marshall, Justin

    2011-01-01

    The low fecundity, late maturity, long gestation and long life span of Nautilus suggest that this species is vulnerable to over-exploitation. Demand from the ornamental shell trade has contributed to their rapid decline in localized populations. More data from wild populations are needed to design management plans which ensure Nautilus persistence. We used a variety of techniques including capture-mark-recapture, baited remote underwater video systems, ultrasonic telemetry and remotely operated vehicles to estimate population size, growth rates, distribution and demographic characteristics of an unexploited Nautilus pompilius population at Osprey Reef (Coral Sea, Australia). We estimated a small and dispersed population of between 844 and 4467 individuals (14.6–77.4 km−2) dominated by males (83∶17 male∶female) and comprised of few juveniles (<10%).These results provide the first Nautilid population and density estimates which are essential elements for long-term management of populations via sustainable catch models. Results from baited remote underwater video systems provide confidence for their more widespread use to assess efficiently the size and density of exploited and unexploited Nautilus populations worldwide. PMID:21347360

  1. Estimating the Sizes of Populations At Risk of HIV Infection From Multiple Data Sources Using a Bayesian Hierarchical Model.

    PubMed

    Bao, Le; Raftery, Adrian E; Reddy, Amala

    2015-04-01

    In most countries in the world outside of sub-Saharan Africa, HIV is largely concentrated in sub-populations whose behavior puts them at higher risk of contracting and transmitting HIV, such as people who inject drugs, sex workers and men who have sex with men. Estimating the size of these sub-populations is important for assessing overall HIV prevalence and designing effective interventions. We present a Bayesian hierarchical model for estimating the sizes of local and national HIV key affected populations. The model incorporates multiple commonly used data sources including mapping data, surveys, interventions, capture-recapture data, estimates or guesstimates from organizations, and expert opinion. The proposed model is used to estimate the numbers of people who inject drugs in Bangladesh.

  2. Improving size estimates of open animal populations by incorporating information on age

    USGS Publications Warehouse

    Manly, Bryan F.J.; McDonald, Trent L.; Amstrup, Steven C.; Regehr, Eric V.

    2003-01-01

    Around the world, a great deal of effort is expended each year to estimate the sizes of wild animal populations. Unfortunately, population size has proven to be one of the most intractable parameters to estimate. The capture-recapture estimation models most commonly used (of the Jolly-Seber type) are complicated and require numerous, sometimes questionable, assumptions. The derived estimates usually have large variances and lack consistency over time. In capture–recapture studies of long-lived animals, the ages of captured animals can often be determined with great accuracy and relative ease. We show how to incorporate age information into size estimates for open populations, where the size changes through births, deaths, immigration, and emigration. The proposed method allows more precise estimates of population size than the usual models, and it can provide these estimates from two sample occasions rather than the three usually required. Moreover, this method does not require specialized programs for capture-recapture data; researchers can derive their estimates using the logistic regression module in any standard statistical package.

  3. Determining proportions of lunar crater populations by fitting crater size distribution

    NASA Astrophysics Data System (ADS)

    Wang, Nan; Zhou, Ji-Lin

    2016-12-01

    We determine the proportions of two mixed crater populations distinguishable by size distributions on the Moon. A “multiple power-law” model is built to formulate crater size distribution N(D) ∝ D-α whose slope α varies with crater diameter D. This model is then used to fit size distributions of lunar highland craters and Class 1 craters. The former is characterized by α = 1.17 ± 0.04, 1.88 ± 0.07, 3.17 ± 0.10 and 1.40 ± 0.15 for D ranges ˜ 10 - 49, 49 - 120, 120 - 251 and ˜ 251 - 2500 km, while the latter has a single slope α = 1.96 ± 0.14 for about 10 - 100 km. They are considered as Population 1 and 2 crater size distributions, whose sum is then fitted to the global size distribution of lunar craters with D between 10 and 100 km. Estimated crater densities of Population 1 and 2 are 44 × 10-5 and 5 × 10-5 km-2 respectively, leading to the proportion of the latter being 10%. This result underlines the need for more thoroughly investigating Population 1 craters and their related impactors, the primordial main-belt asteroids, which dominated the late heavy bombardment.

  4. Estimation of the size of a closed population when capture probabilities vary among animals

    USGS Publications Warehouse

    Burnham, K.P.; Overton, W.S.

    1978-01-01

    A model which allows capture probabilities to vary by individuals is introduced for multiple recapture studies n closed populations. The set of individual capture probabilities is modelled as a random sample from an arbitrary probability distribution over the unit interval. We show that the capture frequencies are a sufficient statistic. A nonparametric estimator of population size is developed based on the generalized jackknife; this estimator is found to be a linear combination of the capture frequencies. Finally, tests of underlying assumptions are presented.

  5. Effect Size, Statistical Power and Sample Size Requirements for the Bootstrap Likelihood Ratio Test in Latent Class Analysis.

    PubMed

    Dziak, John J; Lanza, Stephanie T; Tan, Xianming

    2014-01-01

    Selecting the number of different classes which will be assumed to exist in the population is an important step in latent class analysis (LCA). The bootstrap likelihood ratio test (BLRT) provides a data-driven way to evaluate the relative adequacy of a (K -1)-class model compared to a K-class model. However, very little is known about how to predict the power or the required sample size for the BLRT in LCA. Based on extensive Monte Carlo simulations, we provide practical effect size measures and power curves which can be used to predict power for the BLRT in LCA given a proposed sample size and a set of hypothesized population parameters. Estimated power curves and tables provide guidance for researchers wishing to size a study to have sufficient power to detect hypothesized underlying latent classes.

  6. Effect Size, Statistical Power and Sample Size Requirements for the Bootstrap Likelihood Ratio Test in Latent Class Analysis

    PubMed Central

    Dziak, John J.; Lanza, Stephanie T.; Tan, Xianming

    2014-01-01

    Selecting the number of different classes which will be assumed to exist in the population is an important step in latent class analysis (LCA). The bootstrap likelihood ratio test (BLRT) provides a data-driven way to evaluate the relative adequacy of a (K −1)-class model compared to a K-class model. However, very little is known about how to predict the power or the required sample size for the BLRT in LCA. Based on extensive Monte Carlo simulations, we provide practical effect size measures and power curves which can be used to predict power for the BLRT in LCA given a proposed sample size and a set of hypothesized population parameters. Estimated power curves and tables provide guidance for researchers wishing to size a study to have sufficient power to detect hypothesized underlying latent classes. PMID:25328371

  7. Impact of the 2010 Deepwater Horizon oil spill on population size and genetic structure of horse flies in Louisiana marshes.

    PubMed

    Husseneder, Claudia; Donaldson, Jennifer R; Foil, Lane D

    2016-01-12

    The greenhead horse fly, Tabanus nigrovittatus Macquart, is frequently found in coastal marshes of the Eastern United States. The greenhead horse fly larvae are top predators in the marsh and thus vulnerable to changes in the environment, and the adults potentially are attracted to polarized surfaces like oil. Therefore, horse fly populations could serve as bioindicators of marsh health and toxic effects of oil intrusion. In this study, we describe the impact of the April 2010 Deep Water Horizon oil spill in the Gulf of Mexico on tabanid population abundance and genetics as well as mating structure. Horse fly populations were sampled biweekly from oiled and unaffected locations immediately after the oil spill in June 2010 until October 2011. Horse fly abundance estimates showed severe crashes of tabanid populations in oiled areas. Microsatellite genotyping of six pristine and seven oiled populations at ten polymorphic loci detected genetic bottlenecks in six of the oiled populations in association with fewer breeding parents, reduced effective population size, lower number of family clusters and fewer migrants among populations. This is the first study assessing the impact of oil contamination at the level of a top arthropod predator of the invertebrate community in salt marshes.

  8. Impact of the 2010 Deepwater Horizon oil spill on population size and genetic structure of horse flies in Louisiana marshes

    PubMed Central

    Husseneder, Claudia; Donaldson, Jennifer R.; Foil, Lane D.

    2016-01-01

    The greenhead horse fly, Tabanus nigrovittatus Macquart, is frequently found in coastal marshes of the Eastern United States. The greenhead horse fly larvae are top predators in the marsh and thus vulnerable to changes in the environment, and the adults potentially are attracted to polarized surfaces like oil. Therefore, horse fly populations could serve as bioindicators of marsh health and toxic effects of oil intrusion. In this study, we describe the impact of the April 2010 Deep Water Horizon oil spill in the Gulf of Mexico on tabanid population abundance and genetics as well as mating structure. Horse fly populations were sampled biweekly from oiled and unaffected locations immediately after the oil spill in June 2010 until October 2011. Horse fly abundance estimates showed severe crashes of tabanid populations in oiled areas. Microsatellite genotyping of six pristine and seven oiled populations at ten polymorphic loci detected genetic bottlenecks in six of the oiled populations in association with fewer breeding parents, reduced effective population size, lower number of family clusters and fewer migrants among populations. This is the first study assessing the impact of oil contamination at the level of a top arthropod predator of the invertebrate community in salt marshes. PMID:26755069

  9. Impact of the 2010 Deepwater Horizon oil spill on population size and genetic structure of horse flies in Louisiana marshes

    NASA Astrophysics Data System (ADS)

    Husseneder, Claudia; Donaldson, Jennifer R.; Foil, Lane D.

    2016-01-01

    The greenhead horse fly, Tabanus nigrovittatus Macquart, is frequently found in coastal marshes of the Eastern United States. The greenhead horse fly larvae are top predators in the marsh and thus vulnerable to changes in the environment, and the adults potentially are attracted to polarized surfaces like oil. Therefore, horse fly populations could serve as bioindicators of marsh health and toxic effects of oil intrusion. In this study, we describe the impact of the April 2010 Deep Water Horizon oil spill in the Gulf of Mexico on tabanid population abundance and genetics as well as mating structure. Horse fly populations were sampled biweekly from oiled and unaffected locations immediately after the oil spill in June 2010 until October 2011. Horse fly abundance estimates showed severe crashes of tabanid populations in oiled areas. Microsatellite genotyping of six pristine and seven oiled populations at ten polymorphic loci detected genetic bottlenecks in six of the oiled populations in association with fewer breeding parents, reduced effective population size, lower number of family clusters and fewer migrants among populations. This is the first study assessing the impact of oil contamination at the level of a top arthropod predator of the invertebrate community in salt marshes.

  10. Size effects in thermal conduction by phonons

    NASA Astrophysics Data System (ADS)

    Allen, Philip B.

    2014-08-01

    Heat transport in nanoscale systems is both hard to measure microscopically, and hard to interpret. Ballistic and diffusive heat flow coexist, adding confusion. This paper looks at a very simple case: a nanoscale crystal repeated periodically. This is a popular model for simulation of bulk heat transport using classical molecular dynamics (MD), and is related to transient thermal grating experiments. Nanoscale effects are seen in perhaps their simplest form. The model is solved by an extension of standard quasiparticle gas theory of bulk solids. Both structure and heat flow are constrained by periodic boundary conditions. Diffusive transport is fully included, while ballistic transport by phonons of a long mean free path is diminished in a specific way. Heat current J (x) and temperature gradient ∇T (x') have a nonlocal relationship, via κ (x-x'), over a distance |x-x'| determined by phonon mean free paths. In MD modeling of bulk conductivity, finite computer resources limit system size. Long mean free paths, comparable to the scale of heating and cooling, cause undesired finite-size effects that have to be removed by extrapolation. The present model allows this extrapolation to be quantified. Calculations based on the Peierls-Boltzmann equation, using a generalized Debye model, show that extrapolation involves fractional powers of 1/L. It is also argued that heating and cooling should be distributed sinusoidally [ė∝cos(2πx/L)] to improve convergence of numerics.

  11. The Population Size of the Lesser Bandicoot (Bandicota bengalensis) in Three Markets in Penang, Malaysia

    PubMed Central

    Khairuddin, Nurul Liyana; Raghazli, Razlina; Sah, Shahrul Anuar Mohd; Shafie, Nur Juliani; Azman, Nur Munira

    2011-01-01

    A study of the population size of Bandicota bengalensis rats in three markets in Penang was conducted from April 2004 through May 2005. Taman Tun Sardon Market (TTS), Batu Lanchang Market (BTLG) and Bayan Lepas Market (BYNLP) were surveyed. Six sampling sessions were conducted in each market for four consecutive nights per session. The total captures of B. bengalensis in TTS, BTLG and BYNLP were 92%, 73% and 89% respectively. The total population of B. bengalensis in TTS was estimated as 265.4 (with a 95% confidence interval of 180.9–424.2). The total population at BTLG was estimated as 69.9 (with a 95% confidence interval of 35.5–148.9). At BYNLP, the total population was estimated as 134.7 (with a 95% confidence interval of 77.8–278.4). In general, adult male rats were captured most frequently at each site (55.19%), followed by adult females (31.69%), juvenile males (9.84%) and juvenile females (3.27%). The results showed that the number of rats captured at each site differed significantly according to sex ratio and maturity (χ2 = 121.45, df = 3, p<0.01). Our results suggest that the population sizes found by the study may not represent the actual population size in each market owing to the low numbers of rats recaptured. This finding might have resulted from the variety of foods available in the markets. PMID:24575219

  12. Minimum sample sizes for population genomics: an empirical study from an Amazonian plant species.

    PubMed

    Nazareno, Alison G; Bemmels, Jordan B; Dick, Christopher W; Lohmann, Lúcia G

    2017-01-12

    High-throughput DNA sequencing facilitates the analysis of large portions of the genome in nonmodel organisms, ensuring high accuracy of population genetic parameters. However, empirical studies evaluating the appropriate sample size for these kinds of studies are still scarce. In this study, we use double-digest restriction-associated DNA sequencing (ddRADseq) to recover thousands of single nucleotide polymorphisms (SNPs) for two physically isolated populations of Amphirrhox longifolia (Violaceae), a nonmodel plant species for which no reference genome is available. We used resampling techniques to construct simulated populations with a random subset of individuals and SNPs to determine how many individuals and biallelic markers should be sampled for accurate estimates of intra- and interpopulation genetic diversity. We identified 3646 and 4900 polymorphic SNPs for the two populations of A. longifolia, respectively. Our simulations show that, overall, a sample size greater than eight individuals has little impact on estimates of genetic diversity within A. longifolia populations, when 1000 SNPs or higher are used. Our results also show that even at a very small sample size (i.e. two individuals), accurate estimates of FST can be obtained with a large number of SNPs (≥1500). These results highlight the potential of high-throughput genomic sequencing approaches to address questions related to evolutionary biology in nonmodel organisms. Furthermore, our findings also provide insights into the optimization of sampling strategies in the era of population genomics.

  13. Developing accurate survey methods for estimating population sizes and trends of the critically endangered Nihoa Millerbird and Nihoa Finch.

    USGS Publications Warehouse

    Gorresen, P. Marcos; Camp, Richard J.; Brinck, Kevin W.; Farmer, Chris

    2012-01-01

    Point-transect surveys indicated that millerbirds were more abundant than shown by the striptransect method, and were estimated at 802 birds in 2010 (95%CI = 652 – 964) and 704 birds in 2011 (95%CI = 579 – 837). Point-transect surveys yielded population estimates with improved precision which will permit trends to be detected in shorter time periods and with greater statistical power than is available from strip-transect survey methods. Mean finch population estimates and associated uncertainty were not markedly different among the three survey methods, but the performance of models used to estimate density and population size are expected to improve as the data from additional surveys are incorporated. Using the pointtransect survey, the mean finch population size was estimated at 2,917 birds in 2010 (95%CI = 2,037 – 3,965) and 2,461 birds in 2011 (95%CI = 1,682 – 3,348). Preliminary testing of the line-transect method in 2011 showed that it would not generate sufficient detections to effectively model bird density, and consequently, relatively precise population size estimates. Both species were fairly evenly distributed across Nihoa and appear to occur in all or nearly all available habitat. The time expended and area traversed by observers was similar among survey methods; however, point-transect surveys do not require that observers walk a straight transect line, thereby allowing them to avoid culturally or biologically sensitive areas and minimize the adverse effects of recurrent travel to any particular area. In general, pointtransect surveys detect more birds than strip-survey methods, thereby improving precision and resulting population size and trend estimation. The method is also better suited for the steep and uneven terrain of Nihoa

  14. Information Conversion, Effective Samples, and Parameter Size

    PubMed Central

    Lin, Xiaodong; Pittman, Jennifer; Clarke, Bertrand

    2008-01-01

    Consider the relative entropy between a posterior density for a parameter given a sample and a second posterior density for the same parameter, based on a different model and a different data set. Then the relative entropy can be minimized over the second sample to get a virtual sample that would make the second posterior as close as possible to the first in an informational sense. If the first posterior is based on a dependent dataset and the second posterior uses an independence model, the effective inferential power of the dependent sample is transferred into the independent sample by the optimization. Examples of this optimization are presented for models with nuisance parameters, finite mixture models, and models for correlated data. Our approach is also used to choose the effective parameter size in a Bayesian hierarchical model. PMID:19079764

  15. Interactions between size-structured predator and prey populations: Experimental test and model comparison

    SciTech Connect

    Rice, J.A.; Crowder, L.B. ); Rose, K.A. )

    1993-05-01

    Because predation mortality is often size-dependent, the survival and size structure of prey populations may vary substantially depending on the size structure of the predator assemblage. We tested this hypothesis in a replicated pond experiment in which a bimodal size distribution of young-of-year spot Leiostomus xanthurus was exposed to two sizes of southern flounder Paralichthys lethostigma, each predator size-group present alone or together, at densities providing equal predation pressure. After 3 weeks, we examined cohort survival and size distributions of remaining spot. In the non-predator controls, spot size-frequency distributions were essentially unchanged, and survival of the large- and small-spot cohorts was similar. However, the size distribution of survivors, and the relative survival of large- and small-spot cohorts, differed markedly with the size structure of the predator assemblage. In the presence of small southern flounders, the large-spot cohort survived 4 times better than the small-spot cohort. In the large-flounder-only treatment, small spot survived 2.4 times better than large spot. When both large and small southern flounders were present, large spot had a net advantage, exceeding small spot survival by 2.4 times. We developed an individual-based model of the flounder-spot size-dependent predation interaction based on data from independent laboratory observations on size-based prey profit-ability, and used it to simulate the results of our experimental treatments. Model predictions of spot survival and size distributions agreed well with the pond experimental results when encounter rates were assumed to scale with spot size and density and with southern flounder density. 37 refs., 5 figs., 2 tabs.

  16. Publication Bias in Psychology: A Diagnosis Based on the Correlation between Effect Size and Sample Size

    PubMed Central

    Kühberger, Anton; Fritz, Astrid; Scherndl, Thomas

    2014-01-01

    Background The p value obtained from a significance test provides no information about the magnitude or importance of the underlying phenomenon. Therefore, additional reporting of effect size is often recommended. Effect sizes are theoretically independent from sample size. Yet this may not hold true empirically: non-independence could indicate publication bias. Methods We investigate whether effect size is independent from sample size in psychological research. We randomly sampled 1,000 psychological articles from all areas of psychological research. We extracted p values, effect sizes, and sample sizes of all empirical papers, and calculated the correlation between effect size and sample size, and investigated the distribution of p values. Results We found a negative correlation of r = −.45 [95% CI: −.53; −.35] between effect size and sample size. In addition, we found an inordinately high number of p values just passing the boundary of significance. Additional data showed that neither implicit nor explicit power analysis could account for this pattern of findings. Conclusion The negative correlation between effect size and samples size, and the biased distribution of p values indicate pervasive publication bias in the entire field of psychology. PMID:25192357

  17. Methods used to estimate the size of the owned cat and dog population: a systematic review

    PubMed Central

    2013-01-01

    Background There are a number of different methods that can be used when estimating the size of the owned cat and dog population in a region, leading to varying population estimates. The aim of this study was to conduct a systematic review to evaluate the methods that have been used for estimating the sizes of owned cat and dog populations and to assess the biases associated with those methods. A comprehensive, systematic search of seven electronic bibliographic databases and the Google search engine was carried out using a range of different search terms for cats, dogs and population. The inclusion criteria were that the studies had involved owned or pet domestic dogs and/or cats, provided an estimate of the size of the owned dog or cat population, collected raw data on dog and cat ownership, and analysed primary data. Data relating to study methodology were extracted and assessed for biases. Results Seven papers were included in the final analysis. Collection methods used to select participants in the included studies were: mailed surveys using a commercial list of contacts, door to door surveys, random digit dialled telephone surveys, and randomised telephone surveys using a commercial list of numbers. Analytical and statistical methods used to estimate the pet population size were: mean number of dogs/cats per household multiplied by the number of households in an area, human density multiplied by number of dogs per human, and calculations using predictors of pet ownership. Conclusion The main biases of the studies included selection bias, non-response bias, measurement bias and biases associated with length of sampling time. Careful design and planning of studies is a necessity before executing a study to estimate pet populations. PMID:23777563

  18. Density-Dependent Effects on Group Size Are Sex-Specific in a Gregarious Ungulate

    PubMed Central

    Vander Wal, Eric; van Beest, Floris M.; Brook, Ryan K.

    2013-01-01

    Density dependence can have marked effects on social behaviors such as group size. We tested whether changes in population density of a large herbivore (elk, Cervus canadensis) affected sex-specific group size and whether the response was density- or frequency-dependent. We quantified the probability and strength of changes in group sizes and dispersion as population density changed for each sex. We used group size data from a population of elk in Manitoba, Canada, that was experimentally reduced from 1.20 to 0.67 elk/km2 between 2002 and 2009. Our results indicated that functional responses of group size to population density are sex-specific. Females showed a positive density-dependent response in group size at population densities ≥0.70 elk/km2 and we found evidence for a minimum group size at population density ≤0.70 elk/km2. Changes in male group size were also density-dependent; however, the strength of the relationship was lower than for females. Density dependence in male group size was predominantly a result of fusion of solitary males into larger groups, rather than fusion among existing groups. Our study revealed that density affects group size of a large herbivore differently between males and females, which has important implications for the benefits e.g., alleviating predation risk, and costs of social behaviors e.g., competition for resources and mates, and intra-specific pathogen transmission. PMID:23326502

  19. Density-dependent effects on group size are sex-specific in a gregarious ungulate.

    PubMed

    Vander Wal, Eric; van Beest, Floris M; Brook, Ryan K

    2013-01-01

    Density dependence can have marked effects on social behaviors such as group size. We tested whether changes in population density of a large herbivore (elk, Cervus canadensis) affected sex-specific group size and whether the response was density- or frequency-dependent. We quantified the probability and strength of changes in group sizes and dispersion as population density changed for each sex. We used group size data from a population of elk in Manitoba, Canada, that was experimentally reduced from 1.20 to 0.67 elk/km(2) between 2002 and 2009. Our results indicated that functional responses of group size to population density are sex-specific. Females showed a positive density-dependent response in group size at population densities ≥0.70 elk/km(2) and we found evidence for a minimum group size at population density ≤0.70 elk/km(2). Changes in male group size were also density-dependent; however, the strength of the relationship was lower than for females. Density dependence in male group size was predominantly a result of fusion of solitary males into larger groups, rather than fusion among existing groups. Our study revealed that density affects group size of a large herbivore differently between males and females, which has important implications for the benefits e.g., alleviating predation risk, and costs of social behaviors e.g., competition for resources and mates, and intra-specific pathogen transmission.

  20. Alpha values as a function of sample size, effect size, and power: accuracy over inference.

    PubMed

    Bradley, M T; Brand, A

    2013-06-01

    Tables of alpha values as a function of sample size, effect size, and desired power were presented. The tables indicated expected alphas for small, medium, and large effect sizes given a variety of sample sizes. It was evident that sample sizes for most psychological studies are adequate for large effect sizes defined at .8. The typical alpha level of .05 and desired power of 90% can be achieved with 70 participants in two groups. It was perhaps doubtful if these ideal levels of alpha and power have generally been achieved for medium effect sizes in actual research, since 170 participants would be required. Small effect sizes have rarely been tested with an adequate number of participants or power. Implications were discussed.

  1. Pollen flow and effects of population structure on selfing rates and female and male reproductive success in fragmented Magnolia stellata populations

    PubMed Central

    2013-01-01

    Background Fragmentation of plant populations may affect mating patterns and female and male reproductive success. To improve understanding of fragmentation effects on plant reproduction, we investigated the pollen flow patterns in six adjacent local populations of Magnolia stellata, an insect-pollinated, threatened tree species in Japan, and assessed effects of maternal plant (genet) size, local genet density, population size and neighboring population size on female reproductive success (seed production rates), and effects of mating distance, paternal genet size, population size and separation of populations on male reproductive success. Results The seed production rate, i.e. the proportion of ovules that successfully turned into seeds, varied between 1.0 and 6.5%, and increased with increasing population size and neighboring population size, and with decreasing maternal genet size and local genet density. The selfing rate varied between 3.6 and 28.9%, and increased with increasing maternal genet size and with declining local genet density. Male reproductive success increased with increasing paternal genet size, and decreased with increasing mating distance and separation of population. Pollen flow between the populations was low (6.1%) and highly leptocurtic. Conclusions Our results indicate that habitat fragmentation, separation and reduced size of populations, affected mating patterns and reproductive success of M. stellata. Local competition for pollinators and plant display size were likely to alter the reproductive success. PMID:23517612

  2. Estimating population size in wastewater-based epidemiology. Valencia metropolitan area as a case study.

    PubMed

    Rico, María; Andrés-Costa, María Jesús; Picó, Yolanda

    2017-02-05

    Wastewater can provide a wealth of epidemiologic data on common drugs consumed and on health and nutritional problems based on the biomarkers excreted into community sewage systems. One of the biggest uncertainties of these studies is the estimation of the number of inhabitants served by the treatment plants. Twelve human urine biomarkers -5-hydroxyindoleacetic acid (5-HIAA), acesulfame, atenolol, caffeine, carbamazepine, codeine, cotinine, creatinine, hydrochlorothiazide (HCTZ), naproxen, salicylic acid (SA) and hydroxycotinine (OHCOT)- were determined by liquid chromatography-tandem mass spectrometry (LC-MS/MS) to estimate population size. The results reveal that populations calculated from cotinine, 5-HIAA and caffeine are commonly in agreement with those calculated by the hydrochemical parameters. Creatinine is too unstable to be applicable. HCTZ, naproxen, codeine, OHCOT and carbamazepine, under or overestimate the population compared to the hydrochemical population estimates but showed constant results through the weekdays. The consumption of cannabis, cocaine, heroin and bufotenine in Valencia was estimated for a week using different population calculations.

  3. METER-SIZED MOONLET POPULATION IN SATURN'S C RING AND CASSINI DIVISION

    SciTech Connect

    Baillie, Kevin; Colwell, Joshua E.; Esposito, Larry W.; Lewis, Mark C.

    2013-06-01

    Stellar occultations observed by the Cassini Ultraviolet Imaging Spectrograph reveal the presence of transparent holes a few meters to a few tens of meters in radial extent in otherwise optically thick regions of the C ring and the Cassini Division. We attribute the holes to gravitational disturbances generated by a population of {approx}10 m boulders in the rings that is intermediate in size between the background ring particle size distribution and the previously observed {approx}100 m propeller moonlets in the A ring. The size distribution of these boulders is described by a shallower power-law than the one that describes the ring particle size distribution. The number and size distribution of these boulders could be explained by limited accretion processes deep within Saturn's Roche zone.

  4. Dynamics of a stochastic tuberculosis model with constant recruitment and varying total population size

    NASA Astrophysics Data System (ADS)

    Liu, Qun; Jiang, Daqing; Shi, Ningzhong; Hayat, Tasawar; Alsaedi, Ahmed

    2017-03-01

    In this paper, we develop a mathematical model for a tuberculosis model with constant recruitment and varying total population size by incorporating stochastic perturbations. By constructing suitable stochastic Lyapunov functions, we establish sufficient conditions for the existence of an ergodic stationary distribution as well as extinction of the disease to the stochastic system.

  5. Age modifies effect of body size on fecundity in Culex quinquefasciatus Say (Diptera: Culicidae).

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Fecundity of mosquitoes can vary with many factors, and can have a strong effect on population growth. This study reports the effects of body size, blood meal size and age on reproductive output of nulliparous Culex quinquefasciatus, a vector of arboviruses and other pathogens. Mated adult female m...

  6. Multiple aspects of plasticity in clutch size vary among populations of a globally distributed songbird.

    PubMed

    Westneat, David F; Bókony, Veronika; Burke, Terry; Chastel, Olivier; Jensen, Henrik; Kvalnes, Thomas; Lendvai, Ádám Z; Liker, András; Mock, Douglas; Schroeder, Julia; Schwagmeyer, P L; Sorci, Gabriele; Stewart, Ian R K

    2014-07-01

    Plasticity in life-history characteristics can influence many ecological and evolutionary phenomena, including how invading organisms cope with novel conditions in new locations or how environmental change affects organisms in native locations. Variation in reaction norm attributes is a critical element to understanding plasticity in life history, yet we know relatively little about the ways in which reaction norms vary within and among populations. We amassed data on clutch size from marked females in eight populations of house sparrows (Passer domesticus) from North America and Europe. We exploited repeated measures of clutch size to assess both the extent of within-individual phenotypic plasticity and among-individual variation and to test alternative hypotheses about the underlying causes of reaction norm shape, particularly the decline in clutch size with date. Across all populations, females of this multibrooded species altered their clutch size with respect to date, attempt order, and the interaction of date and order, producing a reaction norm in multidimensional environmental space. The reaction norm fits that predicted by a model in which optimal clutch size is driven by a decline with date hatched in the ability of offspring to recruit. Our results do not fit those predicted for other proposed causes of a seasonal decline in clutch size. We also found significant differences between populations in response to date and the date by attempt order interaction. We tested the prediction that the relationship with date should be increasingly negative as breeding season becomes shorter but found steeper declines in clutch size with date in populations with longer seasons, contrary to the prediction. Populations also differed in the level of among-individual variation in reaction norm intercept, but we found no evidence of among-individual variation in reaction norm slope. We show that complex reaction norms in life-history characters exhibit within- and among-population

  7. Size-Structured Population Model with Distributed States in The Recruitment: Approximation and Parameter Estimation

    NASA Astrophysics Data System (ADS)

    Li, Xinyu

    We consider a size-structured population model where individuals may be recruited into the population at different sizes. First and second order finite difference schemes are developed to approximate the solution of the model. The convergence of the approximations to a unique weak solution is proved. We then show that as the distribution of the new recruits become concentrated at the smallest size, the weak solution of the distributed states-at-birth model converges to the weak solution of the classical Sinko-Streifer type size-structured model in the weak* topology. Numerical simulations are provided to demonstrate the achievement of the desired accuracy of the two methods for smooth solutions as well as the superior performance of the second-order method in resolving solution-discontinuities. A least-squares method is developed for estimating parameters in a size-structured population model with distributed states-at-birth from field data. The first and second order finite difference schemes for approximating solution of the model are utilized in the least-squares problem. Convergence results for the computed parameters are established. Numerical results demonstrating the efficiency of the technique are provided.

  8. Population size drives industrial Saccharomyces cerevisiae alcoholic fermentation and is under genetic control.

    PubMed

    Albertin, Warren; Marullo, Philippe; Aigle, Michel; Dillmann, Christine; de Vienne, Dominique; Bely, Marina; Sicard, Delphine

    2011-04-01

    Alcoholic fermentation (AF) conducted by Saccharomyces cerevisiae has been exploited for millennia in three important human food processes: beer and wine production and bread leavening. Most of the efforts to understand and improve AF have been made separately for each process, with strains that are supposedly well adapted. In this work, we propose a first comparison of yeast AFs in three synthetic media mimicking the dough/wort/grape must found in baking, brewing, and wine making. The fermentative behaviors of nine food-processing strains were evaluated in these media, at the cellular, populational, and biotechnological levels. A large variation in the measured traits was observed, with medium effects usually being greater than the strain effects. The results suggest that human selection targeted the ability to complete fermentation for wine strains and trehalose content for beer strains. Apart from these features, the food origin of the strains did not significantly affect AF, suggesting that an improvement program for a specific food processing industry could exploit the variability of strains used in other industries. Glucose utilization was analyzed, revealing plastic but also genetic variation in fermentation products and indicating that artificial selection could be used to modify the production of glycerol, acetate, etc. The major result was that the overall maximum CO(2) production rate (V(max)) was not related to the maximum CO(2) production rate per cell. Instead, a highly significant correlation between V(max) and the maximum population size was observed in all three media, indicating that human selection targeted the efficiency of cellular reproduction rather than metabolic efficiency. This result opens the way to new strategies for yeast improvement.

  9. Size effects of latex nanomaterials on lung inflammation in mice

    SciTech Connect

    Inoue, Ken-ichiro Takano, Hirohisa; Yanagisawa, Rie; Koike, Eiko; Shimada, Akinori

    2009-01-01

    Effects of nano-sized materials (nanomaterials) on sensitive population have not been well elucidated. This study examined the effects of pulmonary exposure to (latex) nanomaterials on lung inflammation related to lipopolysaccharide (LPS) or allergen in mice, especially in terms of their size-dependency. In protocol 1, ICR male mice were divided into 8 experimental groups that intratracheally received a single exposure to vehicle, latex nanomaterials (250 {mu}g/animal) with three sizes (25, 50, and 100 nm), LPS (75 {mu}g/animal), or LPS plus latex nanomaterials. In protocol 2, ICR male mice were divided into 8 experimental groups that intratracheally received repeated exposure to vehicle, latex nanomaterials (100 {mu}g/animal), allergen (ovalbumin: OVA; 1 {mu}g/animal), or allergen plus latex nanomaterials. In protocol 1, latex nanomaterials with all sizes exacerbated lung inflammation elicited by LPS, showing an overall trend of amplified lung expressions of proinflammatory cytokines. Furthermore, LPS plus nanomaterials, especially with size less than 50 nm, significantly elevated circulatory levels of fibrinogen, macrophage chemoattractant protein-1, and keratinocyte-derived chemoattractant, and von Willebrand factor as compared with LPS alone. The enhancement tended overall to be greater with the smaller nanomaterials than with the larger ones. In protocol 2, latex nanomaterials with all sizes did not significantly enhance the pathophysiology of allergic asthma, characterized by eosinophilic lung inflammation and Igs production, although latex nanomaterials with less than 50 nm significantly induced/enhanced neutrophilic lung inflammation. These results suggest that latex nanomaterials differentially affect two types of (innate and adaptive immunity-dominant) lung inflammation.

  10. Use of the superpopulation approach to estimate breeding population size: An example in asynchronously breeding birds

    USGS Publications Warehouse

    Williams, K.A.; Frederick, P.C.; Nichols, J.D.

    2011-01-01

    Many populations of animals are fluid in both space and time, making estimation of numbers difficult. Much attention has been devoted to estimation of bias in detection of animals that are present at the time of survey. However, an equally important problem is estimation of population size when all animals are not present on all survey occasions. Here, we showcase use of the superpopulation approach to capture-recapture modeling for estimating populations where group membership is asynchronous, and where considerable overlap in group membership among sampling occasions may occur. We estimate total population size of long-legged wading bird (Great Egret and White Ibis) breeding colonies from aerial observations of individually identifiable nests at various times in the nesting season. Initiation and termination of nests were analogous to entry and departure from a population. Estimates using the superpopulation approach were 47-382% larger than peak aerial counts of the same colonies. Our results indicate that the use of the superpopulation approach to model nesting asynchrony provides a considerably less biased and more efficient estimate of nesting activity than traditional methods. We suggest that this approach may also be used to derive population estimates in a variety of situations where group membership is fluid. ?? 2011 by the Ecological Society of America.

  11. Dispersal, niche breadth and population extinction: colonization ratios predict range size in North American dragonflies.

    PubMed

    McCauley, Shannon J; Davis, Christopher J; Werner, Earl E; Robeson, Michael S

    2014-07-01

    Species' range sizes are shaped by fundamental differences in species' ecological and evolutionary characteristics, and understanding the mechanisms determining range size can shed light on the factors responsible for generating and structuring biological diversity. Moreover, because geographic range size is associated with a species' risk of extinction and their ability to respond to global changes in climate and land use, understanding these mechanisms has important conservation implications. Despite the hypotheses that dispersal behaviour is a strong determinant of species range areas, few data are available to directly compare the relationship between dispersal behaviour and range size. Here, we overcome this limitation by combining data from a multispecies dispersal experiment with additional species-level trait data that are commonly hypothesized to affect range size (e.g. niche breadth, local abundance and body size.). This enables us to examine the relationship between these species-level traits and range size across North America for fifteen dragonfly species. Ten models based on a priori predictions about the relationship between species traits and range size were evaluated and two models were identified as good predictors of species range size. These models indicated that only two species' level traits, dispersal behaviour and niche breadth were strongly related to range size. The evidence from these two models indicated that dragonfly species that disperse more often and further had larger North American ranges. Extinction and colonization dynamics are expected to be a key linkage between dispersal behaviour and range size in dragonflies. To evaluate how extinction and colonization dynamics among dragonflies were related to range size we used an independent data set of extinction and colonization rates for eleven dragonfly species and assessed the relationship between these populations rates and North American range areas for these species. We found a

  12. L1 insertion within SPEF2 gene is associated with increased litter size in the Finnish Yorkshire population.

    PubMed

    Sironen, A; Uimari, P; Iso-Touru, T; Vilkki, J

    2012-04-01

    Immotile, short-tail sperm defect (ISTS) expanded in the Finnish Yorkshire population in the end of 1990s. The causal mutation for this defect is a recent L1 insertion within the SPEF2 gene in chromosome 16. Even though all homozygous boars are eliminated from the population because of infertility, the amount of affected boars increased rapidly until marker-assisted selection against the defect was established. To elucidate the associated effects of the ISTS defect on production traits, we have investigated the association of the L1 insertion and PRLR haplotype with reproduction traits in the Finnish Yorkshire population. Two data sets including 357 sows and 491 AI-boars were genotyped for the presence of the L1 insertion and analysed for association with reproduction traits. A Proc Mixed procedure (SAS Inc) and a software package for analysing multivariate mixed models (DMU) were used to study the effect of polymorphisms on reproduction traits. The L1-insertion within SPEF2 gene was associated with litter size in the first parity. The SPEF2 gene is located adjacent to a candidate gene for litter size in the pig, PRLR. Haplotypes within PRLR exon 10 were analysed in data set of 93 AI-boars for the association with reproduction traits. However, no associations were detected within the analysed data set indicating that PRLR sequence variants are not the causal cause for the identified effect on litter size.

  13. Fish population studies using parasites from the Southeastern Pacific Ocean: considering host population changes and species body size as sources of variability of parasite communities.

    PubMed

    George-Nascimento, Mario; Oliva, Marcelo

    2015-01-01

    Research using parasites in fish population studies in the South Eastern Pacific (SEP) is summarized. There are 27 such studies (snapshots mainly) in single host species sampled at different geographic localities and at somewhat similar times. They have been devoted mainly to economically important species, though others on coastal and intertidal fish or on less- or non-commercial species provide insights on scales of temporal and spatial variation of parasite infracommunities. Later, we assess whether the probability of harbouring parasites depends on the host species body size. Our results indicate that a stronger tool for fish population studies may be developed under regular (long term) scrutiny of parasite communities, especially of small fish host species, due to their larger variability in richness, abundance and total biomass, than in large fish species. Finally, it might also be necessary to consider the effects of fishing on parasite communities as well as the natural oscillations (coupled or not) of host and parasite populations.

  14. Research on Grid Size Suitability of Gridded Population Distribution in Urban Area: A Case Study in Urban Area of Xuanzhou District, China

    PubMed Central

    Dong, Nan; Yang, Xiaohuan; Cai, Hongyan; Xu, Fengjiao

    2017-01-01

    The research on the grid size suitability is important to provide improvement in accuracies of gridded population distribution. It contributes to reveal the actual spatial distribution of population. However, currently little research has been done in this area. Many well-modeled gridded population dataset are basically built at a single grid scale. If the grid cell size is not appropriate, it will result in spatial information loss or data redundancy. Therefore, in order to capture the desired spatial variation of population within the area of interest, it is necessary to conduct research on grid size suitability. This study summarized three expressed levels to analyze grid size suitability, which include location expressed level, numeric information expressed level, and spatial relationship expressed level. This study elaborated the reasons for choosing the five indexes to explore expression suitability. These five indexes are consistency measure, shape index rate, standard deviation of population density, patches diversity index, and the average local variance. The suitable grid size was determined by constructing grid size-indicator value curves and suitable grid size scheme. Results revealed that the three expressed levels on 10m grid scale are satisfying. And the population distribution raster data with 10m grid size provide excellent accuracy without loss. The 10m grid size is recommended as the appropriate scale for generating a high-quality gridded population distribution in our study area. Based on this preliminary study, it indicates the five indexes are coordinated with each other and reasonable and effective to assess grid size suitability. We also suggest choosing these five indexes in three perspectives of expressed level to carry out the research on grid size suitability of gridded population distribution. PMID:28122050

  15. Signaling among neighboring plants and the development of size inequalities in plant populations

    SciTech Connect

    Ballare, C.L. |; Scopel, A.L. |; Jordan, E.T.; Vierstra, R.D.

    1994-10-11

    Transgenic tobacco plants that express an oat phytochrome gene (phyA) under control of the cauliflower mosaic virus (CaMV) 35S promoter and display altered photophysiology were used to test the role of light as a vehicle of information in dominance relationships between neighboring plants. Compared with the isogenic wild type, phyA-overexpressing plants showed dramatically reduced morphological responsivity to changes in the red/far red ratio of the incident light and to the proximity of neighboring plants in spacing experiments. In transgenic canopies an increase in stand density caused the small plants of the population to be rapidly suppressed by their neighbors. In wild-type canopies, plants responded to increased density with large morphological changes, and there appeared to be an inverse relationship between the magnitude of this morphological response and the ranking of the individual plant in the population size hierarchy. In these wild-type populations, size inequality increased only moderately with density within the time frame of the experiments. The results suggest that, in crowded stands, the ability of individual plants to acquire information about their light environment via phytochrome plays a central role in driving architectural changes that, at the population level, delay the development of size differences between neighbors.

  16. DNA evidence for historic population size and past ecosystem impacts of gray whales

    PubMed Central

    Alter, S. Elizabeth; Rynes, Eric; Palumbi, Stephen R.

    2007-01-01

    Ecosystem restoration may require returning threatened populations of ecologically pivotal species to near their former abundances, but it is often difficult to estimate historic population size of species that have been heavily exploited. Eastern Pacific gray whales play a key ecological role in their Arctic feeding grounds and are widely thought to have returned to their prewhaling abundance. Recent mortality spikes might signal that the population has reached long-term carrying capacity, but an alternative is that this decline was due to shifting climatic conditions on Arctic feeding grounds. We used a genetic approach to estimate prewhaling abundance of gray whales and report DNA variability at 10 loci that is typical of a population of ≈76,000–118,000 individuals, approximately three to five times more numerous than today's average census size of 22,000. Coalescent simulations indicate these estimates may include the entire Pacific metapopulation, suggesting that our average measurement of ≈96,000 individuals was probably distributed between the eastern and currently endangered western Pacific populations. These levels of genetic variation suggest the eastern population is at most at 28–56% of its historical abundance and should be considered depleted. If used to inform management, this would halve acceptable human-caused mortality for this population from 417 to 208 per year. Potentially profound ecosystem impacts may have resulted from a decline from 96,000 gray whales to the current population. At previous levels, gray whales may have seasonally resuspended 700 million cubic meters of sediment, as much as 12 Yukon Rivers, and provided food to a million sea birds. PMID:17848511

  17. The Estimation of Active Social Network Size of the Iranian Population

    PubMed Central

    Rastegari, Azam; Haji-Maghsoudi, Saiedeh; Haghdoost, Aliakbar; Shatti, Mohsen; Tarjoman, Termeh; Baneshi, Mohammad Reza

    2013-01-01

    Objectives: The size of active network (C) of Iranian population is a very important parameter to estimate the size of unknown population using Network Scale Up (NSU) technique. However, there is little information about this parameter not only in Iran but also in other countries in Middle East region. Based on these needs, the aim of this paper is to estimate C for the Iranian population. Methods: Based on available national statistics, 23 reference groups, with known population sizes were selected. Using multistage sampling method, 7454 individuals were recruited randomly around the country. We asked from our samples how many people they knew from each of the reference groups. Using NSU formulae, we maximized the goodness of fit of our estimation about the size of the reference groups by fitting the best C. However, the final C was set by excluding some of the reference groups with no added information; these inappropriate groups were selected by two techniques; regression, and ratio based approaches. Results: Applying regression and ratio based approaches the estimated C was 308 and 380 respectively. The Pearson correlation coefficient between the real and estimated size of reference groups (based on our C) in both methods was above 0.95. However, results of ratio based had better performance. We saw that the network of males, singles, younger age groups, and those with higher education was larger than those in other groups. Conclusion: It seems that C in Iran is higher than that in developed countries, possibly because of its social structure. Because of cultural and social similarities in Middle East courtiers, C in other countries also might be higher than that in developed countries. PMID:23777738

  18. Male Kirtland's Warblers' patch-level response to landscape structure during periods of varying population size and habitat amounts

    USGS Publications Warehouse

    Donner, D.M.; Ribic, C.A.; Probst, J.R.

    2009-01-01

    Forest planners must evaluate how spatiotemporal changes in habitat amount and configuration across the landscape as a result of timber management will affect species' persistence. However, there are few long-term programs available for evaluation. We investigated the response of male Kirtland's Warbler (Dendroica kirtlandii) to 26 years of changing patch and landscape structure during a large, 26-year forestry-habitat restoration program within the warbler's primary breeding range. We found that the average density of male Kirtland's Warblers was related to a different combination of patch and landscape attributes depending on the species' regional population level and habitat amounts on the landscape (early succession jack pine (Pinus banksiana) forests; 15-42% habitat cover). Specifically, patch age and habitat regeneration type were important at low male population and total habitat amounts, while patch age and distance to an occupied patch were important at relatively high population and habitat amounts. Patch age and size were more important at increasing population levels and an intermediate amount of habitat. The importance of patch age to average male density during all periods reflects the temporal buildup and decline of male numbers as habitat suitability within the patch changed with succession. Habitat selection (i.e., preference for wildfire-regenerated habitat) and availability may explain the importance of habitat type and patch size during lower population and habitat levels. The relationship between male density and distance when there was the most habitat on the landscape and the male population was large and still increasing may be explained by the widening spatial dispersion of the increasing male population at the regional scale. Because creating or preserving habitat is not a random process, management efforts would benefit from more investigations of managed population responses to changes in spatial structure that occur through habitat gain

  19. Linking individual phenotype to density-dependent population growth: the influence of body size on the population dynamics of malaria vectors.

    PubMed

    Russell, Tanya L; Lwetoijera, Dickson W; Knols, Bart G J; Takken, Willem; Killeen, Gerry F; Ferguson, Heather M

    2011-10-22

    Understanding the endogenous factors that drive the population dynamics of malaria mosquitoes will facilitate more accurate predictions about vector control effectiveness and our ability to destabilize the growth of either low- or high-density insect populations. We assessed whether variation in phenotypic traits predict the dynamics of Anopheles gambiae sensu lato mosquitoes, the most important vectors of human malaria. Anopheles gambiae dynamics were monitored over a six-month period of seasonal growth and decline. The population exhibited density-dependent feedback, with the carrying capacity being modified by rainfall (97% wAIC(c) support). The individual phenotypic expression of the maternal (p = 0.0001) and current (p = 0.040) body size positively influenced population growth. Our field-based evidence uniquely demonstrates that individual fitness can have population-level impacts and, furthermore, can mitigate the impact of exogenous drivers (e.g. rainfall) in species whose reproduction depends upon it. Once frontline interventions have suppressed mosquito densities, attempts to eliminate malaria with supplementary vector control tools may be attenuated by increased population growth and individual fitness.

  20. Linking individual phenotype to density-dependent population growth: the influence of body size on the population dynamics of malaria vectors

    PubMed Central

    Russell, Tanya L.; Lwetoijera, Dickson W.; Knols, Bart G. J.; Takken, Willem; Killeen, Gerry F.; Ferguson, Heather M.

    2011-01-01

    Understanding the endogenous factors that drive the population dynamics of malaria mosquitoes will facilitate more accurate predictions about vector control effectiveness and our ability to destabilize the growth of either low- or high-density insect populations. We assessed whether variation in phenotypic traits predict the dynamics of Anopheles gambiae sensu lato mosquitoes, the most important vectors of