Half of 23 Belgian dog breeds has a compromised genetic diversity, as revealed by genealogical and molecular data analysis.

PubMed

Wijnrocx, K; François, L; Stinckens, A; Janssens, S; Buys, N

2016-10-01

The genetic diversity in 23 dog breeds raised in Belgium was investigated using both genealogical analysis and microsatellite markers. Some of these breeds are native breeds, with only small populations maintained. Pedigree and molecular data, obtained from the Belgian kennel club, were used to calculate the inbreeding coefficients, realised effective population size as well as probabilities of gene origin and average observed heterozygosity. Inbreeding coefficients ranged from 0.8 to 44.7% and realised effective population size varied between 3.2 and 829.1, according to the used method and breed. Mean observed heterozygosity ranged from 0.47 to 0.73. Both pedigree and molecular methods reveal low genetic diversity and presence of bottlenecks, especially in native Belgian breeds with small population sizes. Furthermore, principal component analysis on the set of investigated diversity parameters revealed no groups of breeds that could be identified in which similar breeding strategies could be applied to maintain genetic diversity. © 2016 Blackwell Verlag GmbH.

A general methodology for population analysis

NASA Astrophysics Data System (ADS)

Lazov, Petar; Lazov, Igor

2014-12-01

For a given population with N - current and M - maximum number of entities, modeled by a Birth-Death Process (BDP) with size M+1, we introduce utilization parameter ρ, ratio of the primary birth and death rates in that BDP, which, physically, determines (equilibrium) macrostates of the population, and information parameter ν, which has an interpretation as population information stiffness. The BDP, modeling the population, is in the state n, n=0,1,…,M, if N=n. In presence of these two key metrics, applying continuity law, equilibrium balance equations concerning the probability distribution pn, n=0,1,…,M, of the quantity N, pn=Prob{N=n}, in equilibrium, and conservation law, and relying on the fundamental concepts population information and population entropy, we develop a general methodology for population analysis; thereto, by definition, population entropy is uncertainty, related to the population. In this approach, what is its essential contribution, the population information consists of three basic parts: elastic (Hooke's) or absorption/emission part, synchronization or inelastic part and null part; the first two parts, which determine uniquely the null part (the null part connects them), are the two basic components of the Information Spectrum of the population. Population entropy, as mean value of population information, follows this division of the information. A given population can function in information elastic, antielastic and inelastic regime. In an information linear population, the synchronization part of the information and entropy is absent. The population size, M+1, is the third key metric in this methodology. Namely, right supposing a population with infinite size, the most of the key quantities and results for populations with finite size, emerged in this methodology, vanish.

Effects of Group Size and Lack of Sphericity on the Recovery of Clusters in K-Means Cluster Analysis

ERIC Educational Resources Information Center

de Craen, Saskia; Commandeur, Jacques J. F.; Frank, Laurence E.; Heiser, Willem J.

2006-01-01

K-means cluster analysis is known for its tendency to produce spherical and equally sized clusters. To assess the magnitude of these effects, a simulation study was conducted, in which populations were created with varying departures from sphericity and group sizes. An analysis of the recovery of clusters in the samples taken from these…

Effective population size and genetic structure of a Piute ground squirrel (Spermophilus mollis) population

USGS Publications Warehouse

Antolin, Michael F.; Van Horne, Beatrice; Berger, Michael D.

2001-01-01

Piute ground squirrels (Spermophilus mollis) are distributed continuously in habitat dominated by native shrubs and perennial grasses in the Snake River Birds of Prey National Conservation Area in Idaho, U.S.A. This habitat is being fragmented and replaced by exotic annual plants, changing it to a wildfire-dominated system that provides poor habitat for ground squirrels. To assess potential effects of this fragmentation on ground squirrel populations, we combined an estimate of effective population size (Ne) based upon a demographic study with a population genetic analysis. The study area included three subpopulations separated from each other by 8–13 km. The ratio of effective population size to census number (Ne/N) was 0.57. Combining Ne/N with dispersal distances from a radio-tracking study, we calculated that neighborhood size was 62.2 ha, which included between 204 and 480 individuals. Our population genetic analysis (based on randomly amplified polymorphic DNA (RAPD) and microsatellite markers) showed relatively low levels of genetic differentiation (Qpopulations 0.07–0.10) between subpopulations and no inbreeding within subpopulations (f = 0.0003). These estimates of population subdivision translate into an effective migration rate (Nem) of 2.3–3.3 per year, which represents a high level of gene flow. Invasion by exotics will reduce the overall productivity of the habitat, and will lead to isolation among subpopulations if favorable habitat patches become isolated.

Harbor porpoise Phocoena phocoena strandings on the Dutch coast: No genetic structure, but evidence of inbreeding

NASA Astrophysics Data System (ADS)

van der Plas-Duivesteijn, Suzanne J.; Smit, Femmie J. L.; van Alphen, Jacques J. M.; Kraaijeveld, Ken

2015-03-01

Conservation management in the North Sea is often motivated by the population size of marine mammals, like harbor porpoises Phocoena phocoena. In the Dutch part of the North Sea, sighting and stranding data are used to estimate population sizes, but these data give little insight into genetic structuring of the population. In this study we investigated genetic structure among animals stranded at different locations and times of year. We also tested whether there is a link between stranding and necropsy data, and genetic diversity. We made use of both mitochondrial (mtDNA) and microsatellite DNA analysis of samples from dead stranded porpoises along the Dutch coast during 2007. mtDNA analysis showed 6 variable positions in the control region, defining 3 different haplotypes. mtDNA haplotypes were not randomly distributed along the Dutch coastline. However, microsatellite analysis showed that these mtDNA haplotypes did not represent separate groups on a nuclear level. Furthermore, microsatellite analysis revealed no genotypic differences between seasons, locations or genders. The results of this study indicate that the Dutch population is panmictic. In contrast, heterozygosity levels were low, indicating some level of inbreeding in this population. However, this was not corroborated by other indices of inbreeding. This research provided insight into genetic structuring of stranded porpoises in 2007, but data from multiple years should be included to be able to help estimate population sizes.

Size and shape in Melipona quadrifasciata anthidioides Lepeletier, 1836 (Hymenoptera; Meliponini).

PubMed

Nunes, L A; Passos, G B; Carvalho, C A L; Araújo, E D

2013-11-01

This study aimed to identify differences in wing shape among populations of Melipona quadrifasciata anthidioides obtained in 23 locations in the semi-arid region of Bahia state (Brazil). Analysis of the Procrustes distances among mean wing shapes indicated that population structure did not determine shape variation. Instead, populations were structured geographically according to wing size. The Partial Mantel Test between morphometric (shape and size) distance matrices and altitude, taking geographic distances into account, was used for a more detailed understanding of size and shape determinants. A partial Mantel test between morphometris (shape and size) variation and altitude, taking geographic distances into account, revealed that size (but not shape) is largely influenced by altitude (r = 0.54 p < 0.01). These results indicate greater evolutionary constraints for the shape variation, which must be directly associated with aerodynamic issues in this structure. The size, however, indicates that the bees tend to have larger wings in populations located at higher altitudes.

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 (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. PMID:24147115

Experimental demonstration of a two-phase population extinction hazard

PubMed Central

Drake, John M.; Shapiro, Jeff; Griffen, Blaine D.

2011-01-01

Population extinction is a fundamental biological process with applications to ecology, epidemiology, immunology, conservation biology and genetics. Although a monotonic relationship between initial population size and mean extinction time is predicted by virtually all theoretical models, attempts at empirical demonstration have been equivocal. We suggest that this anomaly is best explained with reference to the transient properties of ensembles of populations. Specifically, we submit that under experimental conditions, many populations escape their initially vulnerable state to reach quasi-stationarity, where effects of initial conditions are erased. Thus, extinction of populations initialized far from quasi-stationarity may be exposed to a two-phase extinction hazard. An empirical prediction of this theory is that the fit Cox proportional hazards regression model for the observed survival time distribution of a group of populations will be shown to violate the proportional hazards assumption early in the experiment, but not at later times. We report results of two experiments with the cladoceran zooplankton Daphnia magna designed to exhibit this phenomenon. In one experiment, habitat size was also varied. Statistical analysis showed that in one of these experiments a transformation occurred so that very early in the experiment there existed a transient phase during which the extinction hazard was primarily owing to the initial population size, and that this was gradually replaced by a more stable quasi-stationary phase. In the second experiment, only habitat size unambiguously displayed an effect. Analysis of data pooled from both experiments suggests that the overall extinction time distribution in this system results from the mixture of extinctions during the initial rapid phase, during which the effects of initial population size can be considerable, and a longer quasi-stationary phase, during which only habitat size has an effect. These are the first results, to our knowledge, of a two-phase population extinction process. PMID:21429907

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

Monarch butterfly population decline in North America: identifying the threatening processes

USGS Publications Warehouse

Thogmartin, Wayne E.; Wiederholt, Ruscena; Oberhauser, Karen; Drum, Ryan G.; Diffendorfer, Jay E.; Altizer, Sonia; Taylor, Orley R.; Pleasants, John M.; Semmens, Darius J.; Semmens, Brice X.; Erickson, Richard A.; Libby, Kaitlin; Lopez-Hoffman, Laura

2017-01-01

The monarch butterfly (Danaus plexippus) population in North America has sharply declined over the last two decades. Despite rising concern over the monarch butterfly's status, no comprehensive study of the factors driving this decline has been conducted. Using partial least-squares regressions and time-series analysis, we investigated climatic and habitat-related factors influencing monarch population size from 1993 to 2014. Potential threats included climatic factors, habitat loss (milkweed and overwinter forest), disease and agricultural insecticide use (neonicotinoids). While climatic factors, principally breeding season temperature, were important determinants of annual variation in abundance, our results indicated strong negative relationships between population size and habitat loss variables, principally glyphosate use, but also weaker negative effects from the loss of overwinter forest and breeding season use of neonicotinoids. Further declines in population size because of glyphosate application are not expected. Thus, if remaining threats to habitat are mitigated we expect climate-induced stochastic variation of the eastern migratory population of monarch butterfly around a relatively stationary population size.

Spectral Study of Measles Epidemics: The Dependence of Spectral Gradient on the Population Size of the Community

NASA Astrophysics Data System (ADS)

Sumi, Ayako; Olsen, Lars Folke; Ohtomo, Norio; Tanaka, Yukio; Sawamura, Sadashi

2003-02-01

We have carried out spectral analysis of measles notifications in several communities in Denmark, UK and USA. The results confirm that each power spectral density (PSD) shows exponential characteristics, which are universally observed in the PSD for time series generated from nonlinear dynamical system. The exponential gradient increases with the population size. For almost all communities, many spectral lines observed in each PSD can be fully assigned to linear combinations of several fundamental periods, suggesting that the measles data are substantially noise-free. The optimum least squares fitting curve calculated using these fundamental periods essentially reproduces an underlying variation of the measles data, and an extension of the curve can be used to predict measles epidemics. For the communities with large population sizes, some PSD patterns obtained from segment time series analysis show a close resemblance to the PSD patterns at the initial stages of a period-doubling bifurcation process for the so-called susceptible/exposed/infectious/recovered (SEIR) model with seasonal forcing. The meaning of the relationship between the exponential gradient and the population size is discussed.

The Ecological Genetics of Introduced Populations of the Giant Toad BUFO MARINUS. II. Effective Population Size

PubMed Central

Easteal, Simon

1985-01-01

The allele frequencies are described at ten polymorphic enzyme loci (of a total of 22 loci sampled) in 15 populations of the neotropical giant toad, Bufo marinus, introduced to Hawaii and Australia in the 1930s. The history of establishment of the ten populations is described and used as a framework for the analysis of allele frequency variances. The variances are used to determine the effective sizes of the populations. The estimates obtained (390 and 346) are reasonably precise, homogeneous between localities and much smaller than estimates of neighborhood size obtained previously using ecological methods. This discrepancy is discussed, and it is concluded that the estimates obtained here using genetic methods are the more reliable. PMID:3922852

Towards a Population Dynamics Theory for Evolutionary Computing: Learning from Biological Population Dynamics in Nature

NASA Astrophysics Data System (ADS)

Ma, Zhanshan (Sam)

In evolutionary computing (EC), population size is one of the critical parameters that a researcher has to deal with. Hence, it was no surprise that the pioneers of EC, such as De Jong (1975) and Holland (1975), had already studied the population sizing from the very beginning of EC. What is perhaps surprising is that more than three decades later, we still largely depend on the experience or ad-hoc trial-and-error approach to set the population size. For example, in a recent monograph, Eiben and Smith (2003) indicated: "In almost all EC applications, the population size is constant and does not change during the evolutionary search." Despite enormous research on this issue in recent years, we still lack a well accepted theory for population sizing. In this paper, I propose to develop a population dynamics theory forEC with the inspiration from the population dynamics theory of biological populations in nature. Essentially, the EC population is considered as a dynamic system over time (generations) and space (search space or fitness landscape), similar to the spatial and temporal dynamics of biological populations in nature. With this conceptual mapping, I propose to 'transplant' the biological population dynamics theory to EC via three steps: (i) experimentally test the feasibility—whether or not emulating natural population dynamics improves the EC performance; (ii) comparatively study the underlying mechanisms—why there are improvements, primarily via statistical modeling analysis; (iii) conduct theoretical analysis with theoretical models such as percolation theory and extended evolutionary game theory that are generally applicable to both EC and natural populations. This article is a summary of a series of studies we have performed to achieve the general goal [27][30]-[32]. In the following, I start with an extremely brief introduction on the theory and models of natural population dynamics (Sections 1 & 2). In Sections 4 to 6, I briefly discuss three categories of population dynamics models: deterministic modeling with Logistic chaos map as an example, stochastic modeling with spatial distribution patterns as an example, as well as survival analysis and extended evolutionary game theory (EEGT) modeling. Sample experiment results with Genetic algorithms (GA) are presented to demonstrate the applications of these models. The proposed EC population dynamics approach also makes survival selection largely unnecessary or much simplified since the individuals are naturally selected (controlled) by the mathematical models for EC population dynamics.

Colonial, more widely distributed and less abundant bird species undergo wider population fluctuations independent of their population trend

PubMed Central

Møller, Anders P.

2017-01-01

Understanding temporal variability in population size is important for conservation biology because wide population fluctuations increase the risk of extinction. Previous studies suggested that certain ecological, demographic, life-history and genetic characteristics of species might be related to the degree of their population fluctuations. We checked whether that was the case in a large sample of 231 European breeding bird species while taking a number of potentially confounding factors such as population trends or similarities among species due to common descent into account. When species-specific characteristics were analysed one by one, the magnitude of population fluctuations was positively related to coloniality, habitat, total breeding range, heterogeneity of breeding distribution and natal dispersal, and negatively related to urbanisation, abundance, relative number of subspecies, parasitism and proportion of polymorphic loci. However, when abundance (population size) was included in the analyses of the other parameters, only coloniality, habitat, total breeding range and abundance remained significantly related to population fluctuations. The analysis including all these predictors simultaneously showed that population size fluctuated more in colonial, less abundant species with larger breeding ranges. Other parameters seemed to be related to population fluctuations only because of their association with abundance or coloniality. The unexpected positive relationship between population fluctuations and total breeding range did not seem to be mediated by abundance. The link between population fluctuations and coloniality suggests a previously unrecognized cost of coloniality. The negative relationship between population size and population fluctuations might be explained by at least three types of non-mutually exclusive stochastic processes: demographic, environmental and genetic stochasticity. Measurement error in population indices, which was unknown, may have contributed to the negative relationship between population size and fluctuations, but apparently only to a minor extent. The association between population size and fluctuations suggests that populations might be stabilized by increasing population size. PMID:28253345

Directions for new developments on statistical design and analysis of small population group trials.

PubMed

Hilgers, Ralf-Dieter; Roes, Kit; Stallard, Nigel

2016-06-14

Most statistical design and analysis methods for clinical trials have been developed and evaluated where at least several hundreds of patients could be recruited. These methods may not be suitable to evaluate therapies if the sample size is unavoidably small, which is usually termed by small populations. The specific sample size cut off, where the standard methods fail, needs to be investigated. In this paper, the authors present their view on new developments for design and analysis of clinical trials in small population groups, where conventional statistical methods may be inappropriate, e.g., because of lack of power or poor adherence to asymptotic approximations due to sample size restrictions. Following the EMA/CHMP guideline on clinical trials in small populations, we consider directions for new developments in the area of statistical methodology for design and analysis of small population clinical trials. We relate the findings to the research activities of three projects, Asterix, IDeAl, and InSPiRe, which have received funding since 2013 within the FP7-HEALTH-2013-INNOVATION-1 framework of the EU. As not all aspects of the wide research area of small population clinical trials can be addressed, we focus on areas where we feel advances are needed and feasible. The general framework of the EMA/CHMP guideline on small population clinical trials stimulates a number of research areas. These serve as the basis for the three projects, Asterix, IDeAl, and InSPiRe, which use various approaches to develop new statistical methodology for design and analysis of small population clinical trials. Small population clinical trials refer to trials with a limited number of patients. Small populations may result form rare diseases or specific subtypes of more common diseases. New statistical methodology needs to be tailored to these specific situations. The main results from the three projects will constitute a useful toolbox for improved design and analysis of small population clinical trials. They address various challenges presented by the EMA/CHMP guideline as well as recent discussions about extrapolation. There is a need for involvement of the patients' perspective in the planning and conduct of small population clinical trials for a successful therapy evaluation.

Dispersal and population state of an endangered island lizard following a conservation translocation.

PubMed

Angeli, Nicole F; Lundgren, Ian F; Pollock, Clayton G; Hillis-Starr, Zandy M; Fitzgerald, Lee A

2018-03-01

Population size is widely used as a unit of ecological analysis, yet to estimate population size requires accounting for observed and latent heterogeneity influencing dispersion of individuals across landscapes. In newly established populations, such as when animals are translocated for conservation, dispersal and availability of resources influence patterns of abundance. We developed a process to estimate population size using N-mixture models and spatial models for newly established and dispersing populations. We used our approach to estimate the population size of critically endangered St. Croix ground lizards (Ameiva polops) five years after translocation of 57 individuals to Buck Island, an offshore island of St. Croix, United States Virgin Islands. Estimates of population size incorporated abiotic variables, dispersal limits, and operative environmental temperature available to the lizards to account for low species detection. Operative environmental temperature and distance from the translocation site were always important in fitting the N-mixture model indicating effects of dispersal and species biology on estimates of population size. We found that the population is increasing its range across the island by 5-10% every six months. We spatially interpolated site-specific abundance from the N-mixture model to the entire island, and we estimated 1,473 (95% CI, 940-1,802) St. Croix ground lizards on Buck Island in 2013 corresponding to survey results. This represents a 26-fold increase since the translocation. We predicted the future dispersal of the lizards to all habitats on Buck Island, with the potential for the population to increase by another five times in the future. Incorporating biologically relevant covariates as explicit parameters in population models can improve predictions of population size and the future spread of species introduced to new localities. © 2018 by the Ecological Society of America.

Genetic models reveal historical patterns of sea lamprey population fluctuations within Lake Champlain

PubMed Central

Azodi, Christina B.; Sheldon, Sallie P.; Trombulak, Stephen C.; Ardren, William R.

2015-01-01

The origin of sea lamprey (Petromyzon marinus) in Lake Champlain has been heavily debated over the past decade. Given the lack of historical documentation, two competing hypotheses have emerged in the literature. First, it has been argued that the relatively recent population size increase and concomitant rise in wounding rates on prey populations are indicative of an invasive population that entered the lake through the Champlain Canal. Second, recent genetic evidence suggests a post-glacial colonization at the end of the Pleistocene, approximately 11,000 years ago. One limitation to resolving the origin of sea lamprey in Lake Champlain is a lack of historical and current measures of population size. In this study, the issue of population size was explicitly addressed using nuclear (nDNA) and mitochondrial DNA (mtDNA) markers to estimate historical demography with genetic models. Haplotype network analysis, mismatch analysis, and summary statistics based on mtDNA noncoding sequences for NCI (479 bp) and NCII (173 bp) all indicate a recent population expansion. Coalescent models based on mtDNA and nDNA identified two potential demographic events: a population decline followed by a very recent population expansion. The decline in effective population size may correlate with land-use and fishing pressure changes post-European settlement, while the recent expansion may be associated with the implementation of the salmonid stocking program in the 1970s. These results are most consistent with the hypothesis that sea lamprey are native to Lake Champlain; however, the credibility intervals around parameter estimates demonstrate that there is uncertainty regarding the magnitude and timing of past demographic events. PMID:26539334

Extreme value statistics analysis of fracture strengths of a sintered silicon nitride failing from pores

NASA Technical Reports Server (NTRS)

Chao, Luen-Yuan; Shetty, Dinesh K.

1992-01-01

Statistical analysis and correlation between pore-size distribution and fracture strength distribution using the theory of extreme-value statistics is presented for a sintered silicon nitride. The pore-size distribution on a polished surface of this material was characterized, using an automatic optical image analyzer. The distribution measured on the two-dimensional plane surface was transformed to a population (volume) distribution, using the Schwartz-Saltykov diameter method. The population pore-size distribution and the distribution of the pore size at the fracture origin were correllated by extreme-value statistics. Fracture strength distribution was then predicted from the extreme-value pore-size distribution, usin a linear elastic fracture mechanics model of annular crack around pore and the fracture toughness of the ceramic. The predicted strength distribution was in good agreement with strength measurements in bending. In particular, the extreme-value statistics analysis explained the nonlinear trend in the linearized Weibull plot of measured strengths without postulating a lower-bound strength.

Fatty Acids Modulate Excitability in Guinea-Pig Hippocampal Slices

DTIC Science & Technology

1991-01-01

141-147. 32. Taube J. S. and Schwartzkroin P . A . (1988) M .- hanisms of long-term potentiation: a current-source density analysis. J. Neurosci. 8, 1645...pyrami- given volley size to elicit a synaptic potential, while dale to record the resultant population postsynaptic poten- stearic acid (100 p M) and...population spike amplitude (0) and population PSP size ( A ) with exposure to 250 p M capric acid in a representative experiment. Synaptic potentials

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 imperiled species.

Comparative Analysis of Genome Diversity in Bullmastiff Dogs

PubMed Central

Mortlock, Sally-Anne; Khatkar, Mehar S.; Williamson, Peter

2016-01-01

Management and preservation of genomic diversity in dog breeds is a major objective for maintaining health. The present study was undertaken to characterise genomic diversity in Bullmastiff dogs using both genealogical and molecular analysis. Genealogical analysis of diversity was conducted using a database consisting of 16,378 Bullmastiff pedigrees from year 1980 to 2013. Additionally, a total of 188 Bullmastiff dogs were genotyped using the 170,000 SNP Illumina CanineHD Beadchip. Genealogical parameters revealed a mean inbreeding coefficient of 0.047; 142 total founders (f); an effective number of founders (fe) of 79; an effective number of ancestors (fa) of 62; and an effective population size of the reference population of 41. Genetic diversity and the degree of genome-wide homogeneity within the breed were also investigated using molecular data. Multiple-locus heterozygosity (MLH) was equal to 0.206; runs of homozygosity (ROH) as proportion of the genome, averaged 16.44%; effective population size was 29.1, with an average inbreeding coefficient of 0.035, all estimated using SNP Data. Fine-scale population structure was analysed using NETVIEW, a population analysis pipeline. Visualisation of the high definition network captured relationships among individuals within and between subpopulations. Effects of unequal founder use, and ancestral inbreeding and selection, were evident. While current levels of Bullmastiff heterozygosity, inbreeding and homozygosity are not unusual, a relatively small effective population size indicates that a breeding strategy to reduce the inbreeding rate may be beneficial. PMID:26824579

Population limitation in a non-cyclic arctic fox population in a changing climate.

PubMed

Pálsson, Snæbjörn; Hersteinsson, Páll; Unnsteinsdóttir, Ester R; Nielsen, Ólafur K

2016-04-01

Arctic foxes Vulpes lagopus (L.) display a sharp 3- to 5-year fluctuation in population size where lemmings are their main prey. In areas devoid of lemmings, such as Iceland, they do not experience short-term fluctuations. This study focusses on the population dynamics of the arctic fox in Iceland and how it is shaped by its main prey populations. Hunting statistics from 1958-2003 show that the population size of the arctic fox was at a maximum in the 1950s, declined to a minimum in the 1970s, and increased steadily until 2003. Analysis of the arctic fox population size and their prey populations suggests that fox numbers were limited by rock ptarmigan numbers during the decline period. The recovery of the arctic fox population was traced mostly to an increase in goose populations, and favourable climatic conditions as reflected by the Subpolar Gyre. These results underscore the flexibility of a generalist predator and its responses to shifting food resources and climate changes.

Optimal exploitation strategies for an animal population in a stochastic serially correlated environment

USGS Publications Warehouse

Anderson, D.R.

1974-01-01

Optimal exploitation strategies were studied for an animal population in a stochastic, serially correlated environment. This is a general case and encompasses a number of important cases as simplifications. Data on the mallard (Anas platyrhynchos) were used to explore the exploitation strategies and test several hypotheses because relatively much is known concerning the life history and general ecology of this species and extensive empirical data are available for analysis. The number of small ponds on the central breeding grounds was used as an index to the state of the environment. Desirable properties of an optimal exploitation strategy were defined. A mathematical model was formulated to provide a synthesis of the existing literature, estimates of parameters developed from an analysis of data, and hypotheses regarding the specific effect of exploitation on total survival. Both the literature and the analysis of data were inconclusive concerning the effect of exploitation on survival. Therefore, alternative hypotheses were formulated: (1) exploitation mortality represents a largely additive form of mortality, or (2 ) exploitation mortality is compensatory with other forms of mortality, at least to some threshold level. Models incorporating these two hypotheses were formulated as stochastic dynamic programming models and optimal exploitation strategies were derived numerically on a digital computer. Optimal exploitation strategies were found to exist under rather general conditions. Direct feedback control was an integral component in the optimal decision-making process. Optimal exploitation was found to be substantially different depending upon the hypothesis regarding the effect of exploitation on the population. Assuming that exploitation is largely an additive force of mortality, optimal exploitation decisions are a convex function of the size of the breeding population and a linear or slightly concave function of the environmental conditions. Optimal exploitation under this hypothesis tends to reduce the variance of the size of the population. Under the hypothesis of compensatory mortality forces, optimal exploitation decisions are approximately linearly related to the size of the breeding population. Environmental variables may be somewhat more important than the size of the breeding population to the production of young mallards. In contrast, the size of the breeding population appears to be more important in the exploitation process than is the state of the environment. The form of the exploitation strategy appears to be relatively insensitive to small changes in the production rate. In general, the relative importance of the size of the breeding population may decrease as fecundity increases. The optimal level of exploitation in year t must be based on the observed size of the population and the state of the environment in year t unless the dynamics of the population, the state of the environment, and the result of the exploitation decisions are completely deterministic. Exploitation based on an average harvest, harvest rate, or designed to maintain a constant breeding population size is inefficient.

A cautionary note on Bayesian estimation of population size by removal sampling with diffuse priors.

PubMed

Bord, Séverine; Bioche, Christèle; Druilhet, Pierre

2018-05-01

We consider the problem of estimating a population size by removal sampling when the sampling rate is unknown. Bayesian methods are now widespread and allow to include prior knowledge in the analysis. However, we show that Bayes estimates based on default improper priors lead to improper posteriors or infinite estimates. Similarly, weakly informative priors give unstable estimators that are sensitive to the choice of hyperparameters. By examining the likelihood, we show that population size estimates can be stabilized by penalizing small values of the sampling rate or large value of the population size. Based on theoretical results and simulation studies, we propose some recommendations on the choice of the prior. Then, we applied our results to real datasets. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

GEO Collisional Risk Assessment Based on Analysis of NASA-WISE Data and Modeling

NASA Astrophysics Data System (ADS)

Howard, S.; Murray-Krezan, J.; Dao, P.; Surka, D.

From December 2009 thru 2011 the NASA Wide-Field Infrared Survey Explorer (WISE) gathered radiometrically exquisite measurements of debris in near Earth orbits, substantially augmenting the current catalog of known debris. The WISE GEO-belt debris population adds approximately 2,000 previously uncataloged objects. This paper describes characterization of the WISE GEO-belt orbital debris population in terms of location, epoch, and size. The WISE GEO-belt debris population characteristics are compared with the publically available U.S. catalog and previous descriptions of the GEO-belt debris population. We found that our results differ from previously published debris distributions, suggesting the need for updates to collision probability models and a better measurement-based understanding of the debris population. Previous studies of collisional rate in GEO invoke the presence of a large number of debris in the regime of sizes too small to track, i.e. not in the catalog, but large enough to cause significant damage and fragmentation in a collision. A common approach is to estimate that population of small debris by assuming that it is dominated by fragments and therefore should follow trends observed in fragmentation events or laboratory fragmentation tests. In other words, the population of debris can be extrapolated from trackable sizes to small sizes using an empirically determined trend of population as a function of size. We use new information suggested by the analysis of WISE IR measurements to propose an updated relationship. Our trend is an improvement because we expect that an IR emissive signature is a more reliable indicator of physical size. Based on the revised relationship, we re-estimate the total collisional rate in the GEO belt with the inclusion of projected uncatalogued debris and applying a conjunction assessment technique. Through modeling, we evaluate the hot spots near the geopotential wells and the effects of fragmentation in the GEO graveyard to the collision with GEO objects.

Demographic and genetic status of an isolated population of bog turtles (Glyptemys muhlenbergii): Implications for managing small populations of long-lived animals

USGS Publications Warehouse

Pittman, Shannon E.; King, T.L.; Faurby, S.; Dorcas, M.E.

2011-01-01

In this study, we sought to determine the population stability and genetic diversity of one isolated population of the federally-threatened bog turtle (Glyptemys muhlenbergii) in North Carolina. Using capture-recapture data, we estimated adult survival and population growth rate from 1992 to 2007. We found that the population decreased from an estimated 36 adult turtles in 1994 to approximately 11 adult turtles in 2007. We found a constant adult survival of 0. 893 (SE = 0. 018, 95% confidence interval, 0. 853-0. 924) between 1992 and 2007. Using 18 microsatellite markers, we compared the genetic status of this population with five other bog turtle populations. The target population displayed allelic richness (4. 8 ?? 0. 5) and observed heterozygosity (0. 619 ?? 0. 064) within the range of the other bog turtle populations. Coalescent analysis of population growth rate, effective population size, and timing of population structuring event also indicated the genetics of the target population were comparable to the other populations studied. Estimates of effective population size were a proportion of the census size in all populations except the target population, in which the effective population size was larger than the census size (30 turtles vs. 11 turtles). We attribute the high genetic diversity in the target population to the presence of multiple generations of old turtles. This study illustrates that the demographic status of populations of long-lived species may not be reflected genetically if a decline occurred recently. Consequently, the genetic integrity of populations of long-lived animals experiencing rapid demographic bottlenecks may be preserved through conservation efforts effective in addressing demographic problems. ?? 2011 Springer Science+Business Media B.V.

Population biology of the mangrove crab Ucides cordatus (Decapoda: Ucididae) in an estuary from semiarid northeastern Brazil.

PubMed

Leite, Marcos de Miranda Leão; Rezende, Carla Ferreira; Silva, José Roberto Feitosa

2013-12-01

The mangrove crab Ucides cordatus is an important resource of estuarine regions along the Brazilian coast. U. cordatus is distributed from Florida, U.S.A., to the coast of Santa Catarina, Brazil. The species plays an important role in processing leaf litter in the mangroves, which optimizes the processes of energy transfer and nutrient cycling, and is considered a keystone species in the ecosystem. Population declines have been reported in different parts of the Brazilian coast. In the present study we evaluated aspects of the population structure, sex ratio and size at morphological sexual maturity. We analyzed 977 specimens collected monthly over 24 months (2010-2012), in a mangrove of the Jaguaribe River, in the municipality of Aracati on the East coast of Ceará state, Northeastern Brazil. The study area has a mild semiarid tropical climate, with mean temperatures between 26 and 28 degrees C. The area is located within the eco-region of the semiarid Northeast coast, where mangroves occur in small areas and estuaries are affected by mesomareal regimes. The population structure was evaluated by the frequency distribution of size classes in each month, and the overall sex ratio was analyzed using the chi-square test. Size at morphological sexual maturity was estimated based on the allometry of the cheliped of the males and the abdomen width of the females, using the program REGRANS. The size-frequency distribution was unimodal in both sexes. The overall sex ratio (M:F) (1:0.6) was significantly different from 1:1. Analysis of the sex ratio by size class showed that the proportion of males increased significantly from size class 55-60 mm upward, and this pattern persisted in the larger size classes. In the smaller size classes the sex ratio did not differ from 1:1. The size at morphological sexual maturity was estimated at a carapace width (CW) of 52 mm and 45 mm for males and females, respectively. Analysis of the population parameters indicated that the population of U. cordatus in the Jaguaribe River mangrove is stable. However, constant monitoring of the population is required to detect any changes in the population attributes that may affect this stability.

HIV populations are large and accumulate high genetic diversity in a nonlinear fashion.

PubMed

Maldarelli, Frank; Kearney, Mary; Palmer, Sarah; Stephens, Robert; Mican, JoAnn; Polis, Michael A; Davey, Richard T; Kovacs, Joseph; Shao, Wei; Rock-Kress, Diane; Metcalf, Julia A; Rehm, Catherine; Greer, Sarah E; Lucey, Daniel L; Danley, Kristen; Alter, Harvey; Mellors, John W; Coffin, John M

2013-09-01

HIV infection is characterized by rapid and error-prone viral replication resulting in genetically diverse virus populations. The rate of accumulation of diversity and the mechanisms involved are under intense study to provide useful information to understand immune evasion and the development of drug resistance. To characterize the development of viral diversity after infection, we carried out an in-depth analysis of single genome sequences of HIV pro-pol to assess diversity and divergence and to estimate replicating population sizes in a group of treatment-naive HIV-infected individuals sampled at single (n = 22) or multiple, longitudinal (n = 11) time points. Analysis of single genome sequences revealed nonlinear accumulation of sequence diversity during the course of infection. Diversity accumulated in recently infected individuals at rates 30-fold higher than in patients with chronic infection. Accumulation of synonymous changes accounted for most of the diversity during chronic infection. Accumulation of diversity resulted in population shifts, but the rates of change were low relative to estimated replication cycle times, consistent with relatively large population sizes. Analysis of changes in allele frequencies revealed effective population sizes that are substantially higher than previous estimates of approximately 1,000 infectious particles/infected individual. Taken together, these observations indicate that HIV populations are large, diverse, and slow to change in chronic infection and that the emergence of new mutations, including drug resistance mutations, is governed by both selection forces and drift.

Wastewater analysis to monitor use of caffeine and nicotine and evaluation of their metabolites as biomarkers for population size assessment.

PubMed

Senta, Ivan; Gracia-Lor, Emma; Borsotti, Andrea; Zuccato, Ettore; Castiglioni, Sara

2015-05-01

The use of caffeine, nicotine and some major metabolites was investigated by wastewater analysis in 13 sewage treatment plants (STPs) across Italy, and their suitability was tested as qualitative and quantitative biomarkers for assessing population size and dynamics. A specific analytical method based on mass spectrometry was developed and validated in raw urban wastewater, and included two caffeine metabolites, 1-methylxanthine and 7-methylxanthine, never reported in wastewater before. All these compounds were found widely at the μg/L level. Mass loads, calculated by multiplying concentrations by the wastewater daily flow rate and normalized to the population served by each plant, were used to compare the profiles from different cities. Some regional differences were observed in the mass loads, especially for nicotine metabolites, which were significantly higher in the south than in the center and north of Italy, reflecting smoking prevalences from population surveys. There were no significant weekly trends, although the mean mass loads of caffeine and its metabolites were slightly lower during the weekend. Most caffeine and nicotine metabolites fulfilled the requirements for an ideal biomarker for the assessment of population size, i.e. being easily detectable in wastewater, stable in sewage and during sampling, and reflecting human metabolism. Nicotine metabolites were tested as quantitative biomarkers to estimate population size and the results agreed well with census data. Caffeine and its metabolites were confirmed as good qualitative biomarkers, but additional information is needed on the caffeine metabolism in relation to the multiple sources of its main metabolites. This exploratory study opens the way to the routine use of nicotine metabolites for estimating population size and dynamics. Copyright © 2015 Elsevier Ltd. All rights reserved.

Computer simulation of vasectomy for wolf control

USGS Publications Warehouse

Haight, R.G.; Mech, L.D.

1997-01-01

Recovering gray wolf (Canis lupus) populations in the Lake Superior region of the United States are prompting state management agencies to consider strategies to control population growth. In addition to wolf removal, vasectomy has been proposed. To predict the population effects of different sterilization and removal strategies, we developed a simulation model of wolf dynamics using simple rules for demography and dispersal. Simulations suggested that the effects of vasectomy and removal in a disjunct population depend largely on the degree of annual immigration. With low immigration, periodic sterilization reduced pup production and resulted in lower rates of territory recolonization. Consequently, average pack size, number of packs, and population size were significantly less than those for an untreated population. Periodically removing a proportion of the population produced roughly the same trends as did sterilization; however, more than twice as many wolves had to be removed than sterilized. With high immigration, periodic sterilization reduced pup production but not territory recolonization and produced only moderate reductions in population size relative to an untreated population. Similar reductions in population size were obtained by periodically removing large numbers of wolves. Our analysis does not address the possible effects of vasectomy on larger wolf populations, but it suggests that the subject should be considered through modeling or field testing.

The greater snow goose Anser caerulescens atlanticus: Managing an overabundant population.

PubMed

Lefebvre, Josée; Gauthier, Gilles; Giroux, Jean-François; Reed, Austin; Reed, Eric T; Bélanger, Luc

2017-03-01

Between the early 1900s and the 1990s, the greater snow goose Anser caerulescens atlanticus population grew from 3000 individuals to more than 700 000. Because of concerns about Arctic degradation of natural habitats through overgrazing, a working group recommended the stabilization of the population. Declared overabundant in 1998, special management actions were then implemented in Canada and the United States. Meanwhile, a cost-benefit socioeconomic analysis was performed to set a target population size. Discussions aiming towards attaining a common vision were undertaken with stakeholders at multiple levels. The implemented measures have had varying success; but population size has been generally stable since 1999. To be effective and meet social acceptance, management actions must have a scientific basis, result from a consensus among stakeholders, and include an efficient monitoring programme. In this paper, historical changes in population size and management decisions along with past and current challenges encountered are discussed.

Morphological and genetic divergence in Swedish postglacial stickleback (Pungitius pungitius) populations

PubMed Central

2011-01-01

Background An important objective of evolutionary biology is to understand the processes that govern phenotypic variation in natural populations. We assessed patterns of morphological and genetic divergence among coastal and inland lake populations of nine-spined stickleback in northern Sweden. Coastal populations are either from the Baltic coast (n = 5) or from nearby coastal lakes (n = 3) that became isolated from the Baltic Sea (< 100 years before present, ybp). Inland populations are from freshwater lakes that became isolated from the Baltic approximately 10,000 ybp; either single species lakes without predators (n = 5), or lakes with a recent history of predation (n = 5) from stocking of salmonid predators (~50 ybp). Results Coastal populations showed little variation in 11 morphological traits and had longer spines per unit of body length than inland populations. Inland populations were larger, on average, and showed greater morphological variation than coastal populations. A principal component analysis (PCA) across all populations revealed two major morphological axes related to spine length (PC1, 47.7% variation) and body size (PC2, 32.9% variation). Analysis of PCA scores showed marked similarity in coastal (Baltic coast and coastal lake) populations. PCA scores indicate that inland populations with predators have higher within-group variance in spine length and lower within-group variance in body size than inland populations without predators. Estimates of within-group PST (a proxy for QST) from PCA scores are similar to estimates of FST for coastal lake populations but PST >FST for Baltic coast populations. PST >FST for PC1 and PC2 for inland predator and inland no predator populations, with the exception that PST

Structured population dynamics: continuous size and discontinuous stage structures.

PubMed

Buffoni, Giuseppe; Pasquali, Sara

2007-04-01

A nonlinear stochastic model for the dynamics of a population with either a continuous size structure or a discontinuous stage structure is formulated in the Eulerian formalism. It takes into account dispersion effects due to stochastic variability of the development process of the individuals. The discrete equations of the numerical approximation are derived, and an analysis of the existence and stability of the equilibrium states is performed. An application to a copepod population is illustrated; numerical results of Eulerian and Lagrangian models are compared.

The relative effects of habitat loss and fragmentation on population genetic variation in the red-cockaded woodpecker (Picoides borealis).

PubMed

Bruggeman, Douglas J; Wiegand, Thorsten; Fernández, Néstor

2010-09-01

The relative influence of habitat loss, fragmentation and matrix heterogeneity on the viability of populations is a critical area of conservation research that remains unresolved. Using simulation modelling, we provide an analysis of the influence both patch size and patch isolation have on abundance, effective population size (N(e)) and F(ST). An individual-based, spatially explicit population model based on 15 years of field work on the red-cockaded woodpecker (Picoides borealis) was applied to different landscape configurations. The variation in landscape patterns was summarized using spatial statistics based on O-ring statistics. By regressing demographic and genetics attributes that emerged across the landscape treatments against proportion of total habitat and O-ring statistics, we show that O-ring statistics provide an explicit link between population processes, habitat area, and critical thresholds of fragmentation that affect those processes. Spatial distances among land cover classes that affect biological processes translated into critical scales at which the measures of landscape structure correlated best with genetic indices. Therefore our study infers pattern from process, which contrasts with past studies of landscape genetics. We found that population genetic structure was more strongly affected by fragmentation than population size, which suggests that examining only population size may limit recognition of fragmentation effects that erode genetic variation. If effective population size is used to set recovery goals for endangered species, then habitat fragmentation effects may be sufficiently strong to prevent evaluation of recovery based on the ratio of census:effective population size alone.

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 objects are an empirical extension from larger debris. The extension takes into account the results of micro-debris (from 10 micron to 1 mm) population modeling that is based on shuttle impact data, in the hope of making a smooth transition between micron and millimeter size regimes. This paper also includes a brief discussion on issues and potential future work concerning the analysis and interpretation of Goldstone radar data.

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.

Effect size calculation in meta-analyses of psychotherapy outcome research.

PubMed

Hoyt, William T; Del Re, A C

2018-05-01

Meta-analysis of psychotherapy intervention research normally examines differences between treatment groups and some form of comparison group (e.g., wait list control; alternative treatment group). The effect of treatment is normally quantified as a standardized mean difference (SMD). We describe procedures for computing unbiased estimates of the population SMD from sample data (e.g., group Ms and SDs), and provide guidance about a number of complications that may arise related to effect size computation. These complications include (a) incomplete data in research reports; (b) use of baseline data in computing SMDs and estimating the population standard deviation (σ); (c) combining effect size data from studies using different research designs; and (d) appropriate techniques for analysis of data from studies providing multiple estimates of the effect of interest (i.e., dependent effect sizes). Clinical or Methodological Significance of this article: Meta-analysis is a set of techniques for producing valid summaries of existing research. The initial computational step for meta-analyses of research on intervention outcomes involves computing an effect size quantifying the change attributable to the intervention. We discuss common issues in the computation of effect sizes and provide recommended procedures to address them.

Automated measurement of diatom size

USGS Publications Warehouse

Spaulding, Sarah A.; Jewson, David H.; Bixby, Rebecca J.; Nelson, Harry; McKnight, Diane M.

2012-01-01

Size analysis of diatom populations has not been widely considered, but it is a potentially powerful tool for understanding diatom life histories, population dynamics, and phylogenetic relationships. However, measuring cell dimensions on a light microscope is a time-consuming process. An alternative technique has been developed using digital flow cytometry on a FlowCAM® (Fluid Imaging Technologies) to capture hundreds, or even thousands, of images of a chosen taxon from a single sample in a matter of minutes. Up to 30 morphological measures may be quantified through post-processing of the high resolution images. We evaluated FlowCAM size measurements, comparing them against measurements from a light microscope. We found good agreement between measurement of apical cell length in species with elongated, straight valves, including small Achnanthidium minutissimum (11-21 µm) and largeDidymosphenia geminata (87–137 µm) forms. However, a taxon with curved cells, Hannaea baicalensis (37–96 µm), showed differences of ~ 4 µm between the two methods. Discrepancies appear to be influenced by the choice of feret or geodesic measurement for asymmetric cells. We describe the operating conditions necessary for analysis of size distributions and present suggestions for optimal instrument conditions for size analysis of diatom samples using the FlowCAM. The increased speed of data acquisition through use of imaging flow cytometers like the FlowCAM is an essential step for advancing studies of diatom populations.

Body size and allometric shape variation in the molly Poecilia vivipara along a gradient of salinity and predation.

PubMed

Araújo, Márcio S; Perez, S Ivan; Magazoni, Maria Julia C; Petry, Ana C

2014-12-04

Phenotypic diversity among populations may result from divergent natural selection acting directly on traits or via correlated responses to changes in other traits. One of the most frequent patterns of correlated response is the proportional change in the dimensions of anatomical traits associated with changes in growth or absolute size, known as allometry. Livebearing fishes subject to predation gradients have been shown to repeatedly evolve larger caudal peduncles and smaller cranial regions under high predation regimes. Poecilia vivipara is a livebearing fish commonly found in coastal lagoons in the north of the state of Rio de Janeiro, Brazil. Similar to what is observed in other predation gradients, lagoons inhabited by P. vivipara vary in the presence of piscivorous fishes; contrary to other poeciliid systems, populations of P. vivipara vary greatly in body size, which opens the possibility of strong allometric effects on shape variation. Here we investigated body shape diversification among six populations of P. vivipara along a predation gradient and its relationship with allometric trajectories within and among populations. We found substantial body size variation and correlated shape changes among populations. Multivariate regression analysis showed that size variation among populations accounted for 66% of shape variation in females and 38% in males, suggesting that size is the most important dimension underlying shape variation among populations of P. vivipara in this system. Changes in the relative sizes of the caudal peduncle and cranial regions were only partly in line with predictions from divergent natural selection associated with predation regime. Our results suggest the possibility that adaptive shape variation among populations has been partly constrained by allometry in P. vivipara. Processes governing body size changes are therefore important in the diversification of this species. We conclude that in species characterized by substantial among-population differences in body size, ignoring allometric effects when investigating divergent natural selection's role in phenotypic diversification might not be warranted.

The accuracy of matrix population model projections for coniferous trees in the Sierra Nevada, California

USGS Publications Warehouse

van Mantgem, P.J.; Stephenson, N.L.

2005-01-01

1 We assess the use of simple, size-based matrix population models for projecting population trends for six coniferous tree species in the Sierra Nevada, California. We used demographic data from 16 673 trees in 15 permanent plots to create 17 separate time-invariant, density-independent population projection models, and determined differences between trends projected from initial surveys with a 5-year interval and observed data during two subsequent 5-year time steps. 2 We detected departures from the assumptions of the matrix modelling approach in terms of strong growth autocorrelations. We also found evidence of observation errors for measurements of tree growth and, to a more limited degree, recruitment. Loglinear analysis provided evidence of significant temporal variation in demographic rates for only two of the 17 populations. 3 Total population sizes were strongly predicted by model projections, although population dynamics were dominated by carryover from the previous 5-year time step (i.e. there were few cases of recruitment or death). Fractional changes to overall population sizes were less well predicted. Compared with a null model and a simple demographic model lacking size structure, matrix model projections were better able to predict total population sizes, although the differences were not statistically significant. Matrix model projections were also able to predict short-term rates of survival, growth and recruitment. Mortality frequencies were not well predicted. 4 Our results suggest that simple size-structured models can accurately project future short-term changes for some tree populations. However, not all populations were well predicted and these simple models would probably become more inaccurate over longer projection intervals. The predictive ability of these models would also be limited by disturbance or other events that destabilize demographic rates. ?? 2005 British Ecological Society.

The fall and rise of the Icelandic Arctic fox (Vulpes lagopus): a 50-year demographic study on a non-cyclic Arctic fox population.

PubMed

Unnsteinsdottir, E R; Hersteinsson, P; Pálsson, S; Angerbjörn, A

2016-08-01

In territorial species, observed density dependence is often manifest in lowered reproductive output at high population density where individuals have fewer resources or are forced to inhabit low-quality territories. The Arctic fox (Vulpes lagopus) in Iceland is territorial throughout the year and feeds mostly on birds, since lemmings are absent from the country. Thus, the population does not exhibit short-term population cycles that are evident in most of the species' geographical range. The population has, however, gone through a major long-term fluctuation in population size. Because of the stability in hunting effort and reliable hunting records since 1958, the total number of adult foxes killed annually can be used as an index of population size (N t ). An index of carrying capacity (K) from population growth data for five separate time blocks during 1958-2007 revealed considerable variation in K and allowed a novel definition of population density in terms of K, or N t /K. Correlation analysis suggested that the reproductive rate was largely determined by the proportion of territorial foxes in the population. Variation in litter size and cub mortality was, on the other hand, related to climatic variation. Thus, Arctic foxes in Iceland engage in typical contest competition but can adapt their territory sizes in response to both temporal and spatial variation in carrying capacity, resulting in surprisingly little variation in litter size.

The Statistics and Mathematics of High Dimension Low Sample Size Asymptotics.

PubMed

Shen, Dan; Shen, Haipeng; Zhu, Hongtu; Marron, J S

2016-10-01

The aim of this paper is to establish several deep theoretical properties of principal component analysis for multiple-component spike covariance models. Our new results reveal an asymptotic conical structure in critical sample eigendirections under the spike models with distinguishable (or indistinguishable) eigenvalues, when the sample size and/or the number of variables (or dimension) tend to infinity. The consistency of the sample eigenvectors relative to their population counterparts is determined by the ratio between the dimension and the product of the sample size with the spike size. When this ratio converges to a nonzero constant, the sample eigenvector converges to a cone, with a certain angle to its corresponding population eigenvector. In the High Dimension, Low Sample Size case, the angle between the sample eigenvector and its population counterpart converges to a limiting distribution. Several generalizations of the multi-spike covariance models are also explored, and additional theoretical results are presented.

Individualism in plant populations: using stochastic differential equations to model individual neighbourhood-dependent plant growth.

PubMed

Lv, Qiming; Schneider, Manuel K; Pitchford, Jonathan W

2008-08-01

We study individual plant growth and size hierarchy formation in an experimental population of Arabidopsis thaliana, within an integrated analysis that explicitly accounts for size-dependent growth, size- and space-dependent competition, and environmental stochasticity. It is shown that a Gompertz-type stochastic differential equation (SDE) model, involving asymmetric competition kernels and a stochastic term which decreases with the logarithm of plant weight, efficiently describes individual plant growth, competition, and variability in the studied population. The model is evaluated within a Bayesian framework and compared to its deterministic counterpart, and to several simplified stochastic models, using distributional validation. We show that stochasticity is an important determinant of size hierarchy and that SDE models outperform the deterministic model if and only if structural components of competition (asymmetry; size- and space-dependence) are accounted for. Implications of these results are discussed in the context of plant ecology and in more general modelling situations.

Variability in the Results of Meta-Analysis as a Function of Comparing Effect Sizes Based on Scores from Noncomparable Measures: A Simulation Study

ERIC Educational Resources Information Center

Nugent, William R.

2017-01-01

Meta-analysis is a significant methodological advance that is increasingly important in research synthesis. Fundamental to meta-analysis is the presumption that effect sizes, such as the standardized mean difference (SMD), based on scores from different measures are comparable. It has been argued that population observed score SMDs based on scores…

Inferred Paternity and Male Reproductive Success in a Killer Whale (Orcinus orca) Population.

PubMed

Ford, Michael J; Hanson, M Bradley; Hempelmann, Jennifer A; Ayres, Katherine L; Emmons, Candice K; Schorr, Gregory S; Baird, Robin W; Balcomb, Kenneth C; Wasser, Samuel K; Parsons, Kim M; Balcomb-Bartok, Kelly

2011-01-01

We used data from 78 individuals at 26 microsatellite loci to infer parental and sibling relationships within a community of fish-eating ("resident") eastern North Pacific killer whales (Orcinus orca). Paternity analysis involving 15 mother/calf pairs and 8 potential fathers and whole-pedigree analysis of the entire sample produced consistent results. The variance in male reproductive success was greater than expected by chance and similar to that of other aquatic mammals. Although the number of confirmed paternities was small, reproductive success appeared to increase with male age and size. We found no evidence that males from outside this small population sired any of the sampled individuals. In contrast to previous results in a different population, many offspring were the result of matings within the same "pod" (long-term social group). Despite this pattern of breeding within social groups, we found no evidence of offspring produced by matings between close relatives, and the average internal relatedness of individuals was significantly less than expected if mating were random. The population's estimated effective size was <30 or about 1/3 of the current census size. Patterns of allele frequency variation were consistent with a population bottleneck.

Gene flow analysis method, the D-statistic, is robust in a wide parameter space.

PubMed

Zheng, Yichen; Janke, Axel

2018-01-08

We evaluated the sensitivity of the D-statistic, a parsimony-like method widely used to detect gene flow between closely related species. This method has been applied to a variety of taxa with a wide range of divergence times. However, its parameter space and thus its applicability to a wide taxonomic range has not been systematically studied. Divergence time, population size, time of gene flow, distance of outgroup and number of loci were examined in a sensitivity analysis. The sensitivity study shows that the primary determinant of the D-statistic is the relative population size, i.e. the population size scaled by the number of generations since divergence. This is consistent with the fact that the main confounding factor in gene flow detection is incomplete lineage sorting by diluting the signal. The sensitivity of the D-statistic is also affected by the direction of gene flow, size and number of loci. In addition, we examined the ability of the f-statistics, [Formula: see text] and [Formula: see text], to estimate the fraction of a genome affected by gene flow; while these statistics are difficult to implement to practical questions in biology due to lack of knowledge of when the gene flow happened, they can be used to compare datasets with identical or similar demographic background. The D-statistic, as a method to detect gene flow, is robust against a wide range of genetic distances (divergence times) but it is sensitive to population size. The D-statistic should only be applied with critical reservation to taxa where population sizes are large relative to branch lengths in generations.

Frog size on continental islands of the coast of Rio de Janeiro and the generality of the Island Rule

PubMed Central

2018-01-01

Island Rule postulated that individuals on islands tend to dwarfism when individuals from mainland populations are large and to gigantism when mainland populations present small individuals. There has been much discussion about this rule, but only few studies were carried out aiming to reveal this pattern for anurans. Our study focused on measuring the size of individuals on islands and to find a possible pattern of size modification for insular anurans. Individuals were collected on continental islands, measured and compared to mainland populations. We selected four species with different natural history aspects during these analyses. Island parameters were compared to size of individuals in order to find an explanation to size modification. Three of the four species presented size shifting on islands. Ololygon trapicheiroi and Adenomera marmorata showed dwarfism, Boana albomarginata showed gigantism and in Thoropa miliaris there was no evident size modification. Allometric analysis also revealed differential modification, which might be a result of different selective pressures on islands in respect of mainland populations. Regression model explained most of the size modification in B. albomarginata, but not for the other species. Our results indicate that previous assumptions, usually proposed for mammals from older islands, do not fit to the anurans studied here. We support the assumption that size modification on islands are population-specific. Hence, in B. albomarginata some factor associated to competition, living area and isolation time might likely be responsible for gigantism on islands. PMID:29324790

Size Matters: Individual Variation in Ectotherm Growth and Asymptotic Size

PubMed Central

King, Richard B.

2016-01-01

Body size, and, by extension, growth has impacts on physiology, survival, attainment of sexual maturity, fecundity, generation time, and population dynamics, especially in ectotherm animals that often exhibit extensive growth following attainment of sexual maturity. Frequently, growth is analyzed at the population level, providing useful population mean growth parameters but ignoring individual variation that is also of ecological and evolutionary significance. Our long-term study of Lake Erie Watersnakes, Nerodia sipedon insularum, provides data sufficient for a detailed analysis of population and individual growth. We describe population mean growth separately for males and females based on size of known age individuals (847 captures of 769 males, 748 captures of 684 females) and annual growth increments of individuals of unknown age (1,152 males, 730 females). We characterize individual variation in asymptotic size based on repeated measurements of 69 males and 71 females that were each captured in five to nine different years. The most striking result of our analyses is that asymptotic size varies dramatically among individuals, ranging from 631–820 mm snout-vent length in males and from 835–1125 mm in females. Because female fecundity increases with increasing body size, we explore the impact of individual variation in asymptotic size on lifetime reproductive success using a range of realistic estimates of annual survival. When all females commence reproduction at the same age, lifetime reproductive success is greatest for females with greater asymptotic size regardless of annual survival. But when reproduction is delayed in females with greater asymptotic size, lifetime reproductive success is greatest for females with lower asymptotic size when annual survival is low. Possible causes of individual variation in asymptotic size, including individual- and cohort-specific variation in size at birth and early growth, warrant further investigation. PMID:26730712

Size Matters: Individual Variation in Ectotherm Growth and Asymptotic Size.

PubMed

King, Richard B; Stanford, Kristin M; Jones, Peter C; Bekker, Kent

2016-01-01

Body size, and, by extension, growth has impacts on physiology, survival, attainment of sexual maturity, fecundity, generation time, and population dynamics, especially in ectotherm animals that often exhibit extensive growth following attainment of sexual maturity. Frequently, growth is analyzed at the population level, providing useful population mean growth parameters but ignoring individual variation that is also of ecological and evolutionary significance. Our long-term study of Lake Erie Watersnakes, Nerodia sipedon insularum, provides data sufficient for a detailed analysis of population and individual growth. We describe population mean growth separately for males and females based on size of known age individuals (847 captures of 769 males, 748 captures of 684 females) and annual growth increments of individuals of unknown age (1,152 males, 730 females). We characterize individual variation in asymptotic size based on repeated measurements of 69 males and 71 females that were each captured in five to nine different years. The most striking result of our analyses is that asymptotic size varies dramatically among individuals, ranging from 631-820 mm snout-vent length in males and from 835-1125 mm in females. Because female fecundity increases with increasing body size, we explore the impact of individual variation in asymptotic size on lifetime reproductive success using a range of realistic estimates of annual survival. When all females commence reproduction at the same age, lifetime reproductive success is greatest for females with greater asymptotic size regardless of annual survival. But when reproduction is delayed in females with greater asymptotic size, lifetime reproductive success is greatest for females with lower asymptotic size when annual survival is low. Possible causes of individual variation in asymptotic size, including individual- and cohort-specific variation in size at birth and early growth, warrant further investigation.

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 Management Zone as two management units. PMID:27463811

Meta-Analysis of Explicit Memory Studies in Populations with Intellectual Disability

ERIC Educational Resources Information Center

Lifshitz, Hefziba; Shtein, Sarit; Weiss, Izhak; Vakil, Eli

2011-01-01

This meta-analysis combines the effect size (ES) of 40 explicit memory experiments in populations with intellectual disability (ID). Eight meta-analyses were performed, as well as contrast tests between ES. The explicit memory of participants with ID was inferior to that of participants with typical development (TD). Relatively preserved explicit…

Computer based experimental studies of the Fry method of strain analysis on 2- and 3- dimensional grain populations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Longiaru, S.; Bhattacharyya, T.

1985-01-01

Inherent in Fry's (1979) all-object separation method of strain analysis are the subtle conditions that 1) the grains or phenocrysts being counted are of equal diameter and 2) that the true centers of such grains lie within the plane of measurement. When such conditions are met, the technique yields accurate, easily interpreted voids within all-object separation (AOS) plots for both deformed and non-deformed populations. Natural grain or phenocryst populations generally do not conform to these limitation and practical application of the technique from either a cut rock surface or thin section often yields diffuse patterns that are not easily interpreted.more » The authors examine the effect of grain size variation and grain/matrix ratio on AOS diagrams developed from computer generated spherical grain populations constructed in both two and three dimensions. They employ a random number generator and simple fitting algorithm to develop grain populations with known statistical parameters. Such control allows for the modeling of many types of natural grain size populations such as fluvial sandstones, porphyritic ash flow tuffs, augen gneisses, etc. They show that significant grain size variation in a two dimensional population contributes substantial noise in to the AOS diagram and that an additional level of noise is encountered when dealing with slices through populations modeled in three dimensions. Some of this noise can be eliminated by rigorous sampling of only subsets of the total grain population.« less

Reproductive success in a natural population of male three-spined stickleback Gasterosteus aculeatus: effects of nuptial colour, parasites and body size.

PubMed

Sparkes, T C; Rush, V; Kopp, D A; Foster, S A

2013-05-01

The effects of nuptial colour, parasites and body size on reproductive success were examined in a natural population of three-spined stickleback Gasterosteus aculeatus. Reproductive males were collected, with the contents of their nests, during the embryo-guarding stage from Lynne Lake (Cook Inlet, Alaska, U.S.A.), and nuptial colour, infection status and body size were recorded. Regression analysis revealed that male body size was the only predictor, of those measured, of reproductive success in nature. © 2013 The Authors. Journal of Fish Biology © 2013 The Fisheries Society of the British Isles.

Disease invasion risk in a growing population.

PubMed

Yuan, Sanling; van den Driessche, P; Willeboordse, Frederick H; Shuai, Zhisheng; Ma, Junling

2016-09-01

The spread of an infectious disease may depend on the population size. For simplicity, classic epidemic models assume homogeneous mixing, usually standard incidence or mass action. For standard incidence, the contact rate between any pair of individuals is inversely proportional to the population size, and so the basic reproduction number (and thus the initial exponential growth rate of the disease) is independent of the population size. For mass action, this contact rate remains constant, predicting that the basic reproduction number increases linearly with the population size, meaning that disease invasion is easiest when the population is largest. In this paper, we show that neither of these may be true on a slowly evolving contact network: the basic reproduction number of a short epidemic can reach its maximum while the population is still growing. The basic reproduction number is proportional to the spectral radius of a contact matrix, which is shown numerically to be well approximated by the average excess degree of the contact network. We base our analysis on modeling the dynamics of the average excess degree of a random contact network with constant population input, proportional deaths, and preferential attachment for contacts brought in by incoming individuals (i.e., individuals with more contacts attract more incoming contacts). In addition, we show that our result also holds for uniform attachment of incoming contacts (i.e., every individual has the same chance of attracting incoming contacts), and much more general population dynamics. Our results show that a disease spreading in a growing population may evade control if disease control planning is based on the basic reproduction number at maximum population size.

Geographical and functional-morphological variations of the skull in the gray-bellied squirrel.

PubMed

Endo, Hideki; Kimura, Junpei; Oshida, Tatsuo; Stafford, Brian J; Rerkamnuaychoke, Worawut; Nishida, Takao; Sasaki, Motoki; Hayashida, Akiko; Hayashi, Yoshihiro

2004-03-01

The geographical variations of the skulls were osteometrically examined in the gray-bellied squirrel (Callosciurus caniceps) from the populations of Korat, Ranong, southernmost Thailand, and Terutau Island. The skull size was larger in northern population than in the southern population in the continental mainland. The zoogeographical influences of the Isthmus of Kra remained unclear, since the plots from Korat population were intermingled with those from southernmost Thailand population in the principal component charts. Although Korat population has been thought to belong to north group, we suggest that Ranong and southernmost Thailand populations may contain individuals from both north and south groups separated by the ancient Kra barrier. Terutau Island population was similar to southernmost Thailand population in skull size, although Terutau population has been isolated in the island and separated from the south group of the Isthmus of Kra. In the proportional analysis the interorbital space was narrower and the binocular sense has been well-developed in Terutau population. It suggests that this population has been highly adapted to arboreal behavior. In contrast, the skull with larger interorbital space was more adaptive for terrestrial life in Korat population. The canonical discriminant analysis could clearly separate the four populations in the scattergrams of discriminant scores.

The Efficacy of Two Improvement-over-Chance Effect Sizes for Two-Group Univariate Comparisons under Variance Heterogeneity and Nonnormality.

ERIC Educational Resources Information Center

Hess, Brian; Olejnik, Stephen; Huberty, Carl J.

2001-01-01

Studied the efficacy of two improvement-over-chance or "I" effect sizes derived from predictive discriminant analysis and logistic regression analysis for two-group univariate mean comparisons through simulation. Discusses the ways in which the usefulness of each of the indices depends on the population characteristics. (SLD)

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 abundance trends. PMID:23755197

Estimated abundance of wild burros surveyed on Bureau of Land Management Lands in 2014

USGS Publications Warehouse

Griffin, Paul C.

2015-01-01

The Bureau of Land Management (BLM) requires accurate estimates of the numbers of wild horses (Equus ferus caballus) and burros (Equus asinus) living on the lands it manages. For over ten years, BLM in Arizona has used the simultaneous double-observer method of recording wild burros during aerial surveys and has reported population estimates for those surveys that come from two formulations of a Lincoln-Petersen type of analysis (Graham and Bell, 1989). In this report, I provide those same two types of burro population analysis for 2014 aerial survey data from six herd management areas (HMAs) in Arizona, California, Nevada, and Utah. I also provide burro population estimates based on a different form of simultaneous double-observer analysis, now in widespread use for wild horse surveys that takes into account the potential effects on detection probability of sighting covariates including group size, distance, vegetative cover, and other factors (Huggins, 1989, 1991). The true number of burros present in the six areas surveyed was not known, so population estimates made with these three types of analyses cannot be directly tested for accuracy in this report. I discuss theoretical reasons why the Huggins (1989, 1991) type of analysis should provide less biased estimates of population size than the Lincoln-Petersen analyses and why estimates from all forms of double-observer analyses are likely to be lower than the true number of animals present in the surveyed areas. I note reasons why I suggest using burro observations made at all available distances in analyses, not only those within 200 meters of the flight path. For all analytical methods, small sample sizes of observed groups can be problematic, but that sample size can be increased over time for Huggins (1989, 1991) analyses by pooling observations. I note ways by which burro population estimates could be tested for accuracy when there are radio-collared animals in the population or when there are simultaneous double-observer surveys before and after a burro gather and removal.

Population ecology of variegate darter (Etheostoma variatum) in Virginia

USGS Publications Warehouse

Argentina, Jane E.; Angermeier, Paul; Hallerman, Eric M.

2013-01-01

Variegate darters (Etheostoma variatum) were listed as endangered in Virginia in 1992. Reasons for listing included habitat degradation and concerns about current and future impacts of coal mining throughout their Virginia range. Prior to this research, little was known about variegate darter distribution, habitat use, or populations in Virginia. Two primary goals of this research were to gain knowledge about the current population ecology and the relationship between landscape-level factors (e.g., land cover changes, watershed size, isolation from other populations) on current and past variegate darter population sizes.We investigated distribution, habitat suitability, population genetics, and population size and structure of variegate darters in the upper Big Sandy River drainage, Buchanan, Dickenson, and Wise Co., Virginia. Our results indicate variegate darters are primarily found in the Levisa Fork, with highest densities and abundances between its confluence with Dismal Creek and the Virginia-Kentucky border. Sporadic occurrences in smaller tributaries to the Levisa and Tug forks indicate they exist more widely in low densities, especially near the confluence with the Tug and Levisa mainstems. Detection of variegate darters in smaller tributaries was inconsistent, with reach-level occupancy estimates varying among years. We detected young-of-year variegate darters every year we sampled, but age 1+ darters were indistinguishable from older darters based on standard length.Variegate darter population size and stability in Virginia were estimated via multiple methods, including site occupancy surveys, mark-recapture studies, and population genetic analysis. Using mark-recapture methods at five sites, we estimated overall population size in 2011 to be approximately 12,800 individuals in the 35-km reach between the Levisa Fork - Dismal Creek confluence and the Virginia-Kentucky border. Age structure seemed stable, with breeding adults and young-of-year collected annually during 2008-2011. Population genetic analysis indicated variegate darters in the Levisa Fork and its tributaries are part of a single genetic population. Historical and current genetic stability were seen in our analysis of the variegate darter population, with no genetic differentiation among riffles across the upper Levisa Fork watershed, indicating dispersal among these sites is enough to overcome random genetic drift. This population is genetically isolated from downstream populations by the dam at Fishtrap Lake, Pike Co., Kentucky, and is beginning to show genetic isolation from other nearby populations. As expected, the Virginia population is most closely related to those in the Russell Fork and Levisa Fork downstream of the dam.Regular monitoring of variegate darters in the Levisa Fork mainstem from the Dismal Creek confluence to the Virginia-Kentucky border would facilitate better understanding of normal fluctuations of population size and distribution, as well as assessments of population status. This reach encompasses the core of the variegate darter population in Virginia, and its persistence will determine long-term viability of this species. Given that little is known about long-term population trends, we suggest that annual site-occupancy and population size estimates be made at ten randomly selected riffles for at least ten years to understand normal levels of variability. Thereafter, these population parameters could be monitored bi-annually as a way to detect shrinking distribution or abundance, especially after any fish kill or other pollution event in the Levisa Fork. We further suggest that the sites upstream and downstream of the saline diffusor pipe be monitored to detect changes in the extent of the impact zone.Overall, the variegate darter population in Virginia appears stable, although primarily confined to the lower 35 km of the Levisa Fork. Nevertheless, variegate darters in Virginia remain susceptible to extirpation due to catastrophic events, both physical (chemical spill) and biological (disease outbreak or invasive species introduction).

Aboriginal population prospects.

PubMed

Gray, A; Tesfaghiorghis, H

1993-11-01

The authors examine data from the 1986 and 1991 Australian censuses to assess discrepancies between the census data and past projections of the size and structure of the Aboriginal population. They also "comment on ways in which determinants of Aboriginal population change are diverging from the parameters used for previous projections. We pay particular attention to mortality prospects.... We note the evidence for under-enumeration of the Aboriginal population in particular age groups in the 1991 Census as in previous censuses, and estimate the size of adjustments necessary to correct for some, but not all, of these deficiencies. The analysis shows that Aboriginal fertility increased in the second half of the 1980s." excerpt

Estimation of effectiveness of three methods of feral cat population control by use of a simulation model.

PubMed

McCarthy, Robert J; Levine, Stephen H; Reed, J Michael

2013-08-15

To predict effectiveness of 3 interventional methods of population control for feral cat colonies. Population model. Estimates of vital data for feral cats. Data were gathered from the literature regarding the demography and mating behavior of feral cats. An individual-based stochastic simulation model was developed to evaluate the effectiveness of trap-neuter-release (TNR), lethal control, and trap-vasectomy-hysterectomy-release (TVHR) in decreasing the size of feral cat populations. TVHR outperformed both TNR and lethal control at all annual capture probabilities between 10% and 90%. Unless > 57% of cats were captured and neutered annually by TNR or removed by lethal control, there was minimal effect on population size. In contrast, with an annual capture rate of ≥ 35%, TVHR caused population size to decrease. An annual capture rate of 57% eliminated the modeled population in 4,000 days by use of TVHR, whereas > 82% was required for both TNR and lethal control. When the effect of fraction of adult cats neutered on kitten and young juvenile survival rate was included in the analysis, TNR performed progressively worse and could be counterproductive, such that population size increased, compared with no intervention at all. TVHR should be preferred over TNR for management of feral cats if decrease in population size is the goal. This model allowed for many factors related to the trapping program and cats to be varied and should be useful for determining the financial and person-effort commitments required to have a desired effect on a given feral cat population.

Transgenerational Adaptation to Pollution Changes Energy Allocation in Populations of Nematodes.

PubMed

Goussen, Benoit; Péry, Alexandre R R; Bonzom, Jean-Marc; Beaudouin, Rémy

2015-10-20

Assessing the evolutionary responses of long-term exposed populations requires multigeneration ecotoxicity tests. However, the analysis of the data from these tests is not straightforward. Mechanistic models allow the in-depth analysis of the variation of physiological traits over many generations, by quantifying the trend of the physiological and toxicological parameters of the model. In the present study, a bioenergetic mechanistic model has been used to assess the evolution of two populations of the nematode Caenorhabditis elegans in control conditions or exposed to uranium. This evolutionary pressure resulted in a brood size reduction of 60%. We showed an adaptation of individuals of both populations to experimental conditions (increase of maximal length, decrease of growth rate, decrease of brood size, and decrease of the elimination rate). In addition, differential evolution was also highlighted between the two populations once the maternal effects had been diminished after several generations. Thus, individuals that were greater in maximal length, but with apparently a greater sensitivity to uranium were selected in the uranium population. In this study, we showed that this bioenergetics mechanistic modeling approach provided a precise, certain, and powerful analysis of the life strategy of C. elegans populations exposed to heavy metals resulting in an evolutionary pressure across successive generations.

An integrated analysis of phenotypic selection on insect body size and development time.

PubMed

Eck, Daniel J; Shaw, Ruth G; Geyer, Charles J; Kingsolver, Joel G

2015-09-01

Most studies of phenotypic selection do not estimate selection or fitness surfaces for multiple components of fitness within a unified statistical framework. This makes it difficult or impossible to assess how selection operates on traits through variation in multiple components of fitness. We describe a new generation of aster models that can evaluate phenotypic selection by accounting for timing of life-history transitions and their effect on population growth rate, in addition to survival and reproductive output. We use this approach to estimate selection on body size and development time for a field population of the herbivorous insect, Manduca sexta (Lepidoptera: Sphingidae). Estimated fitness surfaces revealed strong and significant directional selection favoring both larger adult size (via effects on egg counts) and more rapid rates of early larval development (via effects on larval survival). Incorporating the timing of reproduction and its influence on population growth rate into the analysis resulted in larger values for size in early larval development at which fitness is maximized, and weaker selection on size in early larval development. These results illustrate how the interplay of different components of fitness can influence selection on size and development time. This integrated modeling framework can be readily applied to studies of phenotypic selection via multiple fitness components in other systems. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

Modeling the Space Debris Environment with MASTER-2009 and ORDEM2010

NASA Technical Reports Server (NTRS)

Flegel, S.; Gelhaus, J.; Wiedemann, C.; Mockel, M.; Vorsmann, P.; Krisko, P.; Xu, Y. -L.; Horstman, M. F.; Opiela, J. N.; Matney, M.;

NASA's New Orbital Debris Engineering Model, ORDEM2010

NASA Technical Reports Server (NTRS)

Krisko, Paula H.

2010-01-01

This paper describes the functionality and use of ORDEM2010, which replaces ORDEM2000, as the NASA Orbital Debris Program Office (ODPO) debris engineering model. Like its predecessor, ORDEM2010 serves the ODPO mission of providing spacecraft designers/operators and debris observers with a publicly available model to calculate orbital debris flux by current-state-of-knowledge methods. The key advance in ORDEM2010 is the input file structure of the yearly debris populations from 1995-2035 of sizes 10 micron - 1 m. These files include debris from low-Earth orbits (LEO) through geosynchronous orbits (GEO). Stable orbital elements (i.e., those that do not randomize on a sub-year timescale) are included in the files as are debris size, debris number, material density, random error and population error. Material density is implemented from ground-test data into the NASA breakup model and assigned to debris fragments accordingly. The random and population errors are due to machine error and uncertainties in debris sizes. These high-fidelity population files call for a much higher-level model analysis than what was possible with the populations of ORDEM2000. Population analysis in the ORDEM2010 model consists of mapping matrices that convert the debris population elements to debris fluxes. One output mode results in a spacecraft encompassing 3-D igloo of debris flux, compartmentalized by debris size, velocity, pitch, and yaw with respect to spacecraft ram direction. The second output mode provides debris flux through an Earth-based telescope/radar beam from LEO through GEO. This paper compares the new ORDEM2010 with ORDEM2000 in terms of processes and results with examples of specific orbits.

Combining waterfowl and breeding bird survey data to estimate wood duck breeding population size in the Atlantic Flyway

USGS Publications Warehouse

Guthrie Zimmerman,; Sauer, John; Fleming, Kathy; Link, William; Pamela R. Garrettson,

2015-01-01

We combined data from the Atlantic Flyway Breeding Waterfowl Survey (AFBWS) and the North American Breeding Bird Survey (BBS) to estimate the number of wood ducks (Aix sponsa) in the United States portion of the Atlantic Flyway from 1993 to 2013. The AFBWS is a plot-based survey that covers most of the northern and central portions of the Flyway; when analyzed with adjustments for survey time of day effects, these data can be used to estimate population size. The BBS provides an index of wood duck abundance along roadside routes. Although factors influencing change in BBS counts over time can be controlled in BBS analysis, BBS indices alone cannot be used to derive population size estimates. We used AFBWS data to scale BBS indices for Bird Conservation Regions (BCR), basing the scaling factors on the ratio of estimated AFBWS population sizes to regional BBS indices for portions of BCRs that were common to both surveys. We summed scaled BBS results for portions of the Flyway not covered by the AFBWS with AFBWS population estimates to estimate a mean yearly total of 1,295,875 (mean 95% CI: 1,013,940–1,727,922) wood ducks. Scaling factors varied among BCRs from 16.7 to 148.0; the mean scaling factor was 68.9 (mean 95% CI: 53.5–90.9). Flyway-wide, population estimates from the combined analysis were consistent with alternative estimates derived from harvest data, and also provide population estimates within states and BCRs. We recommend their use in harvest and habitat management within the Atlantic Flyway.

Precipitation, density, and population dynamics of desert bighorn sheep on San Andres National Wildlife Refuge, New Mexico

USGS Publications Warehouse

Bender, L.C.; Weisenberger, M.E.

2005-01-01

Understanding the determinants of population size and performance for desert bighorn sheep (Ovis canadensis mexicana) is critical to develop effective recovery and management strategies. In arid environments, plant communities and consequently herbivore populations are strongly dependent upon precipitation, which is highly variable seasonally and annually. We conducted a retrospective exploratory analysis of desert bighorn sheep population dynamics on San Andres National Wildlife Refuge (SANWR), New Mexico, 1941-1976, by modeling sheep population size as a function of previous population sizes and precipitation. Population size and trend of desert bighorn were best and well described (R 2=0.89) by a model that included only total annual precipitation as a covariate. Models incorporating density-dependence, delayed density-dependence, and combinations of density and precipitation were less informative than the model containing precipitation alone (??AlCc=8.5-22.5). Lamb:female ratios were positively related to precipitation (current year: F1,34=7.09, P=0.012; previous year: F1,33=3.37, P=0.075) but were unrelated to population size (current year. F1,34=0.04, P=0.843; previous year: F1,33 =0.14, P=0.715). Instantaneous population rate of increase (r) was related to population size (F1,33=5.55; P=0.025). Precipitation limited populations of desert bighorn sheep on SANWR primarily in a density-independent manner by affecting production or survival of lambs, likely through influences on forage quantity and quality. Habitat evaluations and recovery plans for desert bighorn sheep need to consider fundamental influences on desert bighorn populations such as precipitation and food, rather than focus solely on proximate issues such as security cover, predation, and disease. Moreover, the concept of carrying capacity for desert bighorn sheep may need re-evaluation in respect to highly variable (CV =35.6%) localized precipitation patterns. On SANWR carrying capacity for desert bighorn sheep was zero when total annual precipitation was <28.2 cm.

Re-examination of population structure and phylogeography of hawksbill turtles in the wider Caribbean using longer mtDNA sequences.

PubMed

Leroux, Robin A; Dutton, Peter H; Abreu-Grobois, F Alberto; Lagueux, Cynthia J; Campbell, Cathi L; Delcroix, Eric; Chevalier, Johan; Horrocks, Julia A; Hillis-Starr, Zandy; Troëng, Sebastian; Harrison, Emma; Stapleton, Seth

2012-01-01

Management of the critically endangered hawksbill turtle in the Wider Caribbean (WC) has been hampered by knowledge gaps regarding stock structure. We carried out a comprehensive stock structure re-assessment of 11 WC hawksbill rookeries using longer mtDNA sequences, larger sample sizes (N = 647), and additional rookeries compared to previous surveys. Additional variation detected by 740 bp sequences between populations allowed us to differentiate populations such as Barbados-Windward and Guadeloupe (F (st) = 0.683, P < 0.05) that appeared genetically indistinguishable based on shorter 380 bp sequences. POWSIM analysis showed that longer sequences improved power to detect population structure and that when N < 30, increasing the variation detected was as effective in increasing power as increasing sample size. Geographic patterns of genetic variation suggest a model of periodic long-distance colonization coupled with region-wide dispersal and subsequent secondary contact within the WC. Mismatch analysis results for individual clades suggest a general population expansion in the WC following a historic bottleneck about 100 000-300 000 years ago. We estimated an effective female population size (N (ef)) of 6000-9000 for the WC, similar to the current estimated numbers of breeding females, highlighting the importance of these regional rookeries to maintaining genetic diversity in hawksbills. Our results provide a basis for standardizing future work to 740 bp sequence reads and establish a more complete baseline for determining stock boundaries in this migratory marine species. Finally, our findings illustrate the value of maintaining an archive of specimens for re-analysis as new markers become available.

Population size and stopover duration estimation using mark–resight data and Bayesian analysis of a superpopulation model

USGS Publications Warehouse

Lyons, James E.; Kendall, William L.; Royle, J. Andrew; Converse, Sarah J.; Andres, Brad A.; Buchanan, Joseph B.

2016-01-01

We present a novel formulation of a mark–recapture–resight model that allows estimation of population size, stopover duration, and arrival and departure schedules at migration areas. Estimation is based on encounter histories of uniquely marked individuals and relative counts of marked and unmarked animals. We use a Bayesian analysis of a state–space formulation of the Jolly–Seber mark–recapture model, integrated with a binomial model for counts of unmarked animals, to derive estimates of population size and arrival and departure probabilities. We also provide a novel estimator for stopover duration that is derived from the latent state variable representing the interim between arrival and departure in the state–space model. We conduct a simulation study of field sampling protocols to understand the impact of superpopulation size, proportion marked, and number of animals sampled on bias and precision of estimates. Simulation results indicate that relative bias of estimates of the proportion of the population with marks was low for all sampling scenarios and never exceeded 2%. Our approach does not require enumeration of all unmarked animals detected or direct knowledge of the number of marked animals in the population at the time of the study. This provides flexibility and potential application in a variety of sampling situations (e.g., migratory birds, breeding seabirds, sea turtles, fish, pinnipeds, etc.). Application of the methods is demonstrated with data from a study of migratory sandpipers.

Size selection from fishways and potential evolutionary responses in a threatened Atlantic salmon population

USGS Publications Warehouse

Maynard, George A.; Kinnison, M.T.; Zydlewski, Joseph D.

2017-01-01

The evolutionary effects of harvest on wild fish populations have been documented around the world; however, sublethal selective pressures can also cause evolutionary changes in phenotypes. For migratory fishes, passage facilities may represent instances of nonlethal selective pressure. Our analysis of 6 years of passage data suggests that certain fish passage facilities on the Penobscot River have been exerting selective pressure against large-bodied, anadromous Atlantic salmon (Salmo salar). At the second and third dams in the river, a 91-cm salmon was 21%–27% and 12%–16% less likely to pass than a 45-cm salmon, respectively. Fish size positively influences egg survival and number and is a heritable trait. Therefore, in a wild-reproducing population, exclusion of large fish from spawning areas may have population-level impacts. In the Penobscot River, most returning adults derive from a hatchery program that collects its broodstock after passing the first dam in the river. Analysis of fork lengths of salmon returning to the Penobscot River from 1978 to 2012 provided mixed support for evolution of size at maturity in different age classes in a pattern that may be expected from interactions with conservation hatchery operations. Additionally, slow-maturing and iteroparous individuals that represent the largest salmon size classes were essentially lost from the population during that time, and Penobscot River fish have shorter fork lengths at maturity than Atlantic salmon in undammed systems.

A Re-Evaluation of the Size of the White Shark (Carcharodon carcharias) Population off California, USA

PubMed Central

Burgess, George H.; Bruce, Barry D.; Cailliet, Gregor M.; Goldman, Kenneth J.; Grubbs, R. Dean; Lowe, Christopher G.; MacNeil, M. Aaron; Mollet, Henry F.; Weng, Kevin C.; O'Sullivan, John B.

2014-01-01

White sharks are highly migratory and segregate by sex, age and size. Unlike marine mammals, they neither surface to breathe nor frequent haul-out sites, hindering generation of abundance data required to estimate population size. A recent tag-recapture study used photographic identifications of white sharks at two aggregation sites to estimate abundance in “central California” at 219 mature and sub-adult individuals. They concluded this represented approximately one-half of the total abundance of mature and sub-adult sharks in the entire eastern North Pacific Ocean (ENP). This low estimate generated great concern within the conservation community, prompting petitions for governmental endangered species designations. We critically examine that study and find violations of model assumptions that, when considered in total, lead to population underestimates. We also use a Bayesian mixture model to demonstrate that the inclusion of transient sharks, characteristic of white shark aggregation sites, would substantially increase abundance estimates for the adults and sub-adults in the surveyed sub-population. Using a dataset obtained from the same sampling locations and widely accepted demographic methodology, our analysis indicates a minimum all-life stages population size of >2000 individuals in the California subpopulation is required to account for the number and size range of individual sharks observed at the two sampled sites. Even accounting for methodological and conceptual biases, an extrapolation of these data to estimate the white shark population size throughout the ENP is inappropriate. The true ENP white shark population size is likely several-fold greater as both our study and the original published estimate exclude non-aggregating sharks and those that independently aggregate at other important ENP sites. Accurately estimating the central California and ENP white shark population size requires methodologies that account for biases introduced by sampling a limited number of sites and that account for all life history stages across the species' range of habitats. PMID:24932483

A re-evaluation of the size of the white shark (Carcharodon carcharias) population off California, USA.

PubMed

Burgess, George H; Bruce, Barry D; Cailliet, Gregor M; Goldman, Kenneth J; Grubbs, R Dean; Lowe, Christopher G; MacNeil, M Aaron; Mollet, Henry F; Weng, Kevin C; O'Sullivan, John B

2014-01-01

White sharks are highly migratory and segregate by sex, age and size. Unlike marine mammals, they neither surface to breathe nor frequent haul-out sites, hindering generation of abundance data required to estimate population size. A recent tag-recapture study used photographic identifications of white sharks at two aggregation sites to estimate abundance in "central California" at 219 mature and sub-adult individuals. They concluded this represented approximately one-half of the total abundance of mature and sub-adult sharks in the entire eastern North Pacific Ocean (ENP). This low estimate generated great concern within the conservation community, prompting petitions for governmental endangered species designations. We critically examine that study and find violations of model assumptions that, when considered in total, lead to population underestimates. We also use a Bayesian mixture model to demonstrate that the inclusion of transient sharks, characteristic of white shark aggregation sites, would substantially increase abundance estimates for the adults and sub-adults in the surveyed sub-population. Using a dataset obtained from the same sampling locations and widely accepted demographic methodology, our analysis indicates a minimum all-life stages population size of >2000 individuals in the California subpopulation is required to account for the number and size range of individual sharks observed at the two sampled sites. Even accounting for methodological and conceptual biases, an extrapolation of these data to estimate the white shark population size throughout the ENP is inappropriate. The true ENP white shark population size is likely several-fold greater as both our study and the original published estimate exclude non-aggregating sharks and those that independently aggregate at other important ENP sites. Accurately estimating the central California and ENP white shark population size requires methodologies that account for biases introduced by sampling a limited number of sites and that account for all life history stages across the species' range of habitats.

Droplets size evolution of dispersion in a stirred tank

NASA Astrophysics Data System (ADS)

Kysela, Bohus; Konfrst, Jiri; Chara, Zdenek; Sulc, Radek; Jasikova, Darina

2018-06-01

Dispersion of two immiscible liquids is commonly used in chemical industry as wall as in metallurgical industry e. g. extraction process. The governing property is droplet size distribution. The droplet sizes are given by the physical properties of both liquids and flow properties inside a stirred tank. The first investigation stage is focused on in-situ droplet size measurement using image analysis and optimizing of the evaluation method to achieve maximal result reproducibility. The obtained experimental results are compared with multiphase flow simulation based on Euler-Euler approach combined with PBM (Population Balance Modelling). The population balance model was, in that specific case, simplified with assumption of pure breakage of droplets.

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 birds and, more recently, possibly population dynamics of resident bird species, but this is the first evidence for effects of lemming abundance on population size of a migratory bird species. Why lemming cycles are faltering in the last two decades is unclear, but this may be associated with changes in winter climate at Taimyr Peninsula (Siberia). PMID:23419215

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 recently, possibly population dynamics of resident bird species, but this is the first evidence for effects of lemming abundance on population size of a migratory bird species. Why lemming cycles are faltering in the last two decades is unclear, but this may be associated with changes in winter climate at Taimyr Peninsula (Siberia). © 2013 The Authors. Journal of Animal Ecology © 2013 British Ecological Society.

The episode of genetic drift defining the migration of humans out of Africa is derived from a large east African population size.

PubMed

Elhassan, Nuha; Gebremeskel, Eyoab Iyasu; Elnour, Mohamed Ali; Isabirye, Dan; Okello, John; Hussien, Ayman; Kwiatksowski, Dominic; Hirbo, Jibril; Tishkoff, Sara; Ibrahim, Muntaser E

2014-01-01

Human genetic variation particularly in Africa is still poorly understood. This is despite a consensus on the large African effective population size compared to populations from other continents. Based on sequencing of the mitochondrial Cytochrome C Oxidase subunit II (MT-CO2), and genome wide microsatellite data we observe evidence suggesting the effective size (Ne) of humans to be larger than the current estimates, with a foci of increased genetic diversity in east Africa, and a population size of east Africans being at least 2-6 fold larger than other populations. Both phylogenetic and network analysis indicate that east Africans possess more ancestral lineages in comparison to various continental populations placing them at the root of the human evolutionary tree. Our results also affirm east Africa as the likely spot from which migration towards Asia has taken place. The study reflects the spectacular level of sequence variation within east Africans in comparison to the global sample, and appeals for further studies that may contribute towards filling the existing gaps in the database. The implication of these data to current genomic research, as well as the need to carry out defined studies of human genetic variation that includes more African populations; particularly east Africans is paramount.

The genetics of rhizosheath size in a multiparent mapping population of wheat.

PubMed

Delhaize, Emmanuel; Rathjen, Tina M; Cavanagh, Colin R

2015-08-01

Rhizosheaths comprise soil that adheres to plant roots and, in some species, are indicative of root hair length. In this study, the genetics of rhizosheath size in wheat was investigated by screening the progeny of multiparent advanced generation intercrosses (MAGIC). Two MAGIC populations were screened for rhizosheath size using a high throughput method. One MAGIC population was developed from intercrosses between four parents (4-way) and the other from intercrosses between eight parents (8-way). Transgressive segregation for rhizosheath size was observed in both the 4-way and 8-way MAGIC populations. A quantitative trait loci (QTL) analysis of the 4-way population identified six major loci located on chromosomes 2B, 4D, 5A, 5B, 6A, and 7A together accounting for 42% of the variation in rhizosheath size. Rhizosheath size was strongly correlated with root hair length and was robust across different soil types in the absence of chemical constraints. Rhizosheath size in the MAGIC populations was a reliable surrogate for root hair length and, therefore, the QTL identified probably control root hair elongation. Members of the basic helix-loop-helix family of transcription factors have previously been identified to regulate root hair length in Arabidopsis and rice. Since several wheat members of the basic helix-loop-helix family of genes are located within or near the QTL, these genes are candidates for controlling the long root hair trait. The QTL for rhizosheath size identified in this study provides the opportunity to implement marker-assisted selection to increase root hair length for improved phosphate acquisition in wheat. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Genetic structure of Culex erraticus populations across the Americas.

PubMed

Mendenhall, Ian H; Bahl, Justin; Blum, Michael J; Wesson, Dawn M

2012-05-01

Culex erraticus (Dyar & Knab) is a potential competent vector for several arboviruses such as Eastern and Venezuelan equine encephalitis viruses and West Nile virus. It therefore may play a role in the maintenance and spread of viral populations in areas of concern, including the United States where it occurs in >33 states. However, little information is available on potential barriers to movement across the species' distribution. Here, we analyze genetic variation among Cx. erraticus collected from Colombia, Guatemala, and nine locations in the United States to better understand population structure and connectivity. Comparative sequence analysis of the second internal transcribed spacer and mitochondrial NADH dehydrogenase genes identified two major lineages of sampled populations. One lineage represented the central and eastern United States, whereas the other corresponded to Central America, South America, and the western United States. Hierarchical analysis of genetic variation provided further evidence of regional population structure, although the majority of genetic variation was found to reside within populations, suggestive of large population sizes. Although significant physical barriers such as the Chihuahuan Desert probably constrain the spread of Cx. erraticus, large population sizes and connectivity within regions remain important risk factors that probably contribute to the movement of arboviruses within and between these regions.

The Future of Small- and Medium-Sized Communities in the Prairie Region.

ERIC Educational Resources Information Center

Wellar, Barry S., Ed.

Four papers are featured. The first is a statistical overview and analysis of past, present and future happenings to small communities in the Region; it focuses on two indicators: (1) population growth or declining community class size and, (2) the changing distribution of commercial outlets by community class size. The other three papers report…

Nature of the Martian surface as inferred from the particle-size distribution of lunar-surface material.

NASA Technical Reports Server (NTRS)

Mason, C. C.

1971-01-01

Analysis of lunar particle size distribution data indicates that the surface material is composed of two populations. One population is caused by comminution from the impact of the larger-sized meteorites, while the other population is caused by the melting of fine material by the impact of smaller-sized meteorites. The results are referred to Mars, and it is shown that the Martian atmosphere would vaporize the smaller incoming meteorites and retard the incoming meteorites of intermediate and large size, causing comminution and stirring of the particulate layer. The combination of comminution and stirring would result in fine material being sorted out by the prevailing circulation of the Martian atmosphere and the material being transported to regions where it could be deposited. As a result, the Martian surface in regions of prevailing upward circulation is probably covered by either a rubble layer or by desert pavement; regions of prevailing downward circulation are probably covered by sand dunes.

Phenotypic and Transcriptional Analysis of Divergently Selected Maize Populations Reveals the Role of Developmental Timing in Seed Size Determination1[W][OPEN

PubMed Central

Sekhon, Rajandeep S.; Hirsch, Candice N.; Childs, Kevin L.; Breitzman, Matthew W.; Kell, Paul; Duvick, Susan; Spalding, Edgar P.; Buell, C. Robin; de Leon, Natalia; Kaeppler, Shawn M.

2014-01-01

Seed size is a component of grain yield and an important trait in crop domestication. To understand the mechanisms governing seed size in maize (Zea mays), we examined transcriptional and developmental changes during seed development in populations divergently selected for large and small seed size from Krug, a yellow dent maize cultivar. After 30 cycles of selection, seeds of the large seed population (KLS30) have a 4.7-fold greater weight and a 2.6-fold larger size compared with the small seed population (KSS30). Patterns of seed weight accumulation from the time of pollination through 30 d of grain filling showed an earlier onset, slower rate, and earlier termination of grain filling in KSS30 relative to KLS30. This was further supported by transcriptome patterns in seeds from the populations and derived inbreds. Although the onset of key genes was earlier in small seeds, similar maximum transcription levels were observed in large seeds at later stages, suggesting that functionally weaker alleles, rather than transcript abundance, may be the basis of the slow rate of seed filling in KSS30. Gene coexpression networks identified several known genes controlling cellularization and proliferation as well as novel genes that will be useful candidates for biotechnological approaches aimed at altering seed size in maize and other cereals. PMID:24710068

Association between unemployment, income, education level, population size and air pollution in Czech cities: evidence for environmental inequality? A pilot national scale analysis.

PubMed

Branis, Martin; Linhartova, Martina

2012-09-01

We analyzed differentials in exposure to SO(2), PM(10) and NO(2) among Czech urban populations categorized according to education level, unemployment rate, population size and average annual salary. Altogether 39 cities were included in the analysis. The principal component analysis revealed two factors explaining 72.8% of the data variability. The first factor explaining 44.7% of the data variability included SO(2), PM(10), low education level and high unemployment, documenting that inhabitants with unfavorable socioeconomic status mainly reside in smaller cities with higher concentration levels of combustion-related air pollutants. The second factor explaining 28.1% of the data variability included NO(2), high salary, high education level and large population, suggesting that large cities with residents with higher socioeconomic status are exposed to higher levels of traffic-related air pollution. We conclude that, after more than a decade of free-market economy, the Czech Republic, a former Soviet satellite with a centrally planned economy, displays signs of a certain kind of environmental inequality, since environmental hazards are unevenly distributed among the Czech urban populations. Copyright © 2012 Elsevier Ltd. All rights reserved.

The co-evolution of cultures, social network communities, and agent locations in an extension of Axelrod’s model of cultural dissemination

NASA Astrophysics Data System (ADS)

Pfau, Jens; Kirley, Michael; Kashima, Yoshihisa

2013-01-01

We introduce a variant of the Axelrod model of cultural dissemination in which agents change their physical locations, social links, and cultures. Numerical simulations are used to investigate the evolution of social network communities and the cultural diversity within and between these communities. An analysis of the simulation results shows that an initial peak in the cultural diversity within network communities is evident before agents segregate into a final configuration of culturally homogeneous communities. Larger long-range interaction probabilities facilitate the initial emergence of culturally diverse network communities, which leads to a more pronounced initial peak in cultural diversity within communities. At equilibrium, the number of communities, and hence cultures, increases when the initial cultural diversity increases. However, the number of communities decreases when the lattice size or population density increases. A phase transition between two regimes of initial cultural diversity is evident. For initial diversities below a critical value, a single network community and culture emerges that dominates the population. For initial diversities above the critical value, multiple culturally homogeneous communities emerge. The critical value of initial diversity at which this transition occurs increases with increasing lattice size and population density and generally with increasing absolute population size. We conclude that larger initial diversities promote cultural heterogenization, while larger lattice sizes, population densities, and in fact absolute population sizes promote homogenization.

Population and genetic outcomes 20 years after reintroducing bobcats (Lynx rufus) to Cumberland Island, Georgia USA

USGS Publications Warehouse

Diefenbach, Duane R.; Hansen, Leslie A.; Bohling, Justin H.; Miller-Butterworth, Cassandra

2015-01-01

In 1988–1989, 32 bobcats Lynx rufus were reintroduced to Cumberland Island (CUIS), Georgia, USA, from which they had previously been extirpated. They were monitored intensively for 3 years immediately post-reintroduction, but no estimation of the size or genetic diversity of the population had been conducted in over 20 years since reintroduction. We returned to CUIS in 2012 to estimate abundance and effective population size of the present-day population, as well as to quantify genetic diversity and inbreeding. We amplified 12 nuclear microsatellite loci from DNA isolated from scats to establish genetic profiles to identify individuals. We used spatially explicit capture–recapture population estimation to estimate abundance. From nine unique genetic profiles, we estimate a population size of 14.4 (SE = 3.052) bobcats, with an effective population size (Ne) of 5–8 breeding individuals. This is consistent with predictions of a population viability analysis conducted at the time of reintroduction, which estimated the population would average 12–13 bobcats after 10 years. We identified several pairs of related bobcats (parent-offspring and full siblings), but ~75% of the pairwise comparisons were typical of unrelated individuals, and only one individual appeared inbred. Despite the small population size and other indications that it has likely experienced a genetic bottleneck, levels of genetic diversity in the CUIS bobcat population remain high compared to other mammalian carnivores. The reintroduction of bobcats to CUIS provides an opportunity to study changes in genetic diversity in an insular population without risk to this common species. Opportunities for natural immigration to the island are limited; therefore, continued monitoring and supplemental bobcat reintroductions could be used to evaluate the effect of different management strategies to maintain genetic diversity and population viability. The successful reintroduction and maintenance of a bobcat population on CUIS illustrates the suitability of translocation as a management tool for re-establishing felid populations.

Risk of population extinction from fixation of deleterious and reverse mutations.

PubMed

Lande, R

1998-01-01

A model is developed for alternate fixations of mildly deleterious and wild-type alleles arising by forward and reverse mutation in a finite population. For almost all parameter values, this gives an equilibrium load that agrees closely with the general expression derived from diffusion theory. Nearly neutral mutations with selection coefficient a few times larger than 1/(2N(e)) do the most damage by increasing the equilibrium load. The model of alternate fixations facilitates dynamical analysis of the expected load and the mean time to extinction in a population that has been suddenly reduced from a very large size to a small size. Reverse mutation can substantially improve population viability, increasing the mean time to extinction by an order of magnitude or more, but because many mutations are irreversible the effects may not be large. Populations with initially high mean fitness and small effective size, N(e) below a few hundred individuals, may be at serious risk of extinction from fixation of deleterious mutations within 10(3) to 10(4) generations.

Estimation of population trajectories from count data

USGS Publications Warehouse

Link, W.A.; Sauer, J.R.

1997-01-01

Monitoring of changes in animal population size is rarely possible through complete censuses; frequently, the only feasible means of monitoring changes in population size is to use counts of animals obtained by skilled observers as indices to abundance. Analysis of changes in population size can be severely biased if factors related to the acquisition of data are not adequately controlled for. In particular we identify two types of observer effects: these correspond to baseline differences in observer competence, and to changes through time in the ability of individual observers. We present a family of models for count data in which the first of these observer effects is treated as a nuisance parameter. Conditioning on totals of negative binomial counts yields a Dirichlet compound multinomial vector for each observer. Quasi-likelihood is used to estimate parameters related to population trajectory and other parameters of interest; model selection is carried out on the basis of Akaike's information criterion. An example is presented using data on Wood thrush from the North American Breeding Bird Survey.

Sampling intraspecific variability in leaf functional traits: Practical suggestions to maximize collected information.

PubMed

Petruzzellis, Francesco; Palandrani, Chiara; Savi, Tadeja; Alberti, Roberto; Nardini, Andrea; Bacaro, Giovanni

2017-12-01

The choice of the best sampling strategy to capture mean values of functional traits for a species/population, while maintaining information about traits' variability and minimizing the sampling size and effort, is an open issue in functional trait ecology. Intraspecific variability (ITV) of functional traits strongly influences sampling size and effort. However, while adequate information is available about intraspecific variability between individuals (ITV BI ) and among populations (ITV POP ), relatively few studies have analyzed intraspecific variability within individuals (ITV WI ). Here, we provide an analysis of ITV WI of two foliar traits, namely specific leaf area (SLA) and osmotic potential (π), in a population of Quercus ilex L. We assessed the baseline ITV WI level of variation between the two traits and provided the minimum and optimal sampling size in order to take into account ITV WI , comparing sampling optimization outputs with those previously proposed in the literature. Different factors accounted for different amount of variance of the two traits. SLA variance was mostly spread within individuals (43.4% of the total variance), while π variance was mainly spread between individuals (43.2%). Strategies that did not account for all the canopy strata produced mean values not representative of the sampled population. The minimum size to adequately capture the studied functional traits corresponded to 5 leaves taken randomly from 5 individuals, while the most accurate and feasible sampling size was 4 leaves taken randomly from 10 individuals. We demonstrate that the spatial structure of the canopy could significantly affect traits variability. Moreover, different strategies for different traits could be implemented during sampling surveys. We partially confirm sampling sizes previously proposed in the recent literature and encourage future analysis involving different traits.

The relationship between central corneal thickness and optic disc size in patients with primary open-angle glaucoma in a hospital-based population.

PubMed

Terai, Naim; Spoerl, Eberhard; Pillunat, Lutz E; Kuhlisch, Eberhard; Schmidt, Eckart; Boehm, Andreas G

2011-09-01

To investigate the relationship between central corneal thickness (CCT) and optic disc size in patients with primary open-angle glaucoma (POAG) in a hospital-based population. Data for the right eyes of 1435 White patients with POAG were included in a retrospective hospital-based study. All eyes underwent optic nerve head imaging using Heidelberg Retina Tomograph II (HRT II; Heidelberg Engineering, Heidelberg, Germany) and CCT measurement by ultrasound corneal pachymetry. Eyes with prior intraocular or corneal surgery were excluded. Low-quality HRT II images were also excluded. The impact of age, gender, CCT, intraocular pressure, cylindrical and spherical refractive error as independent factors on optic disc size was investigated in a multiple linear regression analysis. The data for 1104 right eyes qualified for participation in the study. The median age of these patients was 65 years. The median CCT was 547 μm (25th-75th percentile 522-575 μm). The median optic disc size was 2.21 mm(2) (25th-75th percentile 1.89-2.60 mm(2)). Multiple linear regression analysis revealed that age (p = 0.001), CCT (p = 0.001) and spherical equivalent (p = 0.049) were correlated to disc size according to the following formula: disc area = -0.004 × age - 0.001 × CCT - 0.014 × spherical equivalent +3.290. R(2) of the whole model was 0.021. Univariate regression analysis between age and disc area provided R(2) = 0.008 with p = 0.002. Univariate regression analysis between disc area and CCT provided R(2) = 0.005 with p = 0.02. In this retrospective hospital-based study we could not detect a clinically relevant correlation between optic disc size and CCT. The correlation between CCT and disc size and between age and disc size were statistically significant, but the R(2) values were very low. The results of the study are biased because of its hospital-based design, so the results of the study need to be confirmed in a large population-based study. © 2009 The Authors. Journal compilation © 2009 Acta Ophthalmol.

Chromosome 9p21 In Ischemic Stroke: Population Structure and Meta-Analysis

PubMed Central

Anderson, CD; Biffi, A; Rost, NS; Cortellini, L; Furie, KL; Rosand, J

2011-01-01

Background and Purpose Sequence variants on chromosome 9p21.3 are implicated in coronary artery disease (CAD) and myocardial infarction (MI), but studies in ischemic stroke have produced inconsistent results. We investigated whether these conflicting findings were due to false positive studies confounded by population stratification, or false negative studies that failed to account for effects specific to certain stroke subtypes. Methods After assessing for population stratification at 9p21.3 using genome-wide data, we meta-analyzed 8 ischemic stroke studies. This analysis focused on two single nucleotide polymorphisms (SNPs), rs1537378 and rs10757278, as these variants are in strong linkage disequilibrium with most SNPs analyzed in prior studies of the region. Results Principal component analysis of the genome-wide data showed no evidence of population stratification at that locus. Meta-analysis confirmed that both rs1537378 and rs10757278 are risk factors for ischemic stroke (odds ratios 1.09, [p = 0.0014], and 1.11, [p = 0.001] respectively). Subtype analysis revealed a substantial increase in the effect of each SNP for risk of large artery (LA) stroke, achieving an effect size similar to that seen in CAD/MI. Conclusions Variants on 9p21.3 are associated with ischemic stroke, and restriction of analysis to LA stroke increases effect size towards that observed in prior association studies of CAD/MI. Previous inconsistent findings are best explained by this subtype-specificity rather than any unmeasured confounding by population stratification. PMID:20395606

Ecological correlates of population genetic structure: a comparative approach using a vertebrate metacommunity.

PubMed

Manier, Mollie K; Arnold, Stevan J

2006-12-07

Identifying ecological factors associated with population genetic differentiation is important for understanding microevolutionary processes and guiding the management of threatened populations. We identified ecological correlates of several population genetic parameters for three interacting species (two garter snakes and an anuran) that occupy a common landscape. Using multiple regression analysis, we found that species interactions were more important in explaining variation in population genetic parameters than habitat and nearest-neighbour characteristics. Effective population size was best explained by census size, while migration was associated with differences in species abundance. In contrast, genetic distance was poorly explained by the ecological correlates that we tested, but geographical distance was prominent in models for all species. We found substantially different population dynamics for the prey species relative to the two predators, characterized by larger effective sizes, lower gene flow and a state of migration-drift equilibrium. We also identified an escarpment formed by a series of block faults that serves as a barrier to dispersal for the predators. Our results suggest that successful landscape-level management should incorporate genetic and ecological data for all relevant species, because even closely associated species can exhibit very different population genetic dynamics on the same landscape.

On sample size of the kruskal-wallis test with application to a mouse peritoneal cavity study.

PubMed

Fan, Chunpeng; Zhang, Donghui; Zhang, Cun-Hui

2011-03-01

As the nonparametric generalization of the one-way analysis of variance model, the Kruskal-Wallis test applies when the goal is to test the difference between multiple samples and the underlying population distributions are nonnormal or unknown. Although the Kruskal-Wallis test has been widely used for data analysis, power and sample size methods for this test have been investigated to a much lesser extent. This article proposes new power and sample size calculation methods for the Kruskal-Wallis test based on the pilot study in either a completely nonparametric model or a semiparametric location model. No assumption is made on the shape of the underlying population distributions. Simulation results show that, in terms of sample size calculation for the Kruskal-Wallis test, the proposed methods are more reliable and preferable to some more traditional methods. A mouse peritoneal cavity study is used to demonstrate the application of the methods. © 2010, The International Biometric Society.

[Rural-urban population redistribution between 1970 and 1980 (a micro-regional analysis)].

PubMed

Costa, M A

1982-01-01

Changes in rural-urban population distribution in Brazil from 1970 to 1980 are analyzed using census data. Trends examined include spatial redistribution throughout the country, rapid urbanization, the decline in the size of the rural population in the state of Parana, agricultural expansion in the northern and central-western regions, and the increase of the rural population within metropolitan areas. (summary in ENG)

Generalizing the Network Scale-Up Method: A New Estimator for the Size of Hidden Populations*

PubMed Central

Feehan, Dennis M.; Salganik, Matthew J.

2018-01-01

The network scale-up method enables researchers to estimate the size of hidden populations, such as drug injectors and sex workers, using sampled social network data. The basic scale-up estimator offers advantages over other size estimation techniques, but it depends on problematic modeling assumptions. We propose a new generalized scale-up estimator that can be used in settings with non-random social mixing and imperfect awareness about membership in the hidden population. Further, the new estimator can be used when data are collected via complex sample designs and from incomplete sampling frames. However, the generalized scale-up estimator also requires data from two samples: one from the frame population and one from the hidden population. In some situations these data from the hidden population can be collected by adding a small number of questions to already planned studies. For other situations, we develop interpretable adjustment factors that can be applied to the basic scale-up estimator. We conclude with practical recommendations for the design and analysis of future studies. PMID:29375167

The influence of life history trade-offs and the size of the incubation gravels on egg size variation in sockeye salmon Onchorhynchus nerka

USGS Publications Warehouse

Quinn, Thomas P.; Hendry , Andrew P.; Wetzel, Lisa A.

1995-01-01

Egg size is a critical life history trait, reflecting female investment and affecting off- spring fitness. We investigated several factors which may influence variation in egg weight for sockeye salmon (Oncorhynchus nerka). Comparisons were based on col- lections from 18 Alaskan populations, among which adult migration distance and ju- venile rearing habitat were similar but the size composition of incubation gravels was different. Among populations, most of the variation in egg weight could be explained by a positive correlation with different measures of the size composition of incubation gravels (Pearson's r = 0.45-0.91). In contrast, egg weight was poorly correlated with female body length and with female snout length, a morphological feature used during intra-sexual competition. Within each of the Alaskan populations, however, egg weight and snout length were positively correlated with female body length and hence with each other. A positive association between snout length and egg weight was still evident even after the effects of covariance with body size were removed using resid- uals analysis: for all of the fish pooled and within 6 of the 16 populations. A signifi- cant relationship was not detected in the other populations but the trend was neverthe- less positive in 8 of the other 10. Examination of reproductive traits (gonad weight, egg weight, egg number, snout length and hump size) within another population iden- tified a trade-off between egg weight and egg number for females of a given body length. In contrast, positive correlations between reproductive traits were more com- mon, suggesting that energy-rich individuals produce large eggs and large secondary sexual characteristics rather than sacrificing one for the other.

Estimating black bear population density and genetic diversity at Tensas River, Louisiana using microsatellite DNA markers

USGS Publications Warehouse

Boersen, Mark R.; Clark, Joseph D.; King, Tim L.

2003-01-01

The Recovery Plan for the federally threatened Louisiana black bear (Ursus americanus luteolus) mandates that remnant populations be estimated and monitored. In 1999 we obtained genetic material with barbed-wire hair traps to estimate bear population size and genetic diversity at the 329-km2 Tensas River Tract, Louisiana. We constructed and monitored 122 hair traps, which produced 1,939 hair samples. Of those, we randomly selected 116 subsamples for genetic analysis and used up to 12 microsatellite DNA markers to obtain multilocus genotypes for 58 individuals. We used Program CAPTURE to compute estimates of population size using multiple mark-recapture models. The area of study was almost entirely circumscribed by agricultural land, thus the population was geographically closed. Also, study-area boundaries were biologically discreet, enabling us to accurately estimate population density. Using model Chao Mh to account for possible effects of individual heterogeneity in capture probabilities, we estimated the population size to be 119 (SE=29.4) bears, or 0.36 bears/km2. We were forced to examine a substantial number of loci to differentiate between some individuals because of low genetic variation. Despite the probable introduction of genes from Minnesota bears in the 1960s, the isolated population at Tensas exhibited characteristics consistent with inbreeding and genetic drift. Consequently, the effective population size at Tensas may be as few as 32, which warrants continued monitoring or possibly genetic augmentation.

Estimating the Size of a Large Network and its Communities from a Random Sample

PubMed Central

Chen, Lin; Karbasi, Amin; Crawford, Forrest W.

2017-01-01

Most real-world networks are too large to be measured or studied directly and there is substantial interest in estimating global network properties from smaller sub-samples. One of the most important global properties is the number of vertices/nodes in the network. Estimating the number of vertices in a large network is a major challenge in computer science, epidemiology, demography, and intelligence analysis. In this paper we consider a population random graph G = (V, E) from the stochastic block model (SBM) with K communities/blocks. A sample is obtained by randomly choosing a subset W ⊆ V and letting G(W) be the induced subgraph in G of the vertices in W. In addition to G(W), we observe the total degree of each sampled vertex and its block membership. Given this partial information, we propose an efficient PopULation Size Estimation algorithm, called PULSE, that accurately estimates the size of the whole population as well as the size of each community. To support our theoretical analysis, we perform an exhaustive set of experiments to study the effects of sample size, K, and SBM model parameters on the accuracy of the estimates. The experimental results also demonstrate that PULSE significantly outperforms a widely-used method called the network scale-up estimator in a wide variety of scenarios. PMID:28867924

Estimating the Size of a Large Network and its Communities from a Random Sample.

PubMed

Chen, Lin; Karbasi, Amin; Crawford, Forrest W

2016-01-01

Most real-world networks are too large to be measured or studied directly and there is substantial interest in estimating global network properties from smaller sub-samples. One of the most important global properties is the number of vertices/nodes in the network. Estimating the number of vertices in a large network is a major challenge in computer science, epidemiology, demography, and intelligence analysis. In this paper we consider a population random graph G = ( V, E ) from the stochastic block model (SBM) with K communities/blocks. A sample is obtained by randomly choosing a subset W ⊆ V and letting G ( W ) be the induced subgraph in G of the vertices in W . In addition to G ( W ), we observe the total degree of each sampled vertex and its block membership. Given this partial information, we propose an efficient PopULation Size Estimation algorithm, called PULSE, that accurately estimates the size of the whole population as well as the size of each community. To support our theoretical analysis, we perform an exhaustive set of experiments to study the effects of sample size, K , and SBM model parameters on the accuracy of the estimates. The experimental results also demonstrate that PULSE significantly outperforms a widely-used method called the network scale-up estimator in a wide variety of scenarios.

The Population of Optically Faint GEO Debris

NASA Technical Reports Server (NTRS)

Seitzer, Patrick; Barker, Ed; Buckalew, Brent; Burkhardt, Andrew; Cowardin, Heather; Frith, James; Gomez, Juan; Kaleida, Catherine; Lederer, Susan M.; Lee, Chris H.

2016-01-01

The 6.5-m Magellan telescope 'Walter Baade' at the Las Campanas Observatory in Chile has been used for spot surveys of the GEO orbital regime to study the population of optically faint GEO debris. The goal is to estimate the size of the population of GEO debris at sizes much smaller than can be studied with 1-meter class telescopes. Despite the small size of the field of view of the Magellan instrument (diameter 0.5-degree), a significant population of objects fainter than R = 19th magnitude have been found with angular rates consistent with circular orbits at GEO. We compare the size of this population with the numbers of GEO objects found at brighter magnitudes by smaller telescopes. The observed detections have a wide range in characteristics starting with those appearing as short uniform streaks. But there are a substantial number of detections with variations in brightness, flashers, during the 5-second exposure. The duration of each of these flashes can be extremely brief: sometimes less than half a second. This is characteristic of a rapidly tumbling object with a quite variable projected size times albedo. If the albedo is of the order of 0.2, then the largest projected size of these objects is around 10-cm. The data in this paper was collected over the last several years using Magellan's IMACS camera in f/2 mode. The analysis shows the brightness bins for the observed GEO population as well as the periodicity of the flashers. All objects presented are correlated with the catalog: the focus of the paper will be on the uncorrelated, optically faint, objects. The goal of this project is to better characterize the faint debris population in GEO that access to a 6.5-m optical telescope in a superb site can provide.

Understanding the lessons and limitations of conservation and development.

PubMed

Oldekop, Johan A; Bebbington, Anthony J; Brockington, Dan; Preziosi, Richard F

2010-04-01

The lack of concrete instances in which conservation and development have been successfully merged has strengthened arguments for strict exclusionist conservation policies. Research has focused more on social cooperation and conflict of different management regimes and less on how these factors actually affect the natural environments they seek to conserve. Consequently, it is still unknown which strategies yield better conservation outcomes? We conducted a meta-analysis of 116 published case studies on common resource management regimes from Africa, south and central America, and southern and Southeast Asia. Using ranked sociodemographic, political, and ecological data, we analyzed the effect of land tenure, population size, social heterogeneity, as well as internally devised resource-management rules and regulations (institutions) on conservation outcome. Although land tenure, population size, and social heterogeneity did not significantly affect conservation outcome, institutions were positively associated with better conservation outcomes. There was also a significant interaction effect between population size and institutions, which implies complex relationships between population size and conservation outcome. Our results suggest that communities managing a common resource can play a significant role in conservation and that institutions lead to management regimes with lower environmental impacts.

Population biology and feeding habits of the nephropid lobster Metanephrops thomsoni (Bate, 1888) in the East China Sea.

PubMed

Choi, Jung Hwa; Kim, Jung Nyun; Kim, Mi Hyang; Chang, Dae Soo; Yoo, Joon Taek; Kim, Jin Koo

2008-07-01

Population biology and feeding habits of the nephropidlobsterMetanephrops thomsoni (Bate) was studied from a field survey sampled with bottom trawls in the East China Sea. The female/male ratio was 1.06:1. Three size-class groups were discriminated for both sexes, which may correspond to one to three year-old cohorts. The average stage fecundity was 471 in each brood. Larger than two-year-size-class females are multi broods during the breeding season. Gut analysis showed that this lobster is a common camivore and mainly consume crustaceans and fishes, regardless of sex and carapace length size.

Left atrial size and function: role in prognosis.

PubMed

Hoit, Brian D

2014-02-18

The author examines the ability of left atrial size and function to predict cardiovascular outcomes. Data are sufficient to recommend evaluation of left atrial volume in certain populations, and although analysis of atrial reservoir, conduit, and booster pump function trails in that regard, the gap is rapidly closing. In this state-of-the-art paper, the author reviews the methods used to assess left atrial size and function and discusses their role in predicting cardiovascular events in general and referral populations and in patients with atrial fibrillation, cardiomyopathy, ischemic heart disease, and valvular heart disease. Copyright © 2014 American College of Cardiology Foundation. Published by Elsevier Inc. All rights reserved.

Effects of physiological aging on mismatch negativity: a meta-analysis.

PubMed

Cheng, Chia-Hsiung; Hsu, Wan-Yu; Lin, Yung-Yang

2013-11-01

Mismatch negativity (MMN) is a promising window on how the functional integrity of auditory sensory memory and change discrimination is modulated by age and relevant clinical conditions. However, the effects of aging on MMN have remained somewhat elusive, particularly at short interstimulus intervals (ISIs). We performed a meta-analysis of peer-reviewed MMN studies that had targeted both young and elderly adults to estimate the mean effect size. Nine studies, consisting of 29 individual investigations, were included and the final total study population consisted of 182 young and 165 elderly subjects. The effects of different deviant types and duration of ISIs on the effect size were assessed. The overall mean effect size was 0.63 (95% CI at 0.43-0.82). The effect sizes for long ISI (>2s, effect size 0.68, 95% CI at 0.31-1.06) and short ISI (<2s, effect size 0.61, 95% CI at 0.39-0.84) were both considered moderate. A further analysis showed a prominent aging-related decrease in MMN responses to duration and frequency changes at short ISIs. It was also interesting to note that the effect size was about 25% larger for duration deviant condition compared to the frequency deviant condition. In conclusion, a reduced MMN response to duration and frequency deviants is a robust feature among the aged adults, which suggests that there has been a decline in the functional integrity of central auditory processing in this population. © 2013.

Genome-wide analysis of the diversity and ancestry of Korean dogs.

PubMed

Choi, Bong Hwan; Wijayananda, Hasini I; Lee, Soo Hyun; Lee, Doo Ho; Kim, Jong Seok; Oh, Seok Il; Park, Eung Woo; Lee, Cheul Koo; Lee, Seung Hwan

2017-01-01

There are various hypotheses on dog domestication based on archeological and genetic studies. Although many studies have been conducted on the origin of dogs, the existing literature about the ancestry, diversity, and population structure of Korean dogs is sparse. Therefore, this study is focused on the origin, diversity and population structure of Korean dogs. The study sample comprised four major categories, including non-dogs (coyotes and wolves), ancient, modern and Korean dogs. Selected samples were genotyped using an Illumina CanineHD array containing 173,662 single nucleotide polymorphisms. The genome-wide data were filtered using quality control parameters in PLINK 1.9. Only autosomal chromosomes were used for further analysis. The negative off-diagonal variance of the genetic relationship matrix analysis depicted, the variability of samples in each population. FIS (inbreeding rate within a population) values indicated, a low level of inbreeding within populations, and the patterns were in concordance with the results of Nei's genetic distance analysis. The lowest FST (inbreeding rate between populations) values among Korean and Chinese breeds, using a phylogenetic tree, multi-dimensional scaling, and a TreeMix likelihood tree showed Korean breeds are highly related to Chinese breeds. The Korean breeds possessed a unique and large diversity of admixtures compared with other breeds. The highest and lowest effective population sizes were observed in Korean Jindo Black (485) and Korean Donggyeong White (109), respectively. The historical effective population size of all Korean dogs showed declining trend from the past to present. It is important to take immediate action to protect the Korean dog population while conserving their diversity. Furthermore, this study suggests that Korean dogs have unique diversity and are one of the basal lineages of East Asian dogs, originating from China.

Genome-wide analysis of the diversity and ancestry of Korean dogs

PubMed Central

Lee, Doo Ho; Kim, Jong Seok; Oh, Seok Il; Park, Eung Woo; Lee, Cheul Koo; Lee, Seung Hwan

2017-01-01

There are various hypotheses on dog domestication based on archeological and genetic studies. Although many studies have been conducted on the origin of dogs, the existing literature about the ancestry, diversity, and population structure of Korean dogs is sparse. Therefore, this study is focused on the origin, diversity and population structure of Korean dogs. The study sample comprised four major categories, including non-dogs (coyotes and wolves), ancient, modern and Korean dogs. Selected samples were genotyped using an Illumina CanineHD array containing 173,662 single nucleotide polymorphisms. The genome-wide data were filtered using quality control parameters in PLINK 1.9. Only autosomal chromosomes were used for further analysis. The negative off-diagonal variance of the genetic relationship matrix analysis depicted, the variability of samples in each population. FIS (inbreeding rate within a population) values indicated, a low level of inbreeding within populations, and the patterns were in concordance with the results of Nei’s genetic distance analysis. The lowest FST (inbreeding rate between populations) values among Korean and Chinese breeds, using a phylogenetic tree, multi-dimensional scaling, and a TreeMix likelihood tree showed Korean breeds are highly related to Chinese breeds. The Korean breeds possessed a unique and large diversity of admixtures compared with other breeds. The highest and lowest effective population sizes were observed in Korean Jindo Black (485) and Korean Donggyeong White (109), respectively. The historical effective population size of all Korean dogs showed declining trend from the past to present. It is important to take immediate action to protect the Korean dog population while conserving their diversity. Furthermore, this study suggests that Korean dogs have unique diversity and are one of the basal lineages of East Asian dogs, originating from China. PMID:29182674

Body size and meta-community structure: the allometric scaling of parasitic worm communities in their mammalian hosts.

PubMed

DE Leo, Giulio A; Dobson, Andrew P; Gatto, Marino

2016-06-01

In this paper we derive from first principles the expected body sizes of the parasite communities that can coexist in a mammal of given body size. We use a mixture of mathematical models and known allometric relationships to examine whether host and parasite life histories constrain the diversity of parasite species that can coexist in the population of any host species. The model consists of one differential equation for each parasite species and a single density-dependent nonlinear equation for the affected host under the assumption of exploitation competition. We derive threshold conditions for the coexistence and competitive exclusion of parasite species using invasion criteria and stability analysis of the resulting equilibria. These results are then used to evaluate the range of parasites species that can invade and establish in a target host and identify the 'optimal' size of a parasite species for a host of a given body size; 'optimal' is defined as the body size of a parasite species that cannot be outcompeted by any other parasite species. The expected distributions of parasites body sizes in hosts of different sizes are then compared with those observed in empirical studies. Our analysis predicts the relative abundance of parasites of different size that establish in the host and suggests that increasing the ratio of parasite body size to host body size above a minimum threshold increases the persistence of the parasite population.

Population-regulating processes during the adult phase in flatfish

NASA Astrophysics Data System (ADS)

Rijnsdorp, A. D.

Flatfish support major fisheries and the study of regulatory processes are of paramount importance for evaluating the resilience of the resource to exploitation. This paper reviews the evidence for processes operating during the adult phase that may 1. generate interannual variability in recruitment; 2. contribute to population regulation through density-dependent growth, density-dependent ripening of adults and density-dependent egg production. With regard to (1), there is evidence that in the adult phase processes do occur that may generate recruitment variability through variation in size-specific fecundity, contraction of spawning season, reduction in egg quality, change in sex ratio and size composition of the adult population. However, time series of recruitment do not provide support for this hypothesis. With regard to (2), there is ample evidence that exploitation of flatfish coincides with an increase in growth, although the mechanisms involved are not always clear. The presence of density-dependent growth in the adult phase of unexploited populations appears to be the most likely explanation in some cases. From the early years of exploitation of flatfish stocks inhabiting cold waters, evidence exists that adult fish do not spawn each year. Fecundity schedules show annual variations, but the available information suggests that size-specific fecundity is stable over a broad range of population abundance and may only decrease at high population abundance. The analysis is complicated by the possibility of a trade-off between egg numbers and egg size. Nevertheless, a density-dependent decrease in growth will automatically result in a decrease in absolute fecundity because of the reduced body size. The potential contribution of these regulatory effects on population regulation is explored. Results indicate that density-dependent ripening and absolute fecundity, mediated through density-dependent growth, may control recruitment at high levels of population abundance. The effect of a density-dependent decrease in size-specific fecundity seems to play a minor role, although this role may become important at extremely high levels of population abundance.

Evolutionary dynamics of fearfulness and boldness.

PubMed

Ji, Ting; Zhang, Boyu; Sun, Yuehua; Tao, Yi

2009-02-21

A negative relationship between reproductive effort and survival is consistent with life-history. Evolutionary dynamics and evolutionarily stable strategy (ESS) for the trade-off between survival and reproduction are investigated using a simple model with two phenotypes, fearfulness and boldness. The dynamical stability of the pure strategy model and analysis of ESS conditions reveal that: (i) the simple coexistence of fearfulness and boldness is impossible; (ii) a small population size is favorable to fearfulness, but a large population size is favorable to boldness, i.e., neither fearfulness, nor boldness is always favored by natural selection; and (iii) the dynamics of population density is crucial for a proper understanding of the strategy dynamics.

Finite-size effects and switching times for Moran process with mutation.

PubMed

DeVille, Lee; Galiardi, Meghan

2017-04-01

We consider the Moran process with two populations competing under an iterated Prisoner's Dilemma in the presence of mutation, and concentrate on the case where there are multiple evolutionarily stable strategies. We perform a complete bifurcation analysis of the deterministic system which arises in the infinite population size. We also study the Master equation and obtain asymptotics for the invariant distribution and metastable switching times for the stochastic process in the case of large but finite population. We also show that the stochastic system has asymmetries in the form of a skew for parameter values where the deterministic limit is symmetric.

Regional selection of the brain size regulating gene CASC5 provides new insight into human brain evolution.

PubMed

Shi, Lei; Hu, Enzhi; Wang, Zhenbo; Liu, Jiewei; Li, Jin; Li, Ming; Chen, Hua; Yu, Chunshui; Jiang, Tianzi; Su, Bing

2017-02-01

Human evolution is marked by a continued enlargement of the brain. Previous studies on human brain evolution focused on identifying sequence divergences of brain size regulating genes between humans and nonhuman primates. However, the evolutionary pattern of the brain size regulating genes during recent human evolution is largely unknown. We conducted a comprehensive analysis of the brain size regulating gene CASC5 and found that in recent human evolution, CASC5 has accumulated many modern human specific amino acid changes, including two fixed changes and six polymorphic changes. Among human populations, 4 of the 6 amino acid polymorphic sites have high frequencies of derived alleles in East Asians, but are rare in Europeans and Africans. We proved that this between-population allelic divergence was caused by regional Darwinian positive selection in East Asians. Further analysis of brain image data of Han Chinese showed significant associations of the amino acid polymorphic sites with gray matter volume. Hence, CASC5 may contribute to the morphological and structural changes of the human brain during recent evolution. The observed between-population divergence of CASC5 variants was driven by natural selection that tends to favor a larger gray matter volume in East Asians.

Fish assemblages

USGS Publications Warehouse

McGarvey, Daniel J.; Falke, Jeffrey A.; Li, Hiram W.; Li, Judith; Hauer, F. Richard; Lamberti, G.A.

2017-01-01

Methods to sample fishes in stream ecosystems and to analyze the raw data, focusing primarily on assemblage-level (all fish species combined) analyses, are presented in this chapter. We begin with guidance on sample site selection, permitting for fish collection, and information-gathering steps to be completed prior to conducting fieldwork. Basic sampling methods (visual surveying, electrofishing, and seining) are presented with specific instructions for estimating population sizes via visual, capture-recapture, and depletion surveys, in addition to new guidance on environmental DNA (eDNA) methods. Steps to process fish specimens in the field including the use of anesthesia and preservation of whole specimens or tissue samples (for genetic or stable isotope analysis) are also presented. Data analysis methods include characterization of size-structure within populations, estimation of species richness and diversity, and application of fish functional traits. We conclude with three advanced topics in assemblage-level analysis: multidimensional scaling (MDS), ecological networks, and loop analysis.

Qualitative Meta-Analysis on the Hospital Task: Implications for Research

ERIC Educational Resources Information Center

Noll, Jennifer; Sharma, Sashi

2014-01-01

The "law of large numbers" indicates that as sample size increases, sample statistics become less variable and more closely estimate their corresponding population parameters. Different research studies investigating how people consider sample size when evaluating the reliability of a sample statistic have found a wide range of…

On Using a Pilot Sample Variance for Sample Size Determination in the Detection of Differences between Two Means: Power Consideration

ERIC Educational Resources Information Center

Shieh, Gwowen

2013-01-01

The a priori determination of a proper sample size necessary to achieve some specified power is an important problem encountered frequently in practical studies. To establish the needed sample size for a two-sample "t" test, researchers may conduct the power analysis by specifying scientifically important values as the underlying population means…

Nanoparticle separation with a miniaturized asymmetrical flow field-flow fractionation cartridge

PubMed Central

Müller, David; Cattaneo, Stefano; Meier, Florian; Welz, Roland; de Mello, Andrew J.

2015-01-01

Asymmetrical Flow Field-Flow Fractionation (AF4) is a separation technique applicable to particles over a wide size range. Despite the many advantages of AF4, its adoption in routine particle analysis is somewhat limited by the large footprint of currently available separation cartridges, extended analysis times and significant solvent consumption. To address these issues, we describe the fabrication and characterization of miniaturized AF4 cartridges. Key features of the down-scaled platform include simplified cartridge and reagent handling, reduced analysis costs and higher throughput capacities. The separation performance of the miniaturized cartridge is assessed using certified gold and silver nanoparticle standards. Analysis of gold nanoparticle populations indicates shorter analysis times and increased sensitivity compared to conventional AF4 separation schemes. Moreover, nanoparticulate titanium dioxide populations exhibiting broad size distributions are analyzed in a rapid and efficient manner. Finally, the repeatability and reproducibility of the miniaturized platform are investigated with respect to analysis time and separation efficiency. PMID:26258119

Nanoparticle separation with a miniaturized asymmetrical flow field-flow fractionation cartridge

NASA Astrophysics Data System (ADS)

Müller, David; Cattaneo, Stefano; Meier, Florian; Welz, Roland; deMello, Andrew

2015-07-01

Asymmetrical Flow Field-Flow Fractionation (AF4) is a separation technique applicable to particles over a wide size range. Despite the many advantages of AF4, its adoption in routine particle analysis is somewhat limited by the large footprint of currently available separation cartridges, extended analysis times and significant solvent consumption. To address these issues, we describe the fabrication and characterization of miniaturized AF4 cartridges. Key features of the scale-down platform include simplified cartridge and reagent handling, reduced analysis costs and higher throughput capacities. The separation performance of the miniaturized cartridge is assessed using certified gold and silver nanoparticle standards. Analysis of gold nanoparticle populations indicates shorter analysis times and increased sensitivity compared to conventional AF4 separation schemes. Moreover, nanoparticulate titanium dioxide populations exhibiting broad size distributions are analyzed in a rapid and efficient manner. Finally, the repeatability and reproducibility of the miniaturized platform are investigated with respect to analysis time and separation efficiency.

Contemporary and historic factors influence differently genetic differentiation and diversity in a tropical palm

PubMed Central

da Silva Carvalho, C; Ribeiro, M C; Côrtes, M C; Galetti, M; Collevatti, R G

2015-01-01

Population genetics theory predicts loss in genetic variability because of drift and inbreeding in isolated plant populations; however, it has been argued that long-distance pollination and seed dispersal may be able to maintain gene flow, even in highly fragmented landscapes. We tested how historical effective population size, historical migration and contemporary landscape structure, such as forest cover, patch isolation and matrix resistance, affect genetic variability and differentiation of seedlings in a tropical palm (Euterpe edulis) in a human-modified rainforest. We sampled 16 sites within five landscapes in the Brazilian Atlantic forest and assessed genetic variability and differentiation using eight microsatellite loci. Using a model selection approach, none of the covariates explained the variation observed in inbreeding coefficients among populations. The variation in genetic diversity among sites was best explained by historical effective population size. Allelic richness was best explained by historical effective population size and matrix resistance, whereas genetic differentiation was explained by matrix resistance. Coalescence analysis revealed high historical migration between sites within landscapes and constant historical population sizes, showing that the genetic differentiation is most likely due to recent changes caused by habitat loss and fragmentation. Overall, recent landscape changes have a greater influence on among-population genetic variation than historical gene flow process. As immediate restoration actions in landscapes with low forest amount, the development of more permeable matrices to allow the movement of pollinators and seed dispersers may be an effective strategy to maintain microevolutionary processes. PMID:25873150

Asian Elephants in China: Estimating Population Size and Evaluating Habitat Suitability

PubMed Central

Zhang, Li; Dong, Lu; Lin, Liu; Feng, Limin; Yan, Fan; Wang, Lanxin; Guo, Xianming; Luo, Aidong

2015-01-01

We monitored the last remaining Asian elephant populations in China over the past decade. Using DNA tools and repeat genotyping, we estimated the population sizes from 654 dung samples collected from various areas. Combined with morphological individual identifications from over 6,300 elephant photographs taken in the wild, we estimated that the total Asian elephant population size in China is between 221 and 245. Population genetic structure and diversity were examined using a 556-bp fragment of mitochondrial DNA, and 24 unique haplotypes were detected from DNA analysis of 178 individuals. A phylogenetic analysis revealed two highly divergent clades of Asian elephants, α and β, present in Chinese populations. Four populations (Mengla, Shangyong, Mengyang, and Pu’Er) carried mtDNA from the α clade, and only one population (Nangunhe) carried mtDNA belonging to the β clade. Moreover, high genetic divergence was observed between the Nangunhe population and the other four populations; however, genetic diversity among the five populations was low, possibly due to limited gene flow because of habitat fragmentation. The expansion of rubber plantations, crop cultivation, and villages along rivers and roads had caused extensive degradation of natural forest in these areas. This had resulted in the loss and fragmentation of elephant habitats and had formed artificial barriers that inhibited elephant migration. Using Geographic Information System, Global Positioning System, and Remote Sensing technology, we found that the area occupied by rubber plantations, tea farms, and urban settlements had dramatically increased over the past 40 years, resulting in the loss and fragmentation of elephant habitats and forming artificial barriers that inhibit elephant migration. The restoration of ecological corridors to facilitate gene exchange among isolated elephant populations and the establishment of cross-boundary protected areas between China and Laos to secure their natural habitats are critical for the survival of Asian elephants in this region. PMID:25992617

Asian elephants in China: estimating population size and evaluating habitat suitability.

PubMed

Zhang, Li; Dong, Lu; Lin, Liu; Feng, Limin; Yan, Fan; Wang, Lanxin; Guo, Xianming; Luo, Aidong

2015-01-01

We monitored the last remaining Asian elephant populations in China over the past decade. Using DNA tools and repeat genotyping, we estimated the population sizes from 654 dung samples collected from various areas. Combined with morphological individual identifications from over 6,300 elephant photographs taken in the wild, we estimated that the total Asian elephant population size in China is between 221 and 245. Population genetic structure and diversity were examined using a 556-bp fragment of mitochondrial DNA, and 24 unique haplotypes were detected from DNA analysis of 178 individuals. A phylogenetic analysis revealed two highly divergent clades of Asian elephants, α and β, present in Chinese populations. Four populations (Mengla, Shangyong, Mengyang, and Pu'Er) carried mtDNA from the α clade, and only one population (Nangunhe) carried mtDNA belonging to the β clade. Moreover, high genetic divergence was observed between the Nangunhe population and the other four populations; however, genetic diversity among the five populations was low, possibly due to limited gene flow because of habitat fragmentation. The expansion of rubber plantations, crop cultivation, and villages along rivers and roads had caused extensive degradation of natural forest in these areas. This had resulted in the loss and fragmentation of elephant habitats and had formed artificial barriers that inhibited elephant migration. Using Geographic Information System, Global Positioning System, and Remote Sensing technology, we found that the area occupied by rubber plantations, tea farms, and urban settlements had dramatically increased over the past 40 years, resulting in the loss and fragmentation of elephant habitats and forming artificial barriers that inhibit elephant migration. The restoration of ecological corridors to facilitate gene exchange among isolated elephant populations and the establishment of cross-boundary protected areas between China and Laos to secure their natural habitats are critical for the survival of Asian elephants in this region.

And the Last Shall Be First: Heterochrony and Compensatory Marine Growth in Sea Trout (Salmo trutta)

PubMed Central

Marco-Rius, Francisco; Caballero, Pablo; Morán, Paloma; Garcia de Leaniz, Carlos

2012-01-01

Early juvenile growth is a good indicator of growth later in life in many species because larger than average juveniles tend to have a competitive advantage. However, for migratory species the relationship between juvenile and adult growth remains obscure. We used scale analysis to reconstruct growth trajectories of migratory sea trout (Salmo trutta) from six neighbouring populations, and compared the size individuals attained in freshwater (before migration) with their subsequent growth at sea (after migration). We also calculated the coefficient of variation (CV) to examine how much body size varied across populations and life stages. Specifically, we tested the hypothesis that the CV on body size would differ between freshwater and marine environment, perhaps reflecting different trade-offs during ontogeny. Neighbouring sea trout populations differed significantly in time spent at sea and in age-adjusted size of returning adults, but not on size of seaward migration, which was surprisingly uniform and may be indicative of strong selection pressures. The CV on body size decreased significantly over time and was highest during the first 8 months of life (when juvenile mortality is highest) and lowest during the marine phase. Size attained in freshwater was negatively related to growth during the first marine growing season, suggesting the existence of compensatory growth, whereby individuals that grow poorly in freshwater are able to catch up later at sea. Analysis of 61 datasets indicates that negative or no associations between pre- and post-migratory growth are common amongst migratory salmonids. We suggest that despite a widespread selective advantage of large body size in freshwater, freshwater growth is a poor predictor of final body size amongst migratory fish because selection may favour growth heterochrony during transitions to a novel environment, and marine compensatory growth may negate any initial size advantage acquired in freshwater. PMID:23049680

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.

Reproductive Biology and Its Impact on Body Size: Comparative Analysis of Mammalian, Avian and Dinosaurian Reproduction

PubMed Central

Werner, Jan; Griebeler, Eva Maria

2011-01-01

Janis and Carrano (1992) suggested that large dinosaurs might have faced a lower risk of extinction under ecological changes than similar-sized mammals because large dinosaurs had a higher potential reproductive output than similar-sized mammals (JC hypothesis). First, we tested the assumption underlying the JC hypothesis. We therefore analysed the potential reproductive output (reflected in clutch/litter size and annual offspring number) of extant terrestrial mammals and birds (as “dinosaur analogs”) and of extinct dinosaurs. With the exception of rodents, the differences in the reproductive output of similar-sized birds and mammals proposed by Janis and Carrano (1992) existed even at the level of single orders. Fossil dinosaur clutches were larger than litters of similar-sized mammals, and dinosaur clutch sizes were comparable to those of similar-sized birds. Because the extinction risk of extant species often correlates with a low reproductive output, the latter difference suggests a lower risk of population extinction in dinosaurs than in mammals. Second, we present a very simple, mathematical model that demonstrates the advantage of a high reproductive output underlying the JC hypothesis. It predicts that a species with a high reproductive output that usually faces very high juvenile mortalities will benefit more strongly in terms of population size from reduced juvenile mortalities (e.g., resulting from a stochastic reduction in population size) than a species with a low reproductive output that usually comprises low juvenile mortalities. Based on our results, we suggest that reproductive strategy could have contributed to the evolution of the exceptional gigantism seen in dinosaurs that does not exist in extant terrestrial mammals. Large dinosaurs, e.g., the sauropods, may have easily sustained populations of very large-bodied species over evolutionary time. PMID:22194835

Reproductive biology and its impact on body size: comparative analysis of mammalian, avian and dinosaurian reproduction.

PubMed

Werner, Jan; Griebeler, Eva Maria

2011-01-01

Janis and Carrano (1992) suggested that large dinosaurs might have faced a lower risk of extinction under ecological changes than similar-sized mammals because large dinosaurs had a higher potential reproductive output than similar-sized mammals (JC hypothesis). First, we tested the assumption underlying the JC hypothesis. We therefore analysed the potential reproductive output (reflected in clutch/litter size and annual offspring number) of extant terrestrial mammals and birds (as "dinosaur analogs") and of extinct dinosaurs. With the exception of rodents, the differences in the reproductive output of similar-sized birds and mammals proposed by Janis and Carrano (1992) existed even at the level of single orders. Fossil dinosaur clutches were larger than litters of similar-sized mammals, and dinosaur clutch sizes were comparable to those of similar-sized birds. Because the extinction risk of extant species often correlates with a low reproductive output, the latter difference suggests a lower risk of population extinction in dinosaurs than in mammals. Second, we present a very simple, mathematical model that demonstrates the advantage of a high reproductive output underlying the JC hypothesis. It predicts that a species with a high reproductive output that usually faces very high juvenile mortalities will benefit more strongly in terms of population size from reduced juvenile mortalities (e.g., resulting from a stochastic reduction in population size) than a species with a low reproductive output that usually comprises low juvenile mortalities. Based on our results, we suggest that reproductive strategy could have contributed to the evolution of the exceptional gigantism seen in dinosaurs that does not exist in extant terrestrial mammals. Large dinosaurs, e.g., the sauropods, may have easily sustained populations of very large-bodied species over evolutionary time.

Non-invasive genetic censusing and monitoring of primate populations.

PubMed

Arandjelovic, Mimi; Vigilant, Linda

2018-03-01

Knowing the density or abundance of primate populations is essential for their conservation management and contextualizing socio-demographic and behavioral observations. When direct counts of animals are not possible, genetic analysis of non-invasive samples collected from wildlife populations allows estimates of population size with higher accuracy and precision than is possible using indirect signs. Furthermore, in contrast to traditional indirect survey methods, prolonged or periodic genetic sampling across months or years enables inference of group membership, movement, dynamics, and some kin relationships. Data may also be used to estimate sex ratios, sex differences in dispersal distances, and detect gene flow among locations. Recent advances in capture-recapture models have further improved the precision of population estimates derived from non-invasive samples. Simulations using these methods have shown that the confidence interval of point estimates includes the true population size when assumptions of the models are met, and therefore this range of population size minima and maxima should be emphasized in population monitoring studies. Innovations such as the use of sniffer dogs or anti-poaching patrols for sample collection are important to ensure adequate sampling, and the expected development of efficient and cost-effective genotyping by sequencing methods for DNAs derived from non-invasive samples will automate and speed analyses. © 2018 Wiley Periodicals, Inc.

Are rapid population estimates accurate? A field trial of two different assessment methods.

PubMed

Grais, Rebecca F; Coulombier, Denis; Ampuero, Julia; Lucas, Marcelino E S; Barretto, Avertino T; Jacquier, Guy; Diaz, Francisco; Balandine, Serge; Mahoudeau, Claude; Brown, Vincent

2006-09-01

Emergencies resulting in large-scale displacement often lead to populations resettling in areas where basic health services and sanitation are unavailable. To plan relief-related activities quickly, rapid population size estimates are needed. The currently recommended Quadrat method estimates total population by extrapolating the average population size living in square blocks of known area to the total site surface. An alternative approach, the T-Square, provides a population estimate based on analysis of the spatial distribution of housing units taken throughout a site. We field tested both methods and validated the results against a census in Esturro Bairro, Beira, Mozambique. Compared to the census (population: 9,479), the T-Square yielded a better population estimate (9,523) than the Quadrat method (7,681; 95% confidence interval: 6,160-9,201), but was more difficult for field survey teams to implement. Although applicable only to similar sites, several general conclusions can be drawn for emergency planning.

Genome size evolution in Ontario ferns (Polypodiidae): evolutionary correlations with cell size, spore size, and habitat type and an absence of genome downsizing.

PubMed

Henry, Thomas A; Bainard, Jillian D; Newmaster, Steven G

2014-10-01

Genome size is known to correlate with a number of traits in angiosperms, but less is known about the phenotypic correlates of genome size in ferns. We explored genome size variation in relation to a suite of morphological and ecological traits in ferns. Thirty-six fern taxa were collected from wild populations in Ontario, Canada. 2C DNA content was measured using flow cytometry. We tested for genome downsizing following polyploidy using a phylogenetic comparative analysis to explore the correlation between 1Cx DNA content and ploidy. There was no compelling evidence for the occurrence of widespread genome downsizing during the evolution of Ontario ferns. The relationship between genome size and 11 morphological and ecological traits was explored using a phylogenetic principal component regression analysis. Genome size was found to be significantly associated with cell size, spore size, spore type, and habitat type. These results are timely as past and recent studies have found conflicting support for the association between ploidy/genome size and spore size in fern polyploid complexes; this study represents the first comparative analysis of the trend across a broad taxonomic group of ferns.

Genetic structure, spatial organization, and dispersal in two populations of bat-eared foxes

PubMed Central

Kamler, Jan F; Gray, Melissa M; Oh, Annie; Macdonald, David W

2013-01-01

We incorporated radio-telemetry data with genetic analysis of bat-eared foxes (Otocyon megalotis) from individuals in 32 different groups to examine relatedness and spatial organization in two populations in South Africa that differed in density, home-range sizes, and group sizes. Kin clustering occurred only for female dyads in the high-density population. Relatedness was negatively correlated with distance only for female dyads in the high-density population, and for male and mixed-sex dyads in the low-density population. Home-range overlap of neighboring female dyads was significantly greater in the high compared to low-density population, whereas overlap within other dyads was similar between populations. Amount of home-range overlap between neighbors was positively correlated with genetic relatedness for all dyad-site combinations, except for female and male dyads in the low-density population. Foxes from all age and sex classes dispersed, although females (mostly adults) dispersed farther than males. Yearlings dispersed later in the high-density population, and overall exhibited a male-biased dispersal pattern. Our results indicated that genetic structure within populations of bat-eared foxes was sex-biased, and was interrelated to density and group sizes, as well as sex-biases in philopatry and dispersal distances. We conclude that a combination of male-biased dispersal rates, adult dispersals, and sex-biased dispersal distances likely helped to facilitate inbreeding avoidance in this evolutionarily unique species of Canidae. PMID:24101981

Strong fluctuations in aboveground population size do not limit genetic diversity in populations of an endangered biennial species.

PubMed

Münzbergová, Zuzana; Šurinová, Maria; Husáková, Iveta; Brabec, Jiří

2018-04-26

Assessing genetic diversity within populations of rare species and understanding its determinants are crucial for effective species protection. While a lot is known about the relationships between genetic diversity, fitness, and current population size, very few studies explored the effects of past population size. Knowledge of past population size may, however, improve our ability to predict future population fates. We studied Gentianella praecox subsp. bohemica, a biennial species with extensive seed bank. We tested the effect of current, past minimal and maximal population size, and harmonic mean of population sizes within the last 15 years on genetic diversity and fitness. Maximum population size over the last 15 years was the best predictor of expected heterozygosity of the populations and was significantly related to current population size and management. Plant fitness was significantly related to current as well as maximum population size and expected heterozygosity. The results suggested that information on past population size may improve our understanding of contemporary genetic diversity across populations. They demonstrated that despite the strong fluctuations in population size, large reductions in population size do not result in immediate loss of genetic diversity and reduction of fitness within the populations. This is likely due to the seed bank of the species serving as reservoir of the genetic diversity of the populations. From a conservation point of view, this suggests that the restoration of small populations of short-lived species with permanent seed bank is possible as these populations may still be genetically diverse.

Variables influencing allocation of capital expenditure in Indonesia

NASA Astrophysics Data System (ADS)

Muda, Iskandar; Naibaho, Revmianson

2018-03-01

The purpose of this study is to examine the factors affecting capital expenditure in Indonesia. The independent variables used are The Effects of Financing Surplus, Total Population and Regional Sizes and the dependent variable used is The Effects of Financing Surplus. This type of research is a causal associative research. The type of data used is secondary data in severals provinces in Indonesia with multiple regression analysis. The results show significantly the determinants of capital expenditure allocation in Indonesia are affected by Financing Surplus, Total Population and Regional Sizes.

Projecting the success of plant restoration with population viability analysis

USGS Publications Warehouse

Bell, T.J.; Bowles, M.L.; McEachern, A.K.; Brigham, C.A.; Schwartz, M.W.

2003-01-01

Conserving viable populations of plant species requires that they have high probabilities of long-term persistence within natural habitats, such as a chance of extinction in 100 years of less than 5% (Menges 1991, 1998; Brown 1994; Pavlik 1994; Chap. 1, this Vol.). For endangered and threatened species that have been severely reduces in range and whose habitats have been fragmented, important species conservation strategies may include augmenting existing populations or restoring new viable populations (Bowles and Whelan 1994; Chap. 2, this Vol.). Restoration objectives may include increasing population numbers to reduce extinction probability, deterministic manipulations to develop a staged cohort structure, or more complex restoration of a desired genetic structure to allow outcrossing or increase effective population size (DeMauro 1993, 1994; Bowles et al. 1993, 1998; Pavlik 1994; Knapp and Dyer 1998; Chap. 2, this Vol.). These efforts may require translocation of propagules from existing (in situ) populations, or from ex situ botanic gardens or seed storage facilities (Falk et al. 1996; Guerrant and Pavlik 1998; Chap. 2, this Vol.). Population viability analysis (PVA) can provide a critical foundation for plant restoration, as it models demographic projections used to evaluate the probability of population persistence and links plant life history with restoration strategies. It is unknown how well artificially created populations will meet demographic modeling requirements (e.g., due to artificial cohort transitions) and few, if any, PVAs have been applied to restorations. To guide application of PVA to restored populations and to illustrate potential difficulties, we examine effects of planting different life stages, model initial population sizes needed to achieve population viability, and compare demographic characteristics between natural and restored populations. We develop and compare plant population restoration viability analysis (PRVA) case studies of two plant species listed in the USA for which federal recovery planning calls for population restoration: Cirsium pitcheri, a short-lived semelparous herb, and Asclepias meadii, a long-lived iteroparous herb.

An Analysis of Diet Quality, How It Controls Fatty Acid Profiles, Isotope Signatures and Stoichiometry in the Malaria Mosquito Anopheles arabiensis

PubMed Central

Hood-Nowotny, Rebecca; Schwarzinger, Bettina; Schwarzinger, Clemens; Soliban, Sharon; Madakacherry, Odessa; Aigner, Martina; Watzka, Margarete; Gilles, Jeremie

2012-01-01

Background Knowing the underlying mechanisms of mosquito ecology will ensure effective vector management and contribute to the overall goal of malaria control. Mosquito populations show a high degree of population plasticity in response to environmental variability. However, the principle factors controlling population size and fecundity are for the most part unknown. Larval habitat and diet play a crucial role in subsequent mosquito fitness. Developing the most competitive insects for sterile insect technique programmes requires a “production” orientated perspective, to deduce the most effective larval diet formulation; the information gained from this process offers us some insight into the mechanisms and processes taking place in natural native mosquito habitats. Methodology/Principal Findings Fatty acid profiles and de-novo or direct assimilation pathways, of whole-individual mosquitoes reared on a range of larval diets were determined using pyrolysis gas chromatograph/mass spectrometry. We used elemental analysis and isotope ratio mass spectrometry to measure individual-whole-body carbon, nitrogen and phosphorous values and to assess the impact of dietary quality on subsequent population stoichiometry, size, quality and isotopic signature. Diet had the greatest impact on fatty acid (FA) profiles of the mosquitoes, which exhibited a high degree of dietary routing, characteristic of generalist feeders. De-novo synthesis of a number of important FAs was observed. Mosquito C:N stoichiometry was fixed in the teneral stage. Dietary N content had significant influence on mosquito size, and P was shown to be a flexible pool which limited overall population size. Conclusions/Significance Direct routing of FAs was evident but there was ubiquitous de-novo synthesis suggesting mosquito larvae are competent generalist feeders capable of survival on diet with varying characteristics. It was concluded that nitrogen availability in the larval diet controlled teneral mosquito size and that teneral CN ratio is a sex- and species-specific fixed parameter. This finding has significant implications for overall mosquito competitiveness and environmental management. PMID:23133509

The Importance of Teaching Power in Statistical Hypothesis Testing

ERIC Educational Resources Information Center

Olinsky, Alan; Schumacher, Phyllis; Quinn, John

2012-01-01

In this paper, we discuss the importance of teaching power considerations in statistical hypothesis testing. Statistical power analysis determines the ability of a study to detect a meaningful effect size, where the effect size is the difference between the hypothesized value of the population parameter under the null hypothesis and the true value…

Temporal analysis of genetic structure to assess population dynamics of reintroduced swift foxes.

PubMed

Cullingham, Catherine I; Moehrenschlager, Axel

2013-12-01

Reintroductions are increasingly used to reestablish species, but a paucity of long-term postrelease monitoring has limited understanding of whether and when viable populations subsequently persist. We conducted temporal genetic analyses of reintroduced populations of swift foxes (Vulpes velox) in Canada (Alberta and Saskatchewan) and the United States (Montana). We used samples collected 4 years apart, 17 years from the initiation of the reintroduction, and 3 years after the conclusion of releases. To assess program success, we genotyped 304 hair samples, subsampled from the known range in 2000 and 2001, and 2005 and 2006, at 7 microsatellite loci. We compared diversity, effective population size, and genetic connectivity over time in each population. Diversity remained stable over time and there was evidence of increasing effective population size. We determined population structure in both periods after correcting for differences in sample sizes. The geographic distribution of these populations roughly corresponded with the original release locations, which suggests the release sites had residual effects on the population structure. However, given that both reintroduction sites had similar source populations, habitat fragmentation, due to cropland, may be associated with the population structure we found. Although our results indicate growing, stable populations, future connectivity analyses are warranted to ensure both populations are not subject to negative small-population effects. Our results demonstrate the importance of multiple sampling years to fully capture population dynamics of reintroduced populations. Análisis Temporal de la Estructura Genética para Evaluar la Dinámica Poblacional de Zorros (Vulpes velox) Reintroducidos. © 2013 Society for Conservation Biology.

Comparing life history characteristics of Lake Michigan’s naturalized and stocked Chinook Salmon

USGS Publications Warehouse

Kerns, Janice A; Rogers, Mark W.; Bunnell, David B.; Claramunt, Randall M.; Collingsworth, Paris D.

2016-01-01

Lake Michigan supports popular fisheries for Chinook Salmon Oncorhynchus tshawytscha that have been sustained by stocking since the late 1960s. Natural recruitment of Chinook Salmon in Lake Michigan has increased in the past few decades and currently contributes more than 50% of Chinook Salmon recruits. We hypothesized that selective forces differ for naturalized populations born in the wild and hatchery populations, resulting in divergent life history characteristics with implications for Chinook Salmon population production and the Lake Michigan fishery. First, we conducted a historical analysis to determine if life history characteristics changed through time as the Chinook Salmon population became increasingly naturalized. Next, we conducted a 2-year field study of naturalized and hatchery stocked Chinook Salmon spawning populations to quantify differences in fecundity, egg size, timing of spawning, and size at maturity. In general, our results did not indicate significant life history divergence between naturalized and hatchery-stocked Chinook Salmon populations in Lake Michigan. Although historical changes in adult sex ratio were correlated with the proportion of naturalized individuals, changes in weight at maturity were better explained by density-dependent factors. The field study revealed no divergence in fecundity, timing of spawning, or size at maturity, and only small differences in egg size (hatchery > naturalized). For the near future, our results suggest that the limited life history differences observed between Chinook Salmon of naturalized and hatchery origin will not lead to large differences in characteristics important to the dynamics of the population or fishery.

A modified Wright-Fisher model that incorporates Ne: A variant of the standard model with increased biological realism and reduced computational complexity.

PubMed

Zhao, Lei; Gossmann, Toni I; Waxman, David

2016-03-21

The Wright-Fisher model is an important model in evolutionary biology and population genetics. It has been applied in numerous analyses of finite populations with discrete generations. It is recognised that real populations can behave, in some key aspects, as though their size that is not the census size, N, but rather a smaller size, namely the effective population size, Ne. However, in the Wright-Fisher model, there is no distinction between the effective and census population sizes. Equivalently, we can say that in this model, Ne coincides with N. The Wright-Fisher model therefore lacks an important aspect of biological realism. Here, we present a method that allows Ne to be directly incorporated into the Wright-Fisher model. The modified model involves matrices whose size is determined by Ne. Thus apart from increased biological realism, the modified model also has reduced computational complexity, particularly so when Ne⪡N. For complex problems, it may be hard or impossible to numerically analyse the most commonly-used approximation of the Wright-Fisher model that incorporates Ne, namely the diffusion approximation. An alternative approach is simulation. However, the simulations need to be sufficiently detailed that they yield an effective size that is different to the census size. Simulations may also be time consuming and have attendant statistical errors. The method presented in this work may then be the only alternative to simulations, when Ne differs from N. We illustrate the straightforward application of the method to some problems involving allele fixation and the determination of the equilibrium site frequency spectrum. We then apply the method to the problem of fixation when three alleles are segregating in a population. This latter problem is significantly more complex than a two allele problem and since the diffusion equation cannot be numerically solved, the only other way Ne can be incorporated into the analysis is by simulation. We have achieved good accuracy in all cases considered. In summary, the present work extends the realism and tractability of an important model of evolutionary biology and population genetics. Copyright © 2016 Elsevier Ltd. All rights reserved.

Supplemental materials for the analysis of capture-recapture data for polar bears in Western Hudson Bay, Canada, 1984-2004

USGS Publications Warehouse

Regehr, Eric V.; Lunn, Nicholas J.; Amstrup, Steven C.; Stirling, Ian

2007-01-01

Regehr and others (2007, Survival and population size of polar bears in western Hudson Bay in relation to earlier sea ice breakup: Journal of Wildlife Management, v. 71, no. 8) evaluated survival in relation to climatic conditions and estimated population size for polar bears (Ursus maritimus) in western Hudson Bay, Canada. Here, we provide supplemental materials for the analyses in Regehr and others (2007). We demonstrate how tag-return data from harvested polar bears were used to adjust estimates of total survival for human-caused mortality. We describe the sex and age composition of the capture and harvest samples and provide results for goodness-of-fit tests applied to capture-recapture models. We also describe the capture-recapture model selection procedure and the structure of the most supported model, which was used to estimate survival and population size.

Size matters: insights from an allometric approach to evaluate control methods for invasive Australian Rhinella marina.

PubMed

Beaty, Lynne E; Salice, Christopher J

2013-10-01

Invasive species are costly and difficult to control. In order to gain a mechanistic understanding of potential control measures, individual-based models uniquely parameterized to reflect the salient life-history characteristics of invasive species are useful. Using invasive Australian Rhinella marina as a case study, we constructed a cohort- and individual-based population simulation that incorporates growth and body size of terrestrial stages. We used this allometric approach to examine the efficacy of nontraditional control methods (i.e., tadpole alarm chemicals and native meat ants) that may have indirect effects on population dynamics mediated by effects on body size. We compared population estimates resulting from these control methods with traditional hand removal. We also conducted a sensitivity analysis to investigate the effect that model parameters, specifically those associated with growth and body size, had on adult population estimates. Incremental increases in hand removal of adults and juveniles caused nonlinear decreases in adult population estimates, suggesting less return with increased investment in hand-removal efforts. Applying tadpole alarm chemicals or meat ants decreased adult population estimates on the same level as removing 15-25% of adults and juveniles by hand. The combined application of tadpole alarm chemicals and meat ants resulted in approximately 80% decrease in adult abundance, the largest of any applied control method. In further support of the nontraditional control methods, which greatly affected the metamorph stage, our model was most sensitive to changes in metamorph survival, juvenile survival, metamorph growth rate, and adult survival. Our results highlight the use and insights that can be gained from individual-based models that incorporate growth and body size and the potential success that nontraditional control methods could have in controlling established, invasive Rhinella marina populations.

Eco-evolutionary dynamics in urbanized landscapes: evolution, species sorting and the change in zooplankton body size along urbanization gradients.

PubMed

Brans, Kristien I; Govaert, Lynn; Engelen, Jessie M T; Gianuca, Andros T; Souffreau, Caroline; De Meester, Luc

2017-01-19

Urbanization causes both changes in community composition and evolutionary responses, but most studies focus on these responses in isolation. We performed an integrated analysis assessing the relative contribution of intra- and interspecific trait turnover to the observed change in zooplankton community body size in 83 cladoceran communities along urbanization gradients quantified at seven spatial scales (50-3200 m radii). We also performed a quantitative genetic analysis on 12 Daphnia magna populations along the same urbanization gradient. Body size in zooplankton communities generally declined with increasing urbanization, but the opposite was observed for communities dominated by large species. The contribution of intraspecific trait variation to community body size turnover with urbanization strongly varied with the spatial scale considered, and was highest for communities dominated by large cladoceran species and at intermediate spatial scales. Genotypic size at maturity was smaller for urban than for rural D. magna populations and for animals cultured at 24°C compared with 20°C. While local genetic adaptation likely contributed to the persistence of D. magna in the urban heat islands, buffering for the phenotypic shift to larger body sizes with increasing urbanization, community body size turnover was mainly driven by non-genetic intraspecific trait change.This article is part of the themed issue 'Human influences on evolution, and the ecological and societal consequences'. © 2016 The Author(s).

Eco-evolutionary dynamics in urbanized landscapes: evolution, species sorting and the change in zooplankton body size along urbanization gradients

PubMed Central

Souffreau, Caroline

2017-01-01

Urbanization causes both changes in community composition and evolutionary responses, but most studies focus on these responses in isolation. We performed an integrated analysis assessing the relative contribution of intra- and interspecific trait turnover to the observed change in zooplankton community body size in 83 cladoceran communities along urbanization gradients quantified at seven spatial scales (50–3200 m radii). We also performed a quantitative genetic analysis on 12 Daphnia magna populations along the same urbanization gradient. Body size in zooplankton communities generally declined with increasing urbanization, but the opposite was observed for communities dominated by large species. The contribution of intraspecific trait variation to community body size turnover with urbanization strongly varied with the spatial scale considered, and was highest for communities dominated by large cladoceran species and at intermediate spatial scales. Genotypic size at maturity was smaller for urban than for rural D. magna populations and for animals cultured at 24°C compared with 20°C. While local genetic adaptation likely contributed to the persistence of D. magna in the urban heat islands, buffering for the phenotypic shift to larger body sizes with increasing urbanization, community body size turnover was mainly driven by non-genetic intraspecific trait change. This article is part of the themed issue ‘Human influences on evolution, and the ecological and societal consequences’. PMID:27920375

Genetic variation and population structure in Jamunapari goats using microsatellites, mitochondrial DNA, and milk protein genes.

PubMed

Rout, P K; Thangraj, K; Mandal, A; Roy, R

2012-01-01

Jamunapari, a dairy goat breed of India, has been gradually declining in numbers in its home tract over the years. We have analysed genetic variation and population history in Jamunapari goats based on 17 microsatellite loci, 2 milk protein loci, mitochondrial hypervariable region I (HVRI) sequencing, and three Y-chromosomal gene sequencing. We used the mitochondrial DNA (mtDNA) mismatch distribution, microsatellite data, and bottleneck tests to infer the population history and demography. The mean number of alleles per locus was 9.0 indicating that the allelic variation was high in all the loci and the mean heterozygosity was 0.769 at nuclear loci. Although the population size is smaller than 8,000 individuals, the amount of variability both in terms of allelic richness and gene diversity was high in all the microsatellite loci except ILST 005. The gene diversity and effective number of alleles at milk protein loci were higher than the 10 other Indian goat breeds that they were compared to. Mismatch analysis was carried out and the analysis revealed that the population curve was unimodal indicating the expansion of population. The genetic diversity of Y-chromosome genes was low in the present study. The observed mean M ratio in the population was above the critical significance value (Mc) and close to one indicating that it has maintained a slowly changing population size. The mode-shift test did not detect any distortion of allele frequency and the heterozygosity excess method showed that there was no significant departure from mutation-drift equilibrium detected in the population. However, the effects of genetic bottlenecks were observed in some loci due to decreased heterozygosity and lower level of M ratio. There were two observed genetic subdivisions in the population supporting the observations of farmers in different areas. This base line information on genetic diversity, bottleneck analysis, and mismatch analysis was obtained to assist the conservation decision and management of the breed.

Genetic Variation and Population Structure in Jamunapari Goats Using Microsatellites, Mitochondrial DNA, and Milk Protein Genes

PubMed Central

Rout, P. K.; Thangraj, K.; Mandal, A.; Roy, R.

2012-01-01

Jamunapari, a dairy goat breed of India, has been gradually declining in numbers in its home tract over the years. We have analysed genetic variation and population history in Jamunapari goats based on 17 microsatellite loci, 2 milk protein loci, mitochondrial hypervariable region I (HVRI) sequencing, and three Y-chromosomal gene sequencing. We used the mitochondrial DNA (mtDNA) mismatch distribution, microsatellite data, and bottleneck tests to infer the population history and demography. The mean number of alleles per locus was 9.0 indicating that the allelic variation was high in all the loci and the mean heterozygosity was 0.769 at nuclear loci. Although the population size is smaller than 8,000 individuals, the amount of variability both in terms of allelic richness and gene diversity was high in all the microsatellite loci except ILST 005. The gene diversity and effective number of alleles at milk protein loci were higher than the 10 other Indian goat breeds that they were compared to. Mismatch analysis was carried out and the analysis revealed that the population curve was unimodal indicating the expansion of population. The genetic diversity of Y-chromosome genes was low in the present study. The observed mean M ratio in the population was above the critical significance value (Mc) and close to one indicating that it has maintained a slowly changing population size. The mode-shift test did not detect any distortion of allele frequency and the heterozygosity excess method showed that there was no significant departure from mutation-drift equilibrium detected in the population. However, the effects of genetic bottlenecks were observed in some loci due to decreased heterozygosity and lower level of M ratio. There were two observed genetic subdivisions in the population supporting the observations of farmers in different areas. This base line information on genetic diversity, bottleneck analysis, and mismatch analysis was obtained to assist the conservation decision and management of the breed. PMID:22606053

A genome-wide perspective about the diversity and demographic history of seven Spanish goat breeds.

PubMed

Manunza, Arianna; Noce, Antonia; Serradilla, Juan Manuel; Goyache, Félix; Martínez, Amparo; Capote, Juan; Delgado, Juan Vicente; Jordana, Jordi; Muñoz, Eva; Molina, Antonio; Landi, Vincenzo; Pons, Agueda; Balteanu, Valentin; Traoré, Amadou; Vidilla, Montse; Sánchez-Rodríguez, Manuel; Sànchez, Armand; Cardoso, Tainã Figueiredo; Amills, Marcel

2016-07-25

The main goal of the current work was to infer the demographic history of seven Spanish goat breeds (Malagueña, Murciano-Granadina, Florida, Palmera, Mallorquina, Bermeya and Blanca de Rasquera) based on genome-wide diversity data generated with the Illumina Goat SNP50 BeadChip (population size, N = 176). Five additional populations from Europe (Saanen and Carpathian) and Africa (Tunisian, Djallonké and Sahel) were also included in this analysis (N = 80) for comparative purposes. Our results show that the genetic background of Spanish goats traces back mainly to European breeds although signs of North African admixture were detected in two Andalusian breeds (Malagueña and Murciano-Granadina). In general, observed and expected heterozygosities were quite similar across the seven Spanish goat breeds under analysis irrespective of their population size and conservation status. For the Mallorquina and Blanca de Rasquera breeds, which have suffered strong population declines during the past decades, we observed increased frequencies of large-sized (ROH), a finding that is consistent with recent inbreeding. In contrast, a substantial part of the genome of the Palmera goat breed comprised short ROH, which suggests a strong and ancient founder effect. Admixture with African goats, genetic drift and inbreeding have had different effects across the seven Spanish goat breeds analysed in the current work. This has generated distinct patterns of genome-wide diversity that provide new clues about the demographic history of these populations.

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 comprehensive phylogenetic reconstruction of the evolution of life-history and of the population-genetics environment. PMID:23711670

A three-stage colonization model for the peopling of the Americas.

PubMed

Kitchen, Andrew; Miyamoto, Michael M; Mulligan, Connie J

2008-02-13

We evaluate the process by which the Americas were originally colonized and propose a three-stage model that integrates current genetic, archaeological, geological, and paleoecological data. Specifically, we analyze mitochondrial and nuclear genetic data by using complementary coalescent models of demographic history and incorporating non-genetic data to enhance the anthropological relevance of the analysis. Bayesian skyline plots, which provide dynamic representations of population size changes over time, indicate that Amerinds went through two stages of growth approximately 40,000 and approximately 15,000 years ago separated by a long period of population stability. Isolation-with-migration coalescent analyses, which utilize data from sister populations to estimate a divergence date and founder population sizes, suggest an Amerind population expansion starting approximately 15,000 years ago. These results support a model for the peopling of the New World in which Amerind ancestors diverged from the Asian gene pool prior to 40,000 years ago and experienced a gradual population expansion as they moved into Beringia. After a long period of little change in population size in greater Beringia, Amerinds rapidly expanded into the Americas approximately 15,000 years ago either through an interior ice-free corridor or along the coast. This rapid colonization of the New World was achieved by a founder group with an effective population size of approximately 1,000-5,400 individuals. Our model presents a detailed scenario for the timing and scale of the initial migration to the Americas, substantially refines the estimate of New World founders, and provides a unified theory for testing with future datasets and analytic methods.

Individualized head-related transfer functions based on population grouping.

PubMed

Xu, Song; Li, Zhizhong; Salvendy, Gavriel

2008-11-01

A method is proposed to divide a population into different groups for partial individualization of head-related transfer functions (HRTFs). Borrowing the basic idea in sizing system design, factor analysis is used to identify the most representative measurements which are then in a case study used to group the population. The comparison between the group mean HRTFs and the population mean HRTFs shows that the group mean HRTFs could greatly reduce spectral distortion at most sampled positions.

Heritability of Wing Size and Shape of the Rice and Corn Strains of Spodoptera frugiperda (J.E. Smith) (Lepidoptera: Noctuidae).

PubMed

Cañas-Hoyos, N; Márquez, E J; Saldamando-Benjumea, C I

2016-08-01

Spodoptera frugiperda (J.E. Smith) (Lepidoptera: Noctuidae) represents a pest of economic importance in all Western Hemisphere. This polyphagous species has diverged into two populations that have been mainly recognized with various mitochondrial and nuclear molecular markers and named "the rice" and "the corn" strains. In Colombia, both strains have evolved prezygotic and postzygotic isolation. They differ in tolerance to Bacillus thuringiensis (Cry1Ac and Cry1Ab endotoxins) and the insecticides lambda-cyhalothrin and methomyl. In 2014, a wing morphometric analysis made in 159 individuals from a colony showed that both strains significantly differ in wing shape. The species also exhibits sexual dimorphism in the rice strain as in females wing size is larger than in males. Here, we continued this work with another wing morphometric approach in laboratory-reared strains to calculate wing size and shape heritabilities using a full-sib design and in wild populations to determine if this method distinguishes these strains. Our results show that male heritabilities of both traits were higher than female ones. Wild populations were significantly different in wing shape and size. These results suggest that wing morphometrics can be used as an alternative method to molecular markers to differentiate adults from laboratory-reared populations and wild populations of this pest, particularly in males of this species. Finally, Q ST values obtained for wing size and shape further demonstrated that both strains are genetically differentiated in nature.

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 diversity ascribed to population differences within groups (F SC = 0.106). The results suggest that significant genetic erosion has occurred within the conservation flocks due to inbreeding, pronounced effects of random drift and selection. It might be necessary to introduce new breeding individuals from the respective field populations in order to increase the effective population sizes of the conservation flocks and counter the effects of genetic erosion.

50 CFR 648.200 - Specifications.

Code of Federal Regulations, 2010 CFR

2010-10-01

... estimates of recruitment; virtual population analysis results and other estimates of stock size; sea... herring fishery; (v) Total world export potential by herring producer countries; (vi) Total world import...

Pragmatic perspective on conservation genetics and demographic history of the last surviving population of Kashmir red deer (Cervus elaphus hanglu) in India.

PubMed

Mukesh; Kumar, Ved P; Sharma, Lalit K; Shukla, Malay; Sathyakumar, Sambandam

2015-01-01

The hangul (Cervus elaphus hanglu) is of great conservation concern because it represents the easternmost and only hope for an Asiatic survivor of the red deer species in the Indian subcontinent. Despite the rigorous conservation efforts of the Department of Wildlife Protection in Jammu & Kashmir, the hangul population has experienced a severe decline in numbers and range contraction in the past few decades. The hangul population once abundant in the past has largely become confined to the Dachigam landscape, with a recent population estimate of 218 individuals. We investigated the genetic variability and demographic history of the hangul population and found that it has shown a relatively low diversity estimates when compared to other red deer populations of the world. Neutrality tests, which are used to evaluate demographic effects, did not support population expansion, and the multimodal pattern of mismatch distribution indicated that the hangul population is under demographic equilibrium. Furthermore, the hangul population did not exhibit any signature of bottleneck footprints in the past, and Coalescent Bayesian Skyline plot analysis revealed that the population had not experienced any dramatic changes in the effective population size over the last several thousand years. We observed a strong evidence of sub-structuring in the population, wherein the majority of individuals were assigned to different clusters in Bayesian cluster analysis. Population viability analysis demonstrated insignificant changes in the mean population size, with a positive growth rate projected for the next hundred years. We discuss the phylogenetic status of hangul for the first time among the other red deer subspecies of the world and strongly recommend to upgrade hangul conservation status under IUCN that should be discrete from the other red deer subspecies of the world to draw more conservation attention from national and international bodies.

Symmetry breaking in two interacting populations of quadratic integrate-and-fire neurons.

PubMed

Ratas, Irmantas; Pyragas, Kestutis

2017-10-01

We analyze the dynamics of two coupled identical populations of quadratic integrate-and-fire neurons, which represent the canonical model for class I neurons near the spiking threshold. The populations are heterogeneous; they include both inherently spiking and excitable neurons. The coupling within and between the populations is global via synapses that take into account the finite width of synaptic pulses. Using a recently developed reduction method based on the Lorentzian ansatz, we derive a closed system of equations for the neuron's firing rates and the mean membrane potentials in both populations. The reduced equations are exact in the infinite-size limit. The bifurcation analysis of the equations reveals a rich variety of nonsymmetric patterns, including a splay state, antiphase periodic oscillations, chimera-like states, and chaotic oscillations as well as bistabilities between various states. The validity of the reduced equations is confirmed by direct numerical simulations of the finite-size networks.

Symmetry breaking in two interacting populations of quadratic integrate-and-fire neurons

NASA Astrophysics Data System (ADS)

Ratas, Irmantas; Pyragas, Kestutis

2017-10-01

We analyze the dynamics of two coupled identical populations of quadratic integrate-and-fire neurons, which represent the canonical model for class I neurons near the spiking threshold. The populations are heterogeneous; they include both inherently spiking and excitable neurons. The coupling within and between the populations is global via synapses that take into account the finite width of synaptic pulses. Using a recently developed reduction method based on the Lorentzian ansatz, we derive a closed system of equations for the neuron's firing rates and the mean membrane potentials in both populations. The reduced equations are exact in the infinite-size limit. The bifurcation analysis of the equations reveals a rich variety of nonsymmetric patterns, including a splay state, antiphase periodic oscillations, chimera-like states, and chaotic oscillations as well as bistabilities between various states. The validity of the reduced equations is confirmed by direct numerical simulations of the finite-size networks.

[A comparison of convenience sampling and purposive sampling].

PubMed

Suen, Lee-Jen Wu; Huang, Hui-Man; Lee, Hao-Hsien

2014-06-01

Convenience sampling and purposive sampling are two different sampling methods. This article first explains sampling terms such as target population, accessible population, simple random sampling, intended sample, actual sample, and statistical power analysis. These terms are then used to explain the difference between "convenience sampling" and purposive sampling." Convenience sampling is a non-probabilistic sampling technique applicable to qualitative or quantitative studies, although it is most frequently used in quantitative studies. In convenience samples, subjects more readily accessible to the researcher are more likely to be included. Thus, in quantitative studies, opportunity to participate is not equal for all qualified individuals in the target population and study results are not necessarily generalizable to this population. As in all quantitative studies, increasing the sample size increases the statistical power of the convenience sample. In contrast, purposive sampling is typically used in qualitative studies. Researchers who use this technique carefully select subjects based on study purpose with the expectation that each participant will provide unique and rich information of value to the study. As a result, members of the accessible population are not interchangeable and sample size is determined by data saturation not by statistical power analysis.

Finite-Time and -Size Scalings in the Evaluation of Large Deviation Functions. Numerical Analysis in Continuous Time

NASA Astrophysics Data System (ADS)

Guevara Hidalgo, Esteban; Nemoto, Takahiro; Lecomte, Vivien

Rare trajectories of stochastic systems are important to understand because of their potential impact. However, their properties are by definition difficult to sample directly. Population dynamics provide a numerical tool allowing their study, by means of simulating a large number of copies of the system, which are subjected to a selection rule that favors the rare trajectories of interest. However, such algorithms are plagued by finite simulation time- and finite population size- effects that can render their use delicate. Using the continuous-time cloning algorithm, we analyze the finite-time and finite-size scalings of estimators of the large deviation functions associated to the distribution of the rare trajectories. We use these scalings in order to propose a numerical approach which allows to extract the infinite-time and infinite-size limit of these estimators.

Characterization of Inclusion Populations in Mn-Si Deoxidized Steel

NASA Astrophysics Data System (ADS)

García-Carbajal, Alfonso; Herrera-Trejo, Martín; Castro-Cedeño, Edgar-Ivan; Castro-Román, Manuel; Martinez-Enriquez, Arturo-Isaias

2017-12-01

Four plant heats of Mn-Si deoxidized steel were conducted to follow the evolution of the inclusion population through ladle furnace (LF) treatment and subsequent vacuum treatment (VT). The liquid steel was sampled, and the chemical composition and size distribution of the inclusion populations were characterized. The Gumbel generalized extreme-value (GEV) and generalized Pareto (GP) distributions were used for the statistical analysis of the inclusion size distributions. The inclusions found at the beginning of the LF treatment were mostly fully liquid SiO2-Al2O3-MnO inclusions, which then evolved into fully liquid SiO2-Al2O3-CaO-MgO and partly liquid SiO2-CaO-MgO-(Al2O3-MgO) inclusions detected at the end of the VT. The final fully liquid inclusions had a desirable chemical composition for plastic behavior in subsequent metallurgical operations. The GP distribution was found to be undesirable for statistical analysis. The GEV distribution approach led to shape parameter values different from the zero value hypothesized from the Gumbel distribution. According to the GEV approach, some of the final inclusion size distributions had statistically significant differences, whereas the Gumbel approach predicted no statistically significant differences. The heats were organized according to indicators of inclusion cleanliness and a statistical comparison of the size distributions.

Are heritability and selection related to population size in nature? Meta-analysis and conservation implications.

PubMed

Wood, Jacquelyn L A; Yates, Matthew C; Fraser, Dylan J

2016-06-01

It is widely thought that small populations should have less additive genetic variance and respond less efficiently to natural selection than large populations. Across taxa, we meta-analytically quantified the relationship between adult census population size (N) and additive genetic variance (proxy: h (2)) and found no reduction in h (2) with decreasing N; surveyed populations ranged from four to one million individuals (1735 h (2) estimates, 146 populations, 83 species). In terms of adaptation, ecological conditions may systematically differ between populations of varying N; the magnitude of selection these populations experience may therefore also differ. We thus also meta-analytically tested whether selection changes with N and found little evidence for systematic differences in the strength, direction or form of selection with N across different trait types and taxa (7344 selection estimates, 172 populations, 80 species). Collectively, our results (i) indirectly suggest that genetic drift neither overwhelms selection more in small than in large natural populations, nor weakens adaptive potential/h (2) in small populations, and (ii) imply that natural populations of varying sizes experience a variety of environmental conditions, without consistently differing habitat quality at small N. However, we caution that the data are currently insufficient to determine whether some small populations may retain adaptive potential definitively. Further study is required into (i) selection and genetic variation in completely isolated populations of known N, under-represented taxonomic groups, and nongeneralist species, (ii) adaptive potential using multidimensional approaches and (iii) the nature of selective pressures for specific traits.

Sub-sampling genetic data to estimate black bear population size: A case study

USGS Publications Warehouse

Tredick, C.A.; Vaughan, M.R.; Stauffer, D.F.; Simek, S.L.; Eason, T.

2007-01-01

Costs for genetic analysis of hair samples collected for individual identification of bears average approximately US$50 [2004] per sample. This can easily exceed budgetary allowances for large-scale studies or studies of high-density bear populations. We used 2 genetic datasets from 2 areas in the southeastern United States to explore how reducing costs of analysis by sub-sampling affected precision and accuracy of resulting population estimates. We used several sub-sampling scenarios to create subsets of the full datasets and compared summary statistics, population estimates, and precision of estimates generated from these subsets to estimates generated from the complete datasets. Our results suggested that bias and precision of estimates improved as the proportion of total samples used increased, and heterogeneity models (e.g., Mh[CHAO]) were more robust to reduced sample sizes than other models (e.g., behavior models). We recommend that only high-quality samples (>5 hair follicles) be used when budgets are constrained, and efforts should be made to maximize capture and recapture rates in the field.

Uncertainty in Population Estimates for Endangered Animals and Improving the Recovery Process

PubMed Central

Haines, Aaron M.; Zak, Matthew; Hammond, Katie; Scott, J. Michael; Goble, Dale D.; Rachlow, Janet L.

2013-01-01

Simple Summary The objective of our study was to evaluate the mention of uncertainty (i.e., variance) associated with population size estimates within U.S. recovery plans for endangered animals. To do this we reviewed all finalized recovery plans for listed terrestrial vertebrate species. We found that more recent recovery plans reported more estimates of population size and uncertainty. Also, bird and mammal recovery plans reported more estimates of population size and uncertainty. We recommend that updated recovery plans combine uncertainty of population size estimates with a minimum detectable difference to aid in successful recovery. Abstract United States recovery plans contain biological information for a species listed under the Endangered Species Act and specify recovery criteria to provide basis for species recovery. The objective of our study was to evaluate whether recovery plans provide uncertainty (e.g., variance) with estimates of population size. We reviewed all finalized recovery plans for listed terrestrial vertebrate species to record the following data: (1) if a current population size was given, (2) if a measure of uncertainty or variance was associated with current estimates of population size and (3) if population size was stipulated for recovery. We found that 59% of completed recovery plans specified a current population size, 14.5% specified a variance for the current population size estimate and 43% specified population size as a recovery criterion. More recent recovery plans reported more estimates of current population size, uncertainty and population size as a recovery criterion. Also, bird and mammal recovery plans reported more estimates of population size and uncertainty compared to reptiles and amphibians. We suggest the use of calculating minimum detectable differences to improve confidence when delisting endangered animals and we identified incentives for individuals to get involved in recovery planning to improve access to quantitative data. PMID:26479531

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

Log-Normal Distribution of Cosmic Voids in Simulations and Mocks

NASA Astrophysics Data System (ADS)

Russell, E.; Pycke, J.-R.

2017-01-01

Following up on previous studies, we complete here a full analysis of the void size distributions of the Cosmic Void Catalog based on three different simulation and mock catalogs: dark matter (DM), haloes, and galaxies. Based on this analysis, we attempt to answer two questions: Is a three-parameter log-normal distribution a good candidate to satisfy the void size distributions obtained from different types of environments? Is there a direct relation between the shape parameters of the void size distribution and the environmental effects? In an attempt to answer these questions, we find here that all void size distributions of these data samples satisfy the three-parameter log-normal distribution whether the environment is dominated by DM, haloes, or galaxies. In addition, the shape parameters of the three-parameter log-normal void size distribution seem highly affected by environment, particularly existing substructures. Therefore, we show two quantitative relations given by linear equations between the skewness and the maximum tree depth, and between the variance of the void size distribution and the maximum tree depth, directly from the simulated data. In addition to this, we find that the percentage of voids with nonzero central density in the data sets has a critical importance. If the number of voids with nonzero central density reaches ≥3.84% in a simulation/mock sample, then a second population is observed in the void size distributions. This second population emerges as a second peak in the log-normal void size distribution at larger radius.

Intercomparison of textural parameters of intertidal sediments generated by different statistical procedures, and implications for a unifying descriptive nomenclature

NASA Astrophysics Data System (ADS)

Fan, Daidu; Tu, Junbiao; Cai, Guofu; Shang, Shuai

2015-06-01

Grain-size analysis is a basic routine in sedimentology and related fields, but diverse methods of sample collection, processing and statistical analysis often make direct comparisons and interpretations difficult or even impossible. In this paper, 586 published grain-size datasets from the Qiantang Estuary (East China Sea) sampled and analyzed by the same procedures were merged and their textural parameters calculated by a percentile and two moment methods. The aim was to explore which of the statistical procedures performed best in the discrimination of three distinct sedimentary units on the tidal flats of the middle Qiantang Estuary. A Gaussian curve-fitting method served to simulate mixtures of two normal populations having different modal sizes, sorting values and size distributions, enabling a better understanding of the impact of finer tail components on textural parameters, as well as the proposal of a unifying descriptive nomenclature. The results show that percentile and moment procedures yield almost identical results for mean grain size, and that sorting values are also highly correlated. However, more complex relationships exist between percentile and moment skewness (kurtosis), changing from positive to negative correlations when the proportions of the finer populations decrease below 35% (10%). This change results from the overweighting of tail components in moment statistics, which stands in sharp contrast to the underweighting or complete amputation of small tail components by the percentile procedure. Intercomparisons of bivariate plots suggest an advantage of the Friedman & Johnson moment procedure over the McManus moment method in terms of the description of grain-size distributions, and over the percentile method by virtue of a greater sensitivity to small variations in tail components. The textural parameter scalings of Folk & Ward were translated into their Friedman & Johnson moment counterparts by application of mathematical functions derived by regression analysis of measured and modeled grain-size data, or by determining the abscissa values of intersections between auxiliary lines running parallel to the x-axis and vertical lines corresponding to the descriptive percentile limits along the ordinate of representative bivariate plots. Twofold limits were extrapolated for the moment statistics in relation to single descriptive terms in the cases of skewness and kurtosis by considering both positive and negative correlations between percentile and moment statistics. The extrapolated descriptive scalings were further validated by examining entire size-frequency distributions simulated by mixing two normal populations of designated modal size and sorting values, but varying in mixing ratios. These were found to match well in most of the proposed scalings, although platykurtic and very platykurtic categories were questionable when the proportion of the finer population was below 5%. Irrespective of the statistical procedure, descriptive nomenclatures should therefore be cautiously used when tail components contribute less than 5% to grain-size distributions.

Calculating prevalence of hepatitis B in India: using population weights to look for publication bias in conventional meta-analysis.

PubMed

Batham, Ashish; Gupta, Manoj Anand; Rastogi, Pallav; Garg, Shubham; Sreenivas, V; Puliyel, Jacob M

2009-12-01

Publication bias can result from the propensity of researchers to document what is unusual. This can distort the inferences drawn in systematic reviews. To measure the distortion, it has been suggested that a second analysis be done; using weights proportional to the size of the population from which the samples are drawn. We re-evaluate data from a published meta-analysis on prevalence of hepatitis B in India, to see how this approach alters the results. Prevalence of hepatitis B among tribal and non-tribal populations in different States was analyzed. Weights were then assigned according to population of the State. The overall country prevalence was then calculated. Using population-weights it is estimated that the point-prevalence of hepatitis B among non-tribal populations is 3.07% [95% CI: 2.5-3.64]. Among tribal populations it is 11.85% (CI 10.76-12.93). Overall prevalence was 3.70 (CI: 3.17-4.24) (corresponding to a chronic carrier rate of 2.96%). The present analysis using population-weights has resulted in the estimated prevalence among non tribal populations increasing by 24% and that among tribal populations decreasing by 25.5% when compared to figures of the meta-analysis published earlier. The advantages and drawbacks of this procedure are discussed.

Evolution of stochastic demography with life history tradeoffs in density-dependent age-structured populations.

PubMed

Lande, Russell; Engen, Steinar; Sæther, Bernt-Erik

2017-10-31

We analyze the stochastic demography and evolution of a density-dependent age- (or stage-) structured population in a fluctuating environment. A positive linear combination of age classes (e.g., weighted by body mass) is assumed to act as the single variable of population size, [Formula: see text], exerting density dependence on age-specific vital rates through an increasing function of population size. The environment fluctuates in a stationary distribution with no autocorrelation. We show by analysis and simulation of age structure, under assumptions often met by vertebrate populations, that the stochastic dynamics of population size can be accurately approximated by a univariate model governed by three key demographic parameters: the intrinsic rate of increase and carrying capacity in the average environment, [Formula: see text] and [Formula: see text], and the environmental variance in population growth rate, [Formula: see text] Allowing these parameters to be genetically variable and to evolve, but assuming that a fourth parameter, [Formula: see text], measuring the nonlinearity of density dependence, remains constant, the expected evolution maximizes [Formula: see text] This shows that the magnitude of environmental stochasticity governs the classical trade-off between selection for higher [Formula: see text] versus higher [Formula: see text] However, selection also acts to decrease [Formula: see text], so the simple life-history trade-off between [Formula: see text]- and [Formula: see text]-selection may be obscured by additional trade-offs between them and [Formula: see text] Under the classical logistic model of population growth with linear density dependence ([Formula: see text]), life-history evolution in a fluctuating environment tends to maximize the average population size. Published under the PNAS license.

Place matters: A longitudinal analysis measuring the association between neighbourhood walkability and walking by age group and population center size in Canada.

PubMed

Wasfi, Rania; Steinmetz-Wood, Madeleine; Kestens, Yan

2017-01-01

This study examined the influence of walkability on walking behaviour and assessed whether associations varied according to life-stage and population center (PC) size. Walkability scores were obtained for the six-digit postal codes of residential neighbourhoods of 11,200 Canadians, who participated in biennial assessments of the National Population Health Survey from 1994 to 2010. Participants were stratified by age-group. Mixed-effects logistic regression models were used to estimate the influence of cumulative exposure to neighborhood walkability on utilitarian and exercise walking by PC size and life-stage. Associations of neighbourhood walkability with utilitarian and exercise walking varied according to age-group and PC size. Exposure to high walkable neighborhoods was associated with utilitarian walking in younger and older adults in all PC sizes, except for older adults living in a medium PC. Living in a highly walkable neighborhood in a large PC was associated with walking for exercise in younger (OR: 1.42; 95%CI: 1.20-1.67) and older adults (OR: 2.09; 95%CI: 1.51-2.89). Living in highly walkable neighbourhood in a medium PC was associated with walking for exercise in older adults (OR: 1.62; 95%CI: 1.15-2.29). These results emphasize the need to consider the size and nature of every community, and the age-group of a population when implementing strategies to promote walking.

Place matters: A longitudinal analysis measuring the association between neighbourhood walkability and walking by age group and population center size in Canada

PubMed Central

Steinmetz-Wood, Madeleine; Kestens, Yan

2017-01-01

This study examined the influence of walkability on walking behaviour and assessed whether associations varied according to life-stage and population center (PC) size. Walkability scores were obtained for the six-digit postal codes of residential neighbourhoods of 11,200 Canadians, who participated in biennial assessments of the National Population Health Survey from 1994 to 2010. Participants were stratified by age-group. Mixed-effects logistic regression models were used to estimate the influence of cumulative exposure to neighborhood walkability on utilitarian and exercise walking by PC size and life-stage. Associations of neighbourhood walkability with utilitarian and exercise walking varied according to age-group and PC size. Exposure to high walkable neighborhoods was associated with utilitarian walking in younger and older adults in all PC sizes, except for older adults living in a medium PC. Living in a highly walkable neighborhood in a large PC was associated with walking for exercise in younger (OR: 1.42; 95%CI: 1.20–1.67) and older adults (OR: 2.09; 95%CI: 1.51–2.89). Living in highly walkable neighbourhood in a medium PC was associated with walking for exercise in older adults (OR: 1.62; 95%CI: 1.15–2.29). These results emphasize the need to consider the size and nature of every community, and the age-group of a population when implementing strategies to promote walking. PMID:29261706

An individual-based model for population viability analysis of humpback chub in Grand Canyon

USGS Publications Warehouse

Pine, William Pine; Healy, Brian; Smith, Emily Omana; Trammell, Melissa; Speas, Dave; Valdez, Rich; Yard, Mike; Walters, Carl; Ahrens, Rob; Vanhaverbeke, Randy; Stone, Dennis; Wilson, Wade

2013-01-01

We developed an individual-based population viability analysis model (females only) for evaluating risk to populations from catastrophic events or conservation and research actions. This model tracks attributes (size, weight, viability, etc.) for individual fish through time and then compiles this information to assess the extinction risk of the population across large numbers of simulation trials. Using a case history for the Little Colorado River population of Humpback Chub Gila cypha in Grand Canyon, Arizona, we assessed extinction risk and resiliency to a catastrophic event for this population and then assessed a series of conservation actions related to removing specific numbers of Humpback Chub at different sizes for conservation purposes, such as translocating individuals to establish other spawning populations or hatchery refuge development. Our results suggested that the Little Colorado River population is generally resilient to a single catastrophic event and also to removals of larvae and juveniles for conservation purposes, including translocations to establish new populations. Our results also suggested that translocation success is dependent on similar survival rates in receiving and donor streams and low emigration rates from recipient streams. In addition, translocating either large numbers of larvae or small numbers of large juveniles has generally an equal likelihood of successful population establishment at similar extinction risk levels to the Little Colorado River donor population. Our model created a transparent platform to consider extinction risk to populations from catastrophe or conservation actions and should prove useful to managers assessing these risks for endangered species such as Humpback Chub.

Increasing conclusiveness of clinical breath analysis by improved baseline correction of multi capillary column - ion mobility spectrometry (MCC-IMS) data.

PubMed

Szymańska, Ewa; Tinnevelt, Gerjen H; Brodrick, Emma; Williams, Mark; Davies, Antony N; van Manen, Henk-Jan; Buydens, Lutgarde M C

2016-08-05

Current challenges of clinical breath analysis include large data size and non-clinically relevant variations observed in exhaled breath measurements, which should be urgently addressed with competent scientific data tools. In this study, three different baseline correction methods are evaluated within a previously developed data size reduction strategy for multi capillary column - ion mobility spectrometry (MCC-IMS) datasets. Introduced for the first time in breath data analysis, the Top-hat method is presented as the optimum baseline correction method. A refined data size reduction strategy is employed in the analysis of a large breathomic dataset on a healthy and respiratory disease population. New insights into MCC-IMS spectra differences associated with respiratory diseases are provided, demonstrating the additional value of the refined data analysis strategy in clinical breath analysis. Copyright © 2016 Elsevier B.V. All rights reserved.

Size variation in Middle Pleistocene humans.

PubMed

Arsuaga, J L; Carretero, J M; Lorenzo, C; Gracia, A; Martínez, I; Bermúdez de Castro, J M; Carbonell, E

1997-08-22

It has been suggested that European Middle Pleistocene humans, Neandertals, and prehistoric modern humans had a greater sexual dimorphism than modern humans. Analysis of body size variation and cranial capacity variation in the large sample from the Sima de los Huesos site in Spain showed instead that the sexual dimorphism is comparable in Middle Pleistocene and modern populations.

Determining the linkage of disease-resistance genes to molecular markers: the LOD-SCORE method revisited with regard to necessary sample sizes.

PubMed

Hühn, M

1995-05-01

Some approaches to molecular marker-assisted linkage detection for a dominant disease-resistance trait based on a segregating F2 population are discussed. Analysis of two-point linkage is carried out by the traditional measure of maximum lod score. It depends on (1) the maximum-likelihood estimate of the recombination fraction between the marker and the disease-resistance gene locus, (2) the observed absolute frequencies, and (3) the unknown number of tested individuals. If one replaces the absolute frequencies by expressions depending on the unknown sample size and the maximum-likelihood estimate of recombination value, the conventional rule for significant linkage (maximum lod score exceeds a given linkage threshold) can be resolved for the sample size. For each sub-population used for linkage analysis [susceptible (= recessive) individuals, resistant (= dominant) individuals, complete F2] this approach gives a lower bound for the necessary number of individuals required for the detection of significant two-point linkage by the lod-score method.

Density and population viability of coastal marten: a rare and geographically isolated small carnivore

PubMed Central

Green, David S.; Levi, Taal

2018-01-01

Pacific martens (Martes caurina humboldtensis) in coastal forests of Oregon and northern California in the United States are rare and geographically isolated, prompting a petition for listing under the Endangered Species Act. If listed, regulations have the potential to influence land-use decisions on public and private lands, but no estimates of population size, density, or viability of remnant marten populations are available for evaluating their conservation status. We used GPS and VHF telemetry and spatial mark-resight to estimate home ranges, density, and population size of Pacific martens in the Oregon Dunes National Recreation Area, central coast Oregon, USA. We then estimated population viability at differing levels of human-caused mortality (e.g., vehicle mortality). Marten home ranges were small on average (females = 0.8 km2, males 1.5 km2) and density (1.13 martens/1 km2) was the highest reported for North American populations (M. caurina, M. americana). We estimated 71 adult martens (95% CRI [41–87]) across two subpopulations separated by a large barrier (Umpqua River). Using population viability analysis, extinction risk for a subpopulation of 30 martens, approximately the size of the subpopulation south of the Umpqua River, ranged from 32% to 99% with two or three annual human-caused mortalities within 30 years. Absent population expansion, limiting human-caused mortalities will likely have the greatest conservation impact. PMID:29637018

Human population, grasshopper and plant species richness in European countries

NASA Astrophysics Data System (ADS)

Steck, Claude E.; Pautasso, Marco

2008-11-01

Surprisingly, several studies over large scales have reported a positive spatial correlation of people and biodiversity. This pattern has important implications for conservation and has been documented for well studied taxa such as plants, amphibians, reptiles, birds and mammals. However, it is unknown whether the pattern applies also to invertebrates other than butterflies and more work is needed to establish whether the species-people relationship is explained by both variables correlating with other environmental factors. We studied whether grasshopper species richness (Orthoptera, suborder Caelifera) is related to human population size in European countries. As expected, the number of Caelifera species increases significantly with increasing human population size. But this is not the case when controlling for country area, latitude and number of plant species. Variations in Caelifera species richness are primarily associated with variations in plant species richness. Caelifera species richness also increases with decreasing mean annual precipitation, Gross Domestic Product per capita (used as an indicator for economic development) and net fertility rate of the human population. Our analysis confirms the hypothesis that the broad-scale human population-biodiversity correlations can be explained by concurrent variations in factors other than human population size such as plant species richness, environmental productivity, or habitat heterogeneity. Nonetheless, more populated countries in Europe still have more Caelifera species than less populated countries and this poses a particular challenge for conservation.

Role of patch size, disease, and movement in rapid extinction of bighorn sheep

USGS Publications Warehouse

Singer, F.J.; Zeigenfuss, L.C.; Spicer, L.

2001-01-01

The controversy (Berger 1990, 1999; Wehausen 1999) over rapid extinction in bighorn sheep (Ovis canadensis) has focused on population size alone as a correlate to persistence time. We report on the persistence and population performance of 24 translocated populations of bighorn sheep. Persistence in these sheep was strongly correlated with larger patch sizes, greater distance to domestic sheep, higher population growth rates, and migratory movements, as well as to larger population sizes. Persistence was also positively correlated with larger average home-range size (p = 0.058, n = 10 translocated populations) and home-range size of rams (p = 0.087, n = 8 translocated populations). Greater home-range size and dispersal rates of bighorn sheep were positively correlated to larger patches. We conclude that patch size and thus habitat carrying capacity, not population size per se, is the primary correlate to both population performance and persistence. Because habitat carrying capacity defines the upper limit to population size, clearly the amount of suitable habitat in a patch is ultimately linked to population size. Larger populations (250+ animals) were more likely to recover rapidly to their pre-epizootic survey number following an epizootic (p = 0.019), although the proportion of the population dying in the epizootic also influenced the probability of recovery (p = 0.001). Expensive management efforts to restore or increase bighorn sheep populations should focus on large habitat patches located ≥23 km from domestic sheep, and less effort should be expended on populations in isolated, small patches of habitat.

Ranking procedure for partial discriminant analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Beckman, R.J.; Johnson, M.E.

1981-09-01

A rank procedure developed by Broffitt, Randles, and Hogg (1976) is modified to control the conditional probability of misclassification given that classification has been attempted. This modification leads to a useful solution to the two-population partial discriminant analysis problem for even moderately sized training sets.

Assessment of sampling stability in ecological applications of discriminant analysis

USGS Publications Warehouse

Williams, B.K.; Titus, K.

1988-01-01

A simulation study was undertaken to assess the sampling stability of the variable loadings in linear discriminant function analysis. A factorial design was used for the factors of multivariate dimensionality, dispersion structure, configuration of group means, and sample size. A total of 32,400 discriminant analyses were conducted, based on data from simulated populations with appropriate underlying statistical distributions. A review of 60 published studies and 142 individual analyses indicated that sample sizes in ecological studies often have met that requirement. However, individual group sample sizes frequently were very unequal, and checks of assumptions usually were not reported. The authors recommend that ecologists obtain group sample sizes that are at least three times as large as the number of variables measured.

Application of Lorenz curve to interpret concentration of contraception and fertility in a population.

PubMed

Ghanma, M A; Rider, R V; Sirageldin, I

1984-01-01

The Lorenz Curve, originally developed to measure the concentration of wealth in a population, was used to describe the distribution of contraceptive practice in Jordan. Data from the 1976 Jordan Fertility Study, carried out as part of the World Fertility Survey program, was used in the analysis. The application of the Automatic Interaction Detector program to the survey's sample population of 3611 women of reproductive age divided the sample into 6 mutually exclusive groups on the basis of residence, education, and whether desired family size was attained or not attained. These 3 characteristics accounted for a major portion of the variation in contraceptive practice. These subgroups, in ascending order by the proportion practicing contraception, were: 1) rural women with unattained desired family size; 2) urban, illiterate women with unattained desired family size; 3) rural women with attained desired family size; 4) urban, literate women with unattained desired family size; 5) urban, illiterate women with attained desired family size; and 6) urban, literate women with attained desired family size. The cumulative proportion of the sample in each ordered subdivision was plotted on the X axis of a graph, and the cumulative proportion of those practicing contraception was plotted on the Y axis of the graph. A line connecting the intersection of the points on the X and Y axis was then drawn. The resultant line was a concave ascending line. If contraceptive practice was evenly distributed in the population, the line would be a straight diagonal line. The plotted curved line indicated that contraceptive practice was unevenly distributed in the population. 2 indexes for measuring the area between the diagonal and the line resulting from plotting the observed distribution for each subgroup was used to assess the degree of concentration of contraceptive practice in the population. The indexes also indicated that contraceptive practice was unequally distributed. When separate curves were plotted for the subgroups with attained desired family size and the subgroups without attained desired family size, it was apparent that the distribution of contraceptive practice was more uniform among those with attained desired family size than among the other 3 subgroups. A curve for the distribution of births was then plotted on the same graph. This curve was not a true application of the Lorenz Curve since it was based on the order of the subdivisions by birth rates. The resultant line approached the straight diagonal line and indicated that the distribution of births was fairly evenly distributed in the population. The uneven distribution of contraceptive practice and the uniform distribution of births suggests that contraceptive practice in this population is ineffective. This may be a characteristic of populations in the early stages of fertility control.

The role of body size versus growth on the decision to migrate: a case study with Salmo trutta

NASA Astrophysics Data System (ADS)

Acolas, M. L.; Labonne, J.; Baglinière, J. L.; Roussel, J. M.

2012-01-01

In a population exhibiting partial migration (i.e. migration and residency tactics occur in the same population), the mechanisms underlying the tactical choice are still unclear. Empirical studies have highlighted a variety of factors that could influence the coexistence of resident and migratory individuals, with growth and body size considered to be key factors in the decision to migrate. Most studies suffer from at least one of the two following caveats: (1) survival and capture probabilities are not taken into account in the data analysis, and (2) body size is often used as a proxy for individual growth. We performed a capture-mark-recapture experiment to study partial migration among juvenile brown trout Salmo trutta at the end of their first year, when a portion of the population emigrate from the natal stream while others choose residency tactic. Bayesian multistate capture-recapture models accounting for survival and recaptures probabilities were used to investigate the relative role of body size and individual growth on survival and migration probabilities. Our results show that, despite an apparent effect of both size and growth on migration, growth is the better integrative parameter and acts directly on migration probability whereas body size acts more strongly on survival. Consequently, we recommend caution if size is used as a proxy for growth when studying the factors that drive partial migration in juvenile salmonid species.

Uncertainty in Population Estimates for Endangered Animals and Improving the Recovery Process.

PubMed

Haines, Aaron M; Zak, Matthew; Hammond, Katie; Scott, J Michael; Goble, Dale D; Rachlow, Janet L

2013-08-13

United States recovery plans contain biological information for a species listed under the Endangered Species Act and specify recovery criteria to provide basis for species recovery. The objective of our study was to evaluate whether recovery plans provide uncertainty (e.g., variance) with estimates of population size. We reviewed all finalized recovery plans for listed terrestrial vertebrate species to record the following data: (1) if a current population size was given, (2) if a measure of uncertainty or variance was associated with current estimates of population size and (3) if population size was stipulated for recovery. We found that 59% of completed recovery plans specified a current population size, 14.5% specified a variance for the current population size estimate and 43% specified population size as a recovery criterion. More recent recovery plans reported more estimates of current population size, uncertainty and population size as a recovery criterion. Also, bird and mammal recovery plans reported more estimates of population size and uncertainty compared to reptiles and amphibians. We suggest the use of calculating minimum detectable differences to improve confidence when delisting endangered animals and we identified incentives for individuals to get involved in recovery planning to improve access to quantitative data.

Natural selection and inheritance of breeding time and clutch size in the collared flycatcher.

PubMed

Sheldon, B C; Kruuk, L E B; Merilä, J

2003-02-01

Many characteristics of organisms in free-living populations appear to be under directional selection, possess additive genetic variance, and yet show no evolutionary response to selection. Avian breeding time and clutch size are often-cited examples of such characters. We report analyses of inheritance of, and selection on, these traits in a long-term study of a wild population of the collared flycatcher Ficedula albicollis. We used mixed model analysis with REML estimation ("animal models") to make full use of the information in complex multigenerational pedigrees. Heritability of laying date, but not clutch size, was lower than that estimated previously using parent-offspring regressions, although for both traits there was evidence of substantial additive genetic variance (h2 = 0.19 and 0.29, respectively). Laying date and clutch size were negatively genetically correlated (rA = -0.41 +/- 0.09), implying that selection on one of the traits would cause a correlated response in the other, but there was little evidence to suggest that evolution of either trait would be constrained by correlations with other phenotypic characters. Analysis of selection on these traits in females revealed consistent strong directional fecundity selection for earlier breeding at the level of the phenotype (beta = -0.28 +/- 0.03), but little evidence for stabilising selection on breeding time. We found no evidence that clutch size was independently under selection. Analysis of fecundity selection on breeding values for laying date, estimated from an animal model, indicated that selection acts directly on additive genetic variance underlying breeding time (beta = -0.20 +/- 0.04), but not on clutch size (beta = 0.03 +/- 0.05). In contrast, selection on laying date via adult female survival fluctuated in sign between years, and was opposite in sign for selection on phenotypes (negative) and breeding values (positive). Our data thus suggest that any evolutionary response to selection on laying date is partially constrained by underlying life-history trade-offs, and illustrate the difficulties in using purely phenotypic measures and incomplete fitness estimates to assess evolution of life-history trade-offs. We discuss some of the difficulties associated with understanding the evolution of laying date and clutch size in natural populations.

What determines species richness of parasitic organisms? A meta-analysis across animal, plant and fungal hosts.

PubMed

Kamiya, Tsukushi; O'Dwyer, Katie; Nakagawa, Shinichi; Poulin, Robert

2014-02-01

Although a small set of external factors account for much of the spatial variation in plant and animal diversity, the search continues for general drivers of variation in parasite species richness among host species. Qualitative reviews of existing evidence suggest idiosyncrasies and inconsistent predictive power for all proposed determinants of parasite richness. Here, we provide the first quantitative synthesis of the evidence using a meta-analysis of 62 original studies testing the relationship between parasite richness across animal, plant and fungal hosts, and each of its four most widely used presumed predictors: host body size, host geographical range size, host population density, and latitude. We uncover three universal predictors of parasite richness across host species, namely host body size, geographical range size and population density, applicable regardless of the taxa considered and independently of most aspects of study design. A proper match in the primary studies between the focal predictor and both the spatial scale of study and the level at which parasite species richness was quantified (i.e. within host populations or tallied across a host species' entire range) also affected the magnitude of effect sizes. By contrast, except for a couple of indicative trends in subsets of the full dataset, there was no strong evidence for an effect of latitude on parasite species richness; where found, this effect ran counter to the general latitude gradient in diversity, with parasite species richness tending to be higher further from the equator. Finally, the meta-analysis also revealed a negative relationship between the magnitude of effect sizes and the year of publication of original studies (i.e. a time-lag bias). This temporal bias may be due to the increasing use of phylogenetic correction in comparative analyses of parasite richness over time, as this correction yields more conservative effect sizes. Overall, these findings point to common underlying processes of parasite diversification fundamentally different from those controlling the diversity of free-living organisms. © 2013 The Authors. Biological Reviews © 2013 Cambridge Philosophical Society.

The Game of Contacts: Estimating the Social Visibility of Groups.

PubMed

Salganik, Matthew J; Mello, Maeve B; Abdo, Alexandre H; Bertoni, Neilane; Fazito, Dimitri; Bastos, Francisco I

2011-01-01

Estimating the sizes of hard-to-count populations is a challenging and important problem that occurs frequently in social science, public health, and public policy. This problem is particularly pressing in HIV/AIDS research because estimates of the sizes of the most at-risk populations-illicit drug users, men who have sex with men, and sex workers-are needed for designing, evaluating, and funding programs to curb the spread of the disease. A promising new approach in this area is the network scale-up method, which uses information about the personal networks of respondents to make population size estimates. However, if the target population has low social visibility, as is likely to be the case in HIV/AIDS research, scale-up estimates will be too low. In this paper we develop a game-like activity that we call the game of contacts in order to estimate the social visibility of groups, and report results from a study of heavy drug users in Curitiba, Brazil (n = 294). The game produced estimates of social visibility that were consistent with qualitative expectations but of surprising magnitude. Further, a number of checks suggest that the data are high-quality. While motivated by the specific problem of population size estimation, our method could be used by researchers more broadly and adds to long-standing efforts to combine the richness of social network analysis with the power and scale of sample surveys.

Harvesting, predation and competition effects on a red coral population

NASA Astrophysics Data System (ADS)

Abbiati, M.; Buffoni, G.; Caforio, G.; Di Cola, G.; Santangelo, G.

A Corallium rubrum population, dwelling in the Ligurian Sea, has been under observation since 1987. Biometric descriptors of colonies (base diameter, weight, number of polyps, number of growth rings) have been recorded and correlated. The population size structure was obtained by distributing the colonies into diameter classes, each size class representing the average annual increment of diameter growth. The population was divided into ten classes, including a recruitment class. This size structure showed a fairly regular trend in the first four classes. The irregularity of survival in the older classes agreed with field observations on harvesting and predation. Demographic parameters such as survival, growth plasticity and natality coefficients were estimated from the experimental data. On this basis a discrete nonlinear model was implemented. The model is based on a kind of density-dependent Leslie matrix, where the feedback term only occurs in survival of the first class; the recruitment function is assumed to be dependent on the total biomass and related to inhibiting effects due to competitive interactions. Stability analysis was applied to steady-state solutions. Numerical simulations of population evolution were carried out under different conditions. The dynamics of settlement and the effects of disturbances such as harvesting, predation and environmental variability were studied.

Genetic structure and natal origins of immature hawksbill turtles (Eretmochelys imbricata) in Brazilian waters.

PubMed

Proietti, Maira C; Reisser, Julia; Marins, Luis Fernando; Rodriguez-Zarate, Clara; Marcovaldi, Maria A; Monteiro, Danielle S; Pattiaratchi, Charitha; Secchi, Eduardo R

2014-01-01

Understanding the connections between sea turtle populations is fundamental for their effective conservation. Brazil hosts important hawksbill feeding areas, but few studies have focused on how they connect with nesting populations in the Atlantic. Here, we (1) characterized mitochondrial DNA control region haplotypes of immature hawksbills feeding along the coast of Brazil (five areas ranging from equatorial to temperate latitudes, 157 skin samples), (2) analyzed genetic structure among Atlantic hawksbill feeding populations, and (3) inferred natal origins of hawksbills in Brazilian waters using genetic, oceanographic, and population size information. We report ten haplotypes for the sampled Brazilian sites, most of which were previously observed at other Atlantic feeding grounds and rookeries. Genetic profiles of Brazilian feeding areas were significantly different from those in other regions (Caribbean and Africa), and a significant structure was observed between Brazilian feeding grounds grouped into areas influenced by the South Equatorial/North Brazil Current and those influenced by the Brazil Current. Our genetic analysis estimates that the studied Brazilian feeding aggregations are mostly composed of animals originating from the domestic rookeries Bahia and Pipa, but some contributions from African and Caribbean rookeries were also observed. Oceanographic data corroborated the local origins, but showed higher connection with West Africa and none with the Caribbean. High correlation was observed between origins estimated through genetics/rookery size and oceanographic/rookery size data, demonstrating that ocean currents and population sizes influence haplotype distribution of Brazil's hawksbill populations. The information presented here highlights the importance of national conservation strategies and international cooperation for the recovery of endangered hawksbill turtle populations.

Genetic Structure and Natal Origins of Immature Hawksbill Turtles (Eretmochelys imbricata) in Brazilian Waters

PubMed Central

Proietti, Maira C.; Reisser, Julia; Marins, Luis Fernando; Rodriguez-Zarate, Clara; Marcovaldi, Maria A.; Monteiro, Danielle S.; Pattiaratchi, Charitha; Secchi, Eduardo R.

2014-01-01

Understanding the connections between sea turtle populations is fundamental for their effective conservation. Brazil hosts important hawksbill feeding areas, but few studies have focused on how they connect with nesting populations in the Atlantic. Here, we (1) characterized mitochondrial DNA control region haplotypes of immature hawksbills feeding along the coast of Brazil (five areas ranging from equatorial to temperate latitudes, 157 skin samples), (2) analyzed genetic structure among Atlantic hawksbill feeding populations, and (3) inferred natal origins of hawksbills in Brazilian waters using genetic, oceanographic, and population size information. We report ten haplotypes for the sampled Brazilian sites, most of which were previously observed at other Atlantic feeding grounds and rookeries. Genetic profiles of Brazilian feeding areas were significantly different from those in other regions (Caribbean and Africa), and a significant structure was observed between Brazilian feeding grounds grouped into areas influenced by the South Equatorial/North Brazil Current and those influenced by the Brazil Current. Our genetic analysis estimates that the studied Brazilian feeding aggregations are mostly composed of animals originating from the domestic rookeries Bahia and Pipa, but some contributions from African and Caribbean rookeries were also observed. Oceanographic data corroborated the local origins, but showed higher connection with West Africa and none with the Caribbean. High correlation was observed between origins estimated through genetics/rookery size and oceanographic/rookery size data, demonstrating that ocean currents and population sizes influence haplotype distribution of Brazil's hawksbill populations. The information presented here highlights the importance of national conservation strategies and international cooperation for the recovery of endangered hawksbill turtle populations. PMID:24558419

Allometric shape change and heterochrony in the freeliving coral Trachyphyllia bilobata (Duncan)

NASA Astrophysics Data System (ADS)

Foster, Ann Budd; Johnson, Kenneth G.; Schultz, Lori L.

1988-05-01

Regression analysis has been used to study the relationship between age, size, shape, and surface area in two ancestral-descendant populations of the Neogene Caribbean coral Trachyphyllia bilobata. Analyses of the relationship between size and age show that the relationship is isometric and that little difference occurs between populations in mean corallite length or height and in their rates of growth. Onset of columella growth is significantly earlier, however, in the descendant population. Studies of the relationship between size and shape show that growth is allometric, with shape change occurring in both corallum elongation and pinching of the corallite wall during ontogeny. In the descendant population, pinching and elongation initiate earlier in the ontogeny of the coral. These results suggest that the evolutionary development of the meandroid form in freeliving corals has been accomplished by heterochrony, involving a complex set of disassociated peramorphic changes in ontogeny accompanied by paedomorphic changes in astogeny. Further analyses show that the observed heterochronic changes serve to decrease corallum surface area which may in turn enhance sediment removal and nutrition in unstable habitats.

Comparative tests of ectoparasite species richness in seabirds

PubMed Central

Hughes, Joseph; Page, Roderic DM

2007-01-01

Background The diversity of parasites attacking a host varies substantially among different host species. Understanding the factors that explain these patterns of parasite diversity is critical to identifying the ecological principles underlying biodiversity. Seabirds (Charadriiformes, Pelecaniformes and Procellariiformes) and their ectoparasitic lice (Insecta: Phthiraptera) are ideal model groups in which to study correlates of parasite species richness. We evaluated the relative importance of morphological (body size, body weight, wingspan, bill length), life-history (longevity, clutch size), ecological (population size, geographical range) and behavioural (diving versus non-diving) variables as predictors of louse diversity on 413 seabird hosts species. Diversity was measured at the level of louse suborder, genus, and species, and uneven sampling of hosts was controlled for using literature citations as a proxy for sampling effort. Results The only variable consistently correlated with louse diversity was host population size and to a lesser extent geographic range. Other variables such as clutch size, longevity, morphological and behavioural variables including body mass showed inconsistent patterns dependent on the method of analysis. Conclusion The comparative analysis presented herein is (to our knowledge) the first to test correlates of parasite species richness in seabirds. We believe that the comparative data and phylogeny provide a valuable framework for testing future evolutionary hypotheses relating to the diversity and distribution of parasites on seabirds. PMID:18005412

Do less populous countries receive more development assistance for health per capita? Longitudinal evidence for 143 countries, 1990-2014.

PubMed

Martinsen, Lene; Ottersen, Trygve; Dieleman, Joseph L; Hessel, Philipp; Kinge, Jonas Minet; Skirbekk, Vegard

2018-01-01

Per capita allocation of overall development assistance has been shown to be biased towards countries with lower population size, meaning funders tend to provide proportionally less development assistance to countries with large populations. Individuals that happen to be part of large populations therefore tend to receive less assistance. However, no study has investigated whether this is also true regarding development assistance for health. We examined whether this so-called 'small-country bias' exists in the health aid sector. We analysed the effect of a country's population size on the receipt of development assistance for health per capita (in 2015 US$) among 143 countries over the period 1990-2014. Explanatory variables shown to be associated with receipt of development assistance for health were included: gross domestic product per capita, burden of disease, under-5 mortality rate, maternal mortality ratio, vaccination coverage (diphtheria, tetanus and pertussis) and fertility rate. We used the within-between regression analysis, popularised by Mundluck, as well as a number of robustness tests, including ordinary least squares, random-effects and fixed-effects regressions. Our results suggest there exists significant negative effect of population size on the amount of development assistance for health per capita countries received. According to the within-between estimator, a 1% larger population size is associated with a 0.4% lower per capita development assistance for health between countries (-0.37, 95% CI -0.45 to -0.28), and 2.3% lower per capita development assistance for health within countries (-2.29, 95% CI -3.86 to -0.72). Our findings support the hypothesis that small-country bias exists within international health aid, as has been previously documented for aid in general. In a rapidly changing landscape of global health and development, the inclusion of population size in allocation decisions should be challenged on the basis of equitable access to healthcare and health aid effectiveness.

State Size and Government Level Matter Most: A Structural Equation Model of Local Health Department Policy Behaviors.

PubMed

Meyerson, Beth E; Sayegh, M Aaron

2016-01-01

To explore relationships between local health department policy behaviors, levels of government activity, policy focus areas, and selected health department characteristics. Cross-sectional analysis of secondary data from the 2013 National Association of County & City Health Officials (NACCHO) Profile Survey. Local health departments throughout the United States. A total of 2000 local health departments responding to the 2013 Profile Survey of Local Health Departments. Survey data were gathered by the NACCHO. Secondary analysis of reported policy behaviors for the 2013 NACCHO Profile Survey. A structural equation model tested effects on and between state population size, rurality, census region and policy focus, and the latent variables of policy behavior formed from a confirmatory factor analysis. Policy behaviors, levels of government activity (local, state, and federal), policy focus areas, and selected local health department characteristics. The majority (85.1%) of health departments reported at least one of the possible policy behaviors. State population size increased the probability of local policy behavior, and local behavior increased the probability of state policy behavior. State size increased the likelihood of federal policy behavior and the focus on tobacco, emergency preparedness, and obesity/chronic disease. However, the more rural a state was, the more likely policy behavior was at the state and federal levels and not at local levels. Specific policy behaviors mattered less than the level of government activity. Size of state and rurality of health departments influence the government level of policy behavior.

Introgression Makes Waves in Inferred Histories of Effective Population Size.

PubMed

Hawks, John

2017-01-01

Human populations have a complex history of introgression and of changing population size. Human genetic variation has been affected by both these processes, so inference of past population size depends upon the pattern of gene flow and introgression among past populations. One remarkable aspect of human population history as inferred from genetics is a consistent "wave" of larger effective population sizes, found in both African and non-African populations, that appears to reflect events prior to the last 100,000 years. I carried out a series of simulations to investigate how introgression and gene flow from genetically divergent ancestral populations affect the inference of ancestral effective population size. Both introgression and gene flow from an extinct, genetically divergent population consistently produce a wave in the history of inferred effective population size. The time and amplitude of the wave reflect the time of origin of the genetically divergent ancestral populations and the strength of introgression or gene flow. These results demonstrate that even small fractions of introgression or gene flow from ancient populations may have visible effects on the inference of effective population size.

Local extinction and recolonization, species effective population size, and modern human origins.

PubMed

Eller, Elise; Hawks, John; Relethford, John H

2004-10-01

A primary objection from a population genetics perspective to a multiregional model of modern human origins is that the model posits a large census size, whereas genetic data suggest a small effective population size. The relationship between census size and effective size is complex, but arguments based on an island model of migration show that if the effective population size reflects the number of breeding individuals and the effects of population subdivision, then an effective population size of 10,000 is inconsistent with the census size of 500,000 to 1,000,000 that has been suggested by archeological evidence. However, these models have ignored the effects of population extinction and recolonization, which increase the expected variance among demes and reduce the inbreeding effective population size. Using models developed for population extinction and recolonization, we show that a large census size consistent with the multiregional model can be reconciled with an effective population size of 10,000, but genetic variation among demes must be high, reflecting low interdeme migration rates and a colonization process that involves a small number of colonists or kin-structured colonization. Ethnographic and archeological evidence is insufficient to determine whether such demographic conditions existed among Pleistocene human populations, and further work needs to be done. More realistic models that incorporate isolation by distance and heterogeneity in extinction rates and effective deme sizes also need to be developed. However, if true, a process of population extinction and recolonization has interesting implications for human demographic history.

Genetic Diversity in Introduced Populations with an Allee Effect

PubMed Central

Wittmann, Meike J.; Gabriel, Wilfried; Metzler, Dirk

2014-01-01

A phenomenon that strongly influences the demography of small introduced populations and thereby potentially their genetic diversity is the demographic Allee effect, a reduction in population growth rates at small population sizes. We take a stochastic modeling approach to investigate levels of genetic diversity in populations that successfully overcame either a strong Allee effect, in which populations smaller than a certain critical size are expected to decline, or a weak Allee effect, in which the population growth rate is reduced at small sizes but not negative. Our results indicate that compared to successful populations without an Allee effect, successful populations with a strong Allee effect tend to (1) derive from larger founder population sizes and thus have a higher initial amount of genetic variation, (2) spend fewer generations at small population sizes where genetic drift is particularly strong, and (3) spend more time around the critical population size and thus experience more genetic drift there. In the case of multiple introduction events, there is an additional increase in diversity because Allee-effect populations tend to derive from a larger number of introduction events than other populations. Altogether, a strong Allee effect can either increase or decrease genetic diversity, depending on the average founder population size. By contrast, a weak Allee effect tends to decrease genetic diversity across the entire range of founder population sizes. Finally, we show that it is possible in principle to infer critical population sizes from genetic data, although this would require information from many independently introduced populations. PMID:25009147

A Three-Stage Colonization Model for the Peopling of the Americas

PubMed Central

Kitchen, Andrew; Miyamoto, Michael M.; Mulligan, Connie J.

2008-01-01

Background We evaluate the process by which the Americas were originally colonized and propose a three-stage model that integrates current genetic, archaeological, geological, and paleoecological data. Specifically, we analyze mitochondrial and nuclear genetic data by using complementary coalescent models of demographic history and incorporating non-genetic data to enhance the anthropological relevance of the analysis. Methodology/Findings Bayesian skyline plots, which provide dynamic representations of population size changes over time, indicate that Amerinds went through two stages of growth ≈40,000 and ≈15,000 years ago separated by a long period of population stability. Isolation-with-migration coalescent analyses, which utilize data from sister populations to estimate a divergence date and founder population sizes, suggest an Amerind population expansion starting ≈15,000 years ago. Conclusions/Significance These results support a model for the peopling of the New World in which Amerind ancestors diverged from the Asian gene pool prior to 40,000 years ago and experienced a gradual population expansion as they moved into Beringia. After a long period of little change in population size in greater Beringia, Amerinds rapidly expanded into the Americas ≈15,000 years ago either through an interior ice-free corridor or along the coast. This rapid colonization of the New World was achieved by a founder group with an effective population size of ≈1,000–5,400 individuals. Our model presents a detailed scenario for the timing and scale of the initial migration to the Americas, substantially refines the estimate of New World founders, and provides a unified theory for testing with future datasets and analytic methods. PMID:18270583

DOE Office of Scientific and Technical Information (OSTI.GOV)

Terai, Tsuyoshi; Takahashi, Jun; Itoh, Yoichi, E-mail: tsuyoshi.terai@nao.ac.jp

Main-belt asteroids have been continuously colliding with one another since they were formed. Their size distribution is primarily determined by the size dependence of asteroid strength against catastrophic impacts. The strength scaling law as a function of body size could depend on collision velocity, but the relationship remains unknown, especially under hypervelocity collisions comparable to 10 km s{sup –1}. We present a wide-field imaging survey at an ecliptic latitude of about 25° for investigating the size distribution of small main-belt asteroids that have highly inclined orbits. The analysis technique allowing for efficient asteroid detections and high-accuracy photometric measurements provides sufficientmore » sample data to estimate the size distribution of sub-kilometer asteroids with inclinations larger than 14°. The best-fit power-law slopes of the cumulative size distribution are 1.25 ± 0.03 in the diameter range of 0.6-1.0 km and 1.84 ± 0.27 in 1.0-3.0 km. We provide a simple size distribution model that takes into consideration the oscillations of the power-law slope due to the transition from the gravity-scaled regime to the strength-scaled regime. We find that the high-inclination population has a shallow slope of the primary components of the size distribution compared to the low-inclination populations. The asteroid population exposed to hypervelocity impacts undergoes collisional processes where large bodies have a higher disruptive strength and longer lifespan relative to tiny bodies than the ecliptic asteroids.« less

The size of an ethno-cultural community as a social determinant of health for Chinese seniors.

PubMed

Chau, Shirley; Lai, Daniel W L

2011-12-01

The present study investigated the link between the sizes of the Chinese community to the health of Chinese seniors in Canada. A secondary data analysis of survey data from a representative sample of 2,272 Chinese older adults aged 55 and over was conducted. Hierarchical regression analyses were performed to assess the effects of the size of Chinese communities in Chinese seniors' health. Chinese seniors residing in the community with a small Chinese population reported better physical and mental health than the Chinese seniors residing in communities with a larger Chinese population. The findings were contrary to expectations that health of Chinese seniors should be higher in cities with large Chinese communities. These findings raise new questions for future investigations into the dynamics and impact of ethnic community size, and the importance of studying intragroup differences within ethno-cultural groups to better understand health disparities in ethnic groups.

Geometric morphometric analysis of Colombian Anopheles albimanus (Diptera: Culicidae) reveals significant effect of environmental factors on wing traits and presence of a metapopulation

PubMed Central

Gómez, Giovan F.; Márquez, Edna J.; Gutiérrez, Lina A.; Conn, Jan E.; Correa, Margarita M.

2015-01-01

Anopheles albimanus is a major malaria mosquito vector in Colombia. In the present study, wing variability (size and shape) in An. albimanus populations from Colombian Maracaibo and Chocó bio-geographical eco-regions and the relationship of these phenotypic traits with environmental factors were evaluated. Microsatellite and morphometric data facilitated a comparison of the genetic and phenetic structure of this species. Wing size was influenced by elevation and relative humidity, whereas wing shape was affected by these two variables and also by rainfall, latitude, temperature and eco-region. Significant differences in mean shape between populations and eco-regions were detected, but they were smaller than those at the intra-population level. Correct assignment based on wing shape was low at the population level (<58%) and only slightly higher (>70%) at the eco-regional level, supporting the low population structure inferred from microsatellite data. Wing size was similar among populations with no significant differences between eco-regions. Population relationships in the genetic tree did not agree with those from the morphometric data; however, both datasets consistently reinforced a panmictic population of An. albimanus. Overall, site-specific population differentiation is not strongly supported by wing traits or genotypic data. We hypothesize that the metapopulation structure of An. albimanus throughout these Colombian eco-regions is favoring plasticity in wing traits, a relevant characteristic of species living under variable environmental conditions and colonizing new habitats. PMID:24704285

Estimating the number of tree species in forest populations using current vegetation survey and forest inventory and analysis approximation plots and grid intensities

Treesearch

Hans T. Schreuder; Jin-Mann S. Lin; John Teply

2000-01-01

We estimate number of tree species in National Forest populations using the nonparametric estimator. Data from the Current Vegetation Survey (CVS) of Region 6 of the USDA Forest Service were used to estimate the number of tree species with a plot close in size to the Forest Inventory and Analysis (FIA) plot and the actual CVS plot for the 5.5 km FIA grid and the 2.7 km...

Large exon size does not limit splicing in vivo.

PubMed

Chen, I T; Chasin, L A

1994-03-01

Exon sizes in vertebrate genes are, with a few exceptions, limited to less than 300 bases. It has been proposed that this limitation may derive from the exon definition model of splice site recognition. In this model, a downstream donor site enhances splicing at the upstream acceptor site of the same exon. This enhancement may require contact between factors bound to each end of the exon; an exon size limitation would promote such contact. To test the idea that proximity was required for exon definition, we inserted random DNA fragments from Escherichia coli into a central exon in a three-exon dihydrofolate reductase minigene and tested whether the expanded exons were efficiently spliced. DNA from a plasmid library of expanded minigenes was used to transfect a CHO cell deletion mutant lacking the dhfr locus. PCR analysis of DNA isolated from the pooled stable cotransfectant populations displayed a range of DNA insert sizes from 50 to 1,500 nucleotides. A parallel analysis of the RNA from this population by reverse transcription followed by PCR showed a similar size distribution. Central exons as large as 1,400 bases could be spliced into mRNA. We also tested individual plasmid clones containing exon inserts of defined sizes. The largest exon included in mRNA was 1,200 bases in length, well above the 300-base limit implied by the survey of naturally occurring exons. We conclude that a limitation in exon size is not part of the exon definition mechanism.

Geographic variation in morphology of Alaska-breeding Bar-tailed Godwits (Limosa lapponica) is not maintained on their nonbreeding grounds in New Zealand

USGS Publications Warehouse

Conklin, Jesse R.; Battley, Phil F.; Potter, Murray A.; Ruthrauff, Daniel R.

2011-01-01

Among scolopacid shorebirds, Bar-tailed Godwits (Limosa lapponica) have unusually high intra- and intersexual differences in size and breeding plumage. Despite historical evidence for population structure among Alaska-breeding Bar-tailed Godwits (L. l. baueri), no thorough analysis, or comparison with the population's nonbreeding distribution, has been undertaken. We used live captures, field photography, museum specimens, and individuals tracked from New Zealand to describe geographic variation in size and plumage within the Alaska breeding range. We found a north-south cline in body size in Alaska, in which the smallest individuals of each sex occurred at the highest latitudes. Extent of male breeding plumage (proportion of nonbreeding contour feathers replaced) also increased with latitude, but female breeding plumage was most extensive at mid-latitudes. This population structure was not maintained in the nonbreeding season: morphometrics of captured birds and timing of migratory departures indicated that individuals from a wide range of breeding latitudes occur in each region and site in New Zealand. Links among morphology, phenology, and breeding location suggest the possibility of distinct Alaska breeding populations that mix freely in the nonbreeding season, and also imply that the strongest selection for size occurs in the breeding season.

The effects of Medieval dams on genetic divergence and demographic history in brown trout populations

PubMed Central

2014-01-01

Background Habitat fragmentation has accelerated within the last century, but may have been ongoing over longer time scales. We analyzed the timing and genetic consequences of fragmentation in two isolated lake-dwelling brown trout populations. They are from the same river system (the Gudenå River, Denmark) and have been isolated from downstream anadromous trout by dams established ca. 600–800 years ago. For reference, we included ten other anadromous populations and two hatchery strains. Based on analysis of 44 microsatellite loci we investigated if the lake populations have been naturally genetically differentiated from anadromous trout for thousands of years, or have diverged recently due to the establishment of dams. Results Divergence time estimates were based on 1) Approximate Bayesian Computation and 2) a coalescent-based isolation-with-gene-flow model. Both methods suggested divergence times ca. 600–800 years bp, providing strong evidence for establishment of dams in the Medieval as the factor causing divergence. Bayesian cluster analysis showed influence of stocked trout in several reference populations, but not in the focal lake and anadromous populations. Estimates of effective population size using a linkage disequilibrium method ranged from 244 to > 1,000 in all but one anadromous population, but were lower (153 and 252) in the lake populations. Conclusions We show that genetic divergence of lake-dwelling trout in two Danish lakes reflects establishment of water mills and impassable dams ca. 600–800 years ago rather than a natural genetic population structure. Although effective population sizes of the two lake populations are not critically low they may ultimately limit response to selection and thereby future adaptation. Our results demonstrate that populations may have been affected by anthropogenic disturbance over longer time scales than normally assumed. PMID:24903056

The effects of Medieval dams on genetic divergence and demographic history in brown trout populations.

PubMed

Hansen, Michael M; Limborg, Morten T; Ferchaud, Anne-Laure; Pujolar, José-Martin

2014-06-05

Habitat fragmentation has accelerated within the last century, but may have been ongoing over longer time scales. We analyzed the timing and genetic consequences of fragmentation in two isolated lake-dwelling brown trout populations. They are from the same river system (the Gudenå River, Denmark) and have been isolated from downstream anadromous trout by dams established ca. 600-800 years ago. For reference, we included ten other anadromous populations and two hatchery strains. Based on analysis of 44 microsatellite loci we investigated if the lake populations have been naturally genetically differentiated from anadromous trout for thousands of years, or have diverged recently due to the establishment of dams. Divergence time estimates were based on 1) Approximate Bayesian Computation and 2) a coalescent-based isolation-with-gene-flow model. Both methods suggested divergence times ca. 600-800 years bp, providing strong evidence for establishment of dams in the Medieval as the factor causing divergence. Bayesian cluster analysis showed influence of stocked trout in several reference populations, but not in the focal lake and anadromous populations. Estimates of effective population size using a linkage disequilibrium method ranged from 244 to > 1,000 in all but one anadromous population, but were lower (153 and 252) in the lake populations. We show that genetic divergence of lake-dwelling trout in two Danish lakes reflects establishment of water mills and impassable dams ca. 600-800 years ago rather than a natural genetic population structure. Although effective population sizes of the two lake populations are not critically low they may ultimately limit response to selection and thereby future adaptation. Our results demonstrate that populations may have been affected by anthropogenic disturbance over longer time scales than normally assumed.

Confidence intervals for population allele frequencies: the general case of sampling from a finite diploid population of any size.

PubMed

Fung, Tak; Keenan, Kevin

2014-01-01

The estimation of population allele frequencies using sample data forms a central component of studies in population genetics. These estimates can be used to test hypotheses on the evolutionary processes governing changes in genetic variation among populations. However, existing studies frequently do not account for sampling uncertainty in these estimates, thus compromising their utility. Incorporation of this uncertainty has been hindered by the lack of a method for constructing confidence intervals containing the population allele frequencies, for the general case of sampling from a finite diploid population of any size. In this study, we address this important knowledge gap by presenting a rigorous mathematical method to construct such confidence intervals. For a range of scenarios, the method is used to demonstrate that for a particular allele, in order to obtain accurate estimates within 0.05 of the population allele frequency with high probability (> or = 95%), a sample size of > 30 is often required. This analysis is augmented by an application of the method to empirical sample allele frequency data for two populations of the checkerspot butterfly (Melitaea cinxia L.), occupying meadows in Finland. For each population, the method is used to derive > or = 98.3% confidence intervals for the population frequencies of three alleles. These intervals are then used to construct two joint > or = 95% confidence regions, one for the set of three frequencies for each population. These regions are then used to derive a > or = 95%% confidence interval for Jost's D, a measure of genetic differentiation between the two populations. Overall, the results demonstrate the practical utility of the method with respect to informing sampling design and accounting for sampling uncertainty in studies of population genetics, important for scientific hypothesis-testing and also for risk-based natural resource management.

Use of population viability analysis to evaluate CITES trade-management options for threatened marine fishes.

PubMed

Curtis, Janelle M R; Vincent, Amanda C J

2008-10-01

Achieving multiple conservation objectives can be challenging, particularly under high uncertainty. Having agreed to limit seahorse (Hippocampus) exports to sustainable levels, signatories to the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) were offered the option of a single 10-cm minimum size limit (MSL) as an interim management measure for all Hippocampus species (> or =34). Although diverse stakeholders supported the recommended MSL, its biological and socioeconomic implications were not assessed quantitatively. We combined population viability analysis, model sensitivity analysis, and economic information to evaluate the trade-off between conservation threat to and long-term cumulative income from these exploited marine fishes of high conservation concern. We used the European long-snouted seahorse (Hippocampus guttulatus) as a representative species to compare the performance of MSLs set at alternative biological reference points. Our sensitivity analyses showed that in most of our scenarios, setting the MSL just above size at maturity (9.7 cm in H. guttulatus) would not prevent exploited populations from becoming listed as vulnerable. By contrast, the relative risk of decline and extinction were almost halved--at a cost of only a 5.6% reduction in long-term catches--by increasing the MSL to the size reached after at least one full reproductive season. On the basis of our analysis, a precautionary increase in the MSL could be compatible with sustaining fishers' livelihoods and international trade. Such management tactics that aid species conservation and have minimal effects on long term catch trends may help bolster the case for CITES trade management of other valuable marine fishes.

The Impact of Marine Protected Areas on Reef-Wide Population Structure and Fishing-Induced Phenotypes in Coral-Reef Fishes

NASA Astrophysics Data System (ADS)

Fidler, Robert Young, III

Overfishing and destructive fishing practices threaten the sustainability of fisheries worldwide. In addition to reducing population sizes, anthropogenic fishing effort is highly size-selective, preferentially removing the largest individuals from harvested stocks. Intensive, size-selective mortality induces widespread phenotypic shifts toward the predominance of smaller and earlier-maturing individuals. Fish that reach sexual maturity at smaller size and younger age produce fewer, smaller, and less viable larvae, severely reducing the reproductive capacity of exploited populations. These directional phenotypic alterations, collectively known as "fisheries-induced evolution" (FIE) are among the primary causes of the loss of harvestable fish biomass. Marine protected areas (MPAs) are one of the most widely utilized components of fisheries management programs around the world, and have been proposed as a potential mechanism by which the impacts of FIE may be mitigated. The ability of MPAs to buffer exploited populations against fishing pressure, however, remains debated due to inconsistent results across studies. Additionally, empirical evidence of phenotypic shifts in fishes within MPAs is lacking. This investigation addresses both of these issues by: (1) using a categorical meta-analysis of MPAs to standardize and quantify the magnitude of MPA impacts across studies; and (2) conducting a direct comparison of life-history phenotypes known to be influenced by FIE in six reef-fish species inside and outside of MPAs. The Philippines was used as a model system for analyses due to the country's significance in global marine biodiversity and reliance on MPAs as a fishery management tool. The quantitative impact of Philippine MPAs was assessed using a "reef-wide" meta-analysis. This analysis used pooled visual census data from 39 matched pairs of MPAs and fished reefs surveyed twice over a mean period of 3 years. In 17 of these MPAs, two additional surveys were conducted using size-specific fish counts, allowing for spatiotemporal comparisons of abundance and demographic structure of fish populations across protected and fished areas. Results of the meta-analysis revealed that: (1) although fish density was higher inside MPAs than in fished reefs at each sampling period, reef-wide density often increased or remained stable over time; and (2) increases in large-bodied fish were evident reef-wide between survey periods, indicating that positive demographic shifts occurred simultaneously in both MPAs and adjacent areas. Increases in large-bodied fish were observed across a range of taxa, but were most prominent in families directly targeted by fishermen. These results suggest that over relatively few years of protection, Philippine MPAs promoted beneficial shifts in population structure throughout entire reef systems, rather than simply maintaining stable populations within their borders. Relationships between MPA age and shifts in fish density or demographic structure were rare, but may have been precluded by the relatively short period between replicate surveys. Although increases in fish density inside MPAs were occasionally associated with MPA size, there were no significant relationships between the size of MPAs and reef-wide increases in fish density. The reef-wide framework of MPA assessment used in this study has the advantage of treating MPAs and fished reefs as an integrated system, thus revealing trends that would be indistinguishable in traditional spatial comparisons between MPAs and fished reefs. The impact of MPAs on fishing-induced life-history traits was assessed by comparing growth and maturation patterns exhibited by six reef-fish species inside and outside five MPAs and adjacent, fished reefs in Zambales, Luzon, Philippines. This analysis demonstrated considerable variation in terminal body-sizes (Linf) and growth rates (K) between conspecifics in MPAs and fished reefs. Three of the four experimental species directly targeted for food in the region (Acanthurus nigrofuscus, Ctenochaetus striatus, and Parupeneus multifasciatus) exhibited greater Linf, lower K, or both characteristics inside at least one MPA compared to populations in adjacent, fished reefs. Life-history shifts were concentrated in the oldest and largest MPAs, but occurred at least once in each of the five MPAs that were examined. A fourth species harvested for food (Ctenochaetus binotatus), as well as a species targeted for the aquarium trade (Zebrasoma scopas) and a non-target species (Plectroglyphidodon lacrymatus) did not exhibit differential phenotypes between MPAs and fished reefs. The relatively high frequency of alterations to life-history characteristics across MPAs in harvested species suggests that observed changes in the density and size-structure of harvested fish populations inside MPAs are likely driven by spatial disparities in fishing pressure, and are the result of phenotypic changes rather than increased longevity.

Competition in size-structured populations: mechanisms inducing cohort formation and population cycles.

PubMed

de Roos, André M; Persson, Lennart

2003-02-01

In this paper we investigate the consequences of size-dependent competition among the individuals of a consumer population by analyzing the dynamic properties of a physiologically structured population model. Only 2 size-classes of individuals are distinguished: juveniles and adults. Juveniles and adults both feed on one and the same resource and hence interact by means of exploitative competition. Juvenile individuals allocate all assimilated energy into development and mature on reaching a fixed developmental threshold. The combination of this fixed threshold and the resource-dependent developmental rate, implies that the juvenile delay between birth and the onset of reproduction may vary in time. Adult individuals allocate all assimilated energy to reproduction. Mortality of both juveniles and adults is assumed to be inversely proportional to the amount of energy assimilated. In this setting we study how the dynamics of the population are influenced by the relative foraging capabilities of juveniles and adults. In line with results that we previously obtained in size-structured consumer-resource models with pulsed reproduction, population cycles primarily occur when either juveniles or adults have a distinct competitive advantage. When adults have a larger per capita feeding rate and are hence competitively superior to juveniles, population oscillations occur that are primarily induced by the fact that the duration of the juvenile period changes with changing food conditions. These cycles do not occur when the juvenile delay is a fixed parameter. When juveniles are competitively superior, two different types of population fluctuations can occur: (1) rapid, low-amplitude fluctuations having a period of half the juvenile delay and (2) slow, large-amplitude fluctuations characterized by a period, which is roughly equal to the juvenile delay. The analysis of simplified versions of the structured model indicates that these two types of oscillations also occur if mortality and/or development is independent of food density, i.e. in a situation with a constant juvenile developmental delay and a constant, food-independent background mortality. Thus, the oscillations that occur when juveniles are more competitive are induced by the juvenile delay per se. When juveniles exert a larger foraging pressure on the shared resource, maturation implies an increase not only in adult density, but also in food density and consequently fecundity. Our analysis suggests that this correlation in time between adult density and fecundity is crucial for the occurrence of population cycles when juveniles are competitively superior.

Optimal exploitation strategies for an animal population in a Markovian environment: A theory and an example

USGS Publications Warehouse

Anderson, D.R.

1975-01-01

Optimal exploitation strategies were studied for an animal population in a Markovian (stochastic, serially correlated) environment. This is a general case and encompasses a number of important special cases as simplifications. Extensive empirical data on the Mallard (Anas platyrhynchos) were used as an example of general theory. The number of small ponds on the central breeding grounds was used as an index to the state of the environment. A general mathematical model was formulated to provide a synthesis of the existing literature, estimates of parameters developed from an analysis of data, and hypotheses regarding the specific effect of exploitation on total survival. The literature and analysis of data were inconclusive concerning the effect of exploitation on survival. Therefore, two hypotheses were explored: (1) exploitation mortality represents a largely additive form of mortality, and (2) exploitation mortality is compensatory with other forms of mortality, at least to some threshold level. Models incorporating these two hypotheses were formulated as stochastic dynamic programming models and optimal exploitation strategies were derived numerically on a digital computer. Optimal exploitation strategies were found to exist under the rather general conditions. Direct feedback control was an integral component in the optimal decision-making process. Optimal exploitation was found to be substantially different depending upon the hypothesis regarding the effect of exploitation on the population. If we assume that exploitation is largely an additive force of mortality in Mallards, then optimal exploitation decisions are a convex function of the size of the breeding population and a linear or slight concave function of the environmental conditions. Under the hypothesis of compensatory mortality forces, optimal exploitation decisions are approximately linearly related to the size of the Mallard breeding population. Dynamic programming is suggested as a very general formulation for realistic solutions to the general optimal exploitation problem. The concepts of state vectors and stage transformations are completely general. Populations can be modeled stochastically and the objective function can include extra-biological factors. The optimal level of exploitation in year t must be based on the observed size of the population and the state of the environment in year t unless the dynamics of the population, the state of the environment, and the result of the exploitation decisions are completely deterministic. Exploitation based on an average harvest, or harvest rate, or designed to maintain a constant breeding population size is inefficient.

Effective population size of korean populations.

PubMed

Park, Leeyoung

2014-12-01

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

Estimating the size of hidden populations using respondent-driven sampling data: Case examples from Morocco

PubMed Central

Johnston, Lisa G; McLaughlin, Katherine R; Rhilani, Houssine El; Latifi, Amina; Toufik, Abdalla; Bennani, Aziza; Alami, Kamal; Elomari, Boutaina; Handcock, Mark S

2015-01-01

Background Respondent-driven sampling is used worldwide to estimate the population prevalence of characteristics such as HIV/AIDS and associated risk factors in hard-to-reach populations. Estimating the total size of these populations is of great interest to national and international organizations, however reliable measures of population size often do not exist. Methods Successive Sampling-Population Size Estimation (SS-PSE) along with network size imputation allows population size estimates to be made without relying on separate studies or additional data (as in network scale-up, multiplier and capture-recapture methods), which may be biased. Results Ten population size estimates were calculated for people who inject drugs, female sex workers, men who have sex with other men, and migrants from sub-Sahara Africa in six different cities in Morocco. SS-PSE estimates fell within or very close to the likely values provided by experts and the estimates from previous studies using other methods. Conclusions SS-PSE is an effective method for estimating the size of hard-to-reach populations that leverages important information within respondent-driven sampling studies. The addition of a network size imputation method helps to smooth network sizes allowing for more accurate results. However, caution should be used particularly when there is reason to believe that clustered subgroups may exist within the population of interest or when the sample size is small in relation to the population. PMID:26258908

Kinematic analysis of total knee prosthesis designed for Asian population.

PubMed

Low, F H; Khoo, L P; Chua, C K; Lo, N N

2000-01-01

In designing a total knee replacement (TKR) prosthesis catering for the Asian population, 62 sets of femur were harvested and analyzed. The morphometrical data obtained were found to be in good agreement with dimensions typical of the Asian knee and has reaffirmed the fact that Caucasian knees are generally larger than Asian knees. Subsequently, these data when treated using a multivariate statistical technique resulted in the establishment of major design parameters for six different sizes of femoral implants. An extra-small implant size with established dimensions and geometrical shape has surfaced from the study. The differences between the Asian knees and the Caucasian knees are discussed. Employing the established femoral dimensions and motion path of the knee joint, the articulating tibia profile was generated. All the sizes of implants were modeled using a computer-aided software package. Thereupon, these models that accurately fits the local Asian knee were transported into a dynamic and kinematic analysis software package. The tibiofemoral joint was modeled successfully as a slide curve joint to study intuitively the motion of the femur when articulating on the tibia surface. An optimal tibia profile could be synthesized to mimic the natural knee path motion. Details of the analysis are presented and discussed.

Evaluation of trap capture in a geographically closed population of brown treesnakes on Guam

USGS Publications Warehouse

Tyrrell, C.L.; Christy, M.T.; Rodda, G.H.; Yackel Adams, A.A.; Ellingson, A.R.; Savidge, J.A.; Dean-Bradley, K.; Bischof, R.

2009-01-01

1. Open population mark-recapture analysis of unbounded populations accommodates some types of closure violations (e.g. emigration, immigration). In contrast, closed population analysis of such populations readily allows estimation of capture heterogeneity and behavioural response, but requires crucial assumptions about closure (e.g. no permanent emigration) that are suspect and rarely tested empirically. 2. In 2003, we erected a double-sided barrier to prevent movement of snakes in or out of a 5-ha semi-forested study site in northern Guam. This geographically closed population of >100 snakes was monitored using a series of transects for visual searches and a 13 ?? 13 trapping array, with the aim of marking all snakes within the site. Forty-five marked snakes were also supplemented into the resident population to quantify the efficacy of our sampling methods. We used the program mark to analyse trap captures (101 occasions), referenced to census data from visual surveys, and quantified heterogeneity, behavioural response, and size bias in trappability. Analytical inclusion of untrapped individuals greatly improved precision in the estimation of some covariate effects. 3. A novel discovery was that trap captures for individual snakes consisted of asynchronous bouts of high capture probability lasting about 7 days (ephemeral behavioural effect). There was modest behavioural response (trap happiness) and significant latent (unexplained) heterogeneity, with small influences on capture success of date, gender, residency status (translocated or not), and body condition. 4. Trapping was shown to be an effective tool for eradicating large brown treesnakes Boiga irregularis (>900 mm snout-vent length, SVL). 5. Synthesis and applications. Mark-recapture modelling is commonly used by ecological managers to estimate populations. However, existing models involve making assumptions about either closure violations or response to capture. Physical closure of our population on a landscape scale allowed us to determine the relative importance of covariates influencing capture probability (body size, trappability periods, and latent heterogeneity). This information was used to develop models in which different segments of the population could be assigned different probabilities of capture, and suggests that modelling of open populations should incorporate easily measured, but potentially overlooked, parameters such as body size or condition. ?? 2008 The Authors.

Species delimitation, genetic diversity and population historical dynamics of Cycas diannanensis (Cycadaceae) occurring sympatrically in the Red River region of China

PubMed Central

Liu, Jian; Zhou, Wei; Gong, Xun

2015-01-01

Delimitating species boundaries could be of critical importance when evaluating the species' evolving process and providing guidelines for conservation genetics. Here, species delimitation was carried out on three endemic and endangered Cycas species with resembling morphology and overlapped distribution range along the Red River (Yuanjiang) in China: Cycas diananensis Z. T. Guan et G. D. Tao, Cycas parvula S. L. Yang and Cycas multiovula D. Y. Wang. A total of 137 individuals from 15 populations were genotyped by using three chloroplastic (psbA-trnH, atpI-atpH, and trnL-rps4) and two single copy nuclear (RPB1 and SmHP) DNA sequences. Basing on the carefully morphological comparison and cladistic haplotype aggregation (CHA) analysis, we propose all the populations as one species, with the rest two incorporated into C. diannanensis. Genetic diversity and structure analysis of the conflated C. diannanensis revealed this species possessed a relative lower genetic diversity than estimates of other Cycas species. The higher genetic diversity among populations and relative lower genetic diversity within populations, as well as obvious genetic differentiation among populations inferred from chloroplastic DNA (cpDNA) suggested a recent genetic loss within this protected species. Additionally, a clear genetic structure of C. diannanensis corresponding with geography was detected based on cpDNA, dividing its population ranges into “Yuanjiang-Nanhun” basin and “Ejia-Jiepai” basin groups. Demographical history analyses based on combined cpDNA and one nuclear DNA (nDNA) SmHP both showed the population size of C. diannanensis began to decrease in Quaternary glaciation with no subsequent expansion, while another nDNA RPB1 revealed a more recent sudden expansion after long-term population size contraction, suggesting its probable bottleneck events in history. Our findings offer grounded views for clarifying species boundaries of C. diannanensis when determining the conservation objectives. For operational guidelines, the downstream populations which occupy high and peculiar haplotypes should be given prior in-situ conservation. In addition, ex-situ conservation and reintroduction measures for decades of generations are supplemented for improving the population size and genetic diversity of the endemic and endangered species. PMID:26442013

Species delimitation, genetic diversity and population historical dynamics of Cycas diannanensis (Cycadaceae) occurring sympatrically in the Red River region of China.

PubMed

Liu, Jian; Zhou, Wei; Gong, Xun

2015-01-01

Delimitating species boundaries could be of critical importance when evaluating the species' evolving process and providing guidelines for conservation genetics. Here, species delimitation was carried out on three endemic and endangered Cycas species with resembling morphology and overlapped distribution range along the Red River (Yuanjiang) in China: Cycas diananensis Z. T. Guan et G. D. Tao, Cycas parvula S. L. Yang and Cycas multiovula D. Y. Wang. A total of 137 individuals from 15 populations were genotyped by using three chloroplastic (psbA-trnH, atpI-atpH, and trnL-rps4) and two single copy nuclear (RPB1 and SmHP) DNA sequences. Basing on the carefully morphological comparison and cladistic haplotype aggregation (CHA) analysis, we propose all the populations as one species, with the rest two incorporated into C. diannanensis. Genetic diversity and structure analysis of the conflated C. diannanensis revealed this species possessed a relative lower genetic diversity than estimates of other Cycas species. The higher genetic diversity among populations and relative lower genetic diversity within populations, as well as obvious genetic differentiation among populations inferred from chloroplastic DNA (cpDNA) suggested a recent genetic loss within this protected species. Additionally, a clear genetic structure of C. diannanensis corresponding with geography was detected based on cpDNA, dividing its population ranges into "Yuanjiang-Nanhun" basin and "Ejia-Jiepai" basin groups. Demographical history analyses based on combined cpDNA and one nuclear DNA (nDNA) SmHP both showed the population size of C. diannanensis began to decrease in Quaternary glaciation with no subsequent expansion, while another nDNA RPB1 revealed a more recent sudden expansion after long-term population size contraction, suggesting its probable bottleneck events in history. Our findings offer grounded views for clarifying species boundaries of C. diannanensis when determining the conservation objectives. For operational guidelines, the downstream populations which occupy high and peculiar haplotypes should be given prior in-situ conservation. In addition, ex-situ conservation and reintroduction measures for decades of generations are supplemented for improving the population size and genetic diversity of the endemic and endangered species.

How Reliable Are the Reported Genetic Associations in Disc Degeneration?: The Influence of Phenotypes, Age, Population Size, and Inclusion Sequence in 809 Patients.

PubMed

Rajasekaran, S; Kanna, Rishi Mugesh; Reddy, Ranjani Raja; Natesan, Senthil; Raveendran, Muthuraja; Cheung, Kenneth M C; Chan, Danny; Kao, Patrick Y P; Yee, Anita; Shetty, Ajoy Prasad

2016-11-01

Prospective genetic association study. The aim of this study was to document the variations in the genetic associations, when different magnetic resonance imaging (MRI) phenotypes, age stratification, cohort size, and sequence of cohort inclusion are varied in the same study population. Genetic associations with disc degeneration have shown high inconsistency, generally attributed to hereditary factors and ethnic variations. However, the effect of different phenotypes, size of the study population, age of the cohort, etc have not been documented clearly. Seventy-one single-nucleotide polymorphisms (SNPs) of 41 candidate genes were correlated to six MRI markers of disc degeneration (annular tears, Pfirmann grading, Schmorl nodes, Modic changes, Total Endplate Damage score, and disc bulge) in 809 patients with back pain and/or sciatica. In the same study group, the correlations were then retested for different age groups, different sample, size and sequence of subject inclusion (first 404 and the second 405) and the differences documented. The mean age of population (M: 455, F: 354) was 36.7 ± 10.8 years. Different genetic associations were found with different phenotypes: disc bulge with three SNPs of CILP; annular tears with rs2249350 of ADAMTS5 and rs11247361 IGF1R; modic changes with VDR and MMP20; Pfirmann grading with three SNPs of MMP20 and Schmorl node with SNPs of CALM1 and FN1 and none with Total End Plate Score.Subgroup analysis based on three age groups and dividing the total population into two groups also completely changed the associations for all the six radiographic parameters. In the same study population, SNP associations completely change with different phenotypes. Variations in age, inclusion sequence, and sample size resulted in change of genetic associations. Our study questions the validity of previous studies and necessitates the need for standardizing the description of disc degeneration, phenotype selection, study sample size, age, and other variables in future studies. 4.

Demographic Divergence History of Pied Flycatcher and Collared Flycatcher Inferred from Whole-Genome Re-sequencing Data

PubMed Central

Nadachowska-Brzyska, Krystyna; Burri, Reto; Olason, Pall I.; Kawakami, Takeshi; Smeds, Linnéa; Ellegren, Hans

2013-01-01

Profound knowledge of demographic history is a prerequisite for the understanding and inference of processes involved in the evolution of population differentiation and speciation. Together with new coalescent-based methods, the recent availability of genome-wide data enables investigation of differentiation and divergence processes at unprecedented depth. We combined two powerful approaches, full Approximate Bayesian Computation analysis (ABC) and pairwise sequentially Markovian coalescent modeling (PSMC), to reconstruct the demographic history of the split between two avian speciation model species, the pied flycatcher and collared flycatcher. Using whole-genome re-sequencing data from 20 individuals, we investigated 15 demographic models including different levels and patterns of gene flow, and changes in effective population size over time. ABC provided high support for recent (mode 0.3 my, range <0.7 my) species divergence, declines in effective population size of both species since their initial divergence, and unidirectional recent gene flow from pied flycatcher into collared flycatcher. The estimated divergence time and population size changes, supported by PSMC results, suggest that the ancestral species persisted through one of the glacial periods of middle Pleistocene and then split into two large populations that first increased in size before going through severe bottlenecks and expanding into their current ranges. Secondary contact appears to have been established after the last glacial maximum. The severity of the bottlenecks at the last glacial maximum is indicated by the discrepancy between current effective population sizes (20,000–80,000) and census sizes (5–50 million birds) of the two species. The recent divergence time challenges the supposition that avian speciation is a relatively slow process with extended times for intrinsic postzygotic reproductive barriers to evolve. Our study emphasizes the importance of using genome-wide data to unravel tangled demographic histories. Moreover, it constitutes one of the first examples of the inference of divergence history from genome-wide data in non-model species. PMID:24244198

Demographic divergence history of pied flycatcher and collared flycatcher inferred from whole-genome re-sequencing data.

PubMed

Nadachowska-Brzyska, Krystyna; Burri, Reto; Olason, Pall I; Kawakami, Takeshi; Smeds, Linnéa; Ellegren, Hans

2013-11-01

Profound knowledge of demographic history is a prerequisite for the understanding and inference of processes involved in the evolution of population differentiation and speciation. Together with new coalescent-based methods, the recent availability of genome-wide data enables investigation of differentiation and divergence processes at unprecedented depth. We combined two powerful approaches, full Approximate Bayesian Computation analysis (ABC) and pairwise sequentially Markovian coalescent modeling (PSMC), to reconstruct the demographic history of the split between two avian speciation model species, the pied flycatcher and collared flycatcher. Using whole-genome re-sequencing data from 20 individuals, we investigated 15 demographic models including different levels and patterns of gene flow, and changes in effective population size over time. ABC provided high support for recent (mode 0.3 my, range <0.7 my) species divergence, declines in effective population size of both species since their initial divergence, and unidirectional recent gene flow from pied flycatcher into collared flycatcher. The estimated divergence time and population size changes, supported by PSMC results, suggest that the ancestral species persisted through one of the glacial periods of middle Pleistocene and then split into two large populations that first increased in size before going through severe bottlenecks and expanding into their current ranges. Secondary contact appears to have been established after the last glacial maximum. The severity of the bottlenecks at the last glacial maximum is indicated by the discrepancy between current effective population sizes (20,000-80,000) and census sizes (5-50 million birds) of the two species. The recent divergence time challenges the supposition that avian speciation is a relatively slow process with extended times for intrinsic postzygotic reproductive barriers to evolve. Our study emphasizes the importance of using genome-wide data to unravel tangled demographic histories. Moreover, it constitutes one of the first examples of the inference of divergence history from genome-wide data in non-model species.

PICALM gene rs3851179 polymorphism contributes to Alzheimer's disease in an Asian population.

PubMed

Liu, Guiyou; Zhang, Shuyan; Cai, Zhiyou; Ma, Guoda; Zhang, Liangcai; Jiang, Yongshuai; Feng, Rennan; Liao, Mingzhi; Chen, Zugen; Zhao, Bin; Li, Keshen

2013-06-01

PICALM gene rs3851179 polymorphism was reported to an Alzheimer's disease (AD) susceptibility locus in a Caucasian population. However, recent studies reported consistent and inconsistent results in an Asian population. Four studies indicated no association between rs3851179 and AD in a Chinese population and one study reported weak association in a Japanese population. We consider that the failure to replicate the significant association between rs3851179 and AD may be caused by at least two reasons. The first reason may be the genetic heterogeneity in AD among different populations, and the second may be the relatively small sample size compared with large-scale GWAS in Caucasian ancestry. In order to confirm this view, in this research, we first evaluated the genetic heterogeneity of rs3851179 polymorphism in Caucasian and Asian populations. We then investigated rs3851179 polymorphism in an Asian population by a pooled analysis method and a meta-analysis method. We did not observe significant genetic heterogeneity of rs3851179 in the Caucasian and Asian populations. Our results indicate that rs3851179 polymorphism is significantly associated with AD in the Asian population by both pooled analysis and meta-analysis methods. We believe that our findings will be very useful for future genetic studies in AD.

Hierarchical distance-sampling models to estimate population size and habitat-specific abundance of an island endemic

USGS Publications Warehouse

Sillett, Scott T.; Chandler, Richard B.; Royle, J. Andrew; Kéry, Marc; Morrison, Scott A.

2012-01-01

Population size and habitat-specific abundance estimates are essential for conservation management. A major impediment to obtaining such estimates is that few statistical models are able to simultaneously account for both spatial variation in abundance and heterogeneity in detection probability, and still be amenable to large-scale applications. The hierarchical distance-sampling model of J. A. Royle, D. K. Dawson, and S. Bates provides a practical solution. Here, we extend this model to estimate habitat-specific abundance and rangewide population size of a bird species of management concern, the Island Scrub-Jay (Aphelocoma insularis), which occurs solely on Santa Cruz Island, California, USA. We surveyed 307 randomly selected, 300 m diameter, point locations throughout the 250-km2 island during October 2008 and April 2009. Population size was estimated to be 2267 (95% CI 1613-3007) and 1705 (1212-2369) during the fall and spring respectively, considerably lower than a previously published but statistically problematic estimate of 12 500. This large discrepancy emphasizes the importance of proper survey design and analysis for obtaining reliable information for management decisions. Jays were most abundant in low-elevation chaparral habitat; the detection function depended primarily on the percent cover of chaparral and forest within count circles. Vegetation change on the island has been dramatic in recent decades, due to release from herbivory following the eradication of feral sheep (Ovis aries) from the majority of the island in the mid-1980s. We applied best-fit fall and spring models of habitat-specific jay abundance to a vegetation map from 1985, and estimated the population size of A. insularis was 1400-1500 at that time. The 20-30% increase in the jay population suggests that the species has benefited from the recovery of native vegetation since sheep removal. Nevertheless, this jay's tiny range and small population size make it vulnerable to natural disasters and to habitat alteration related to climate change. Our results demonstrate that hierarchical distance-sampling models hold promise for estimating population size and spatial density variation at large scales. Our statistical methods have been incorporated into the R package unmarked to facilitate their use by animal ecologists, and we provide annotated code in the Supplement.

High-throughput nanoparticle sizing using lensfree holographic microscopy and liquid nanolenses (Conference Presentation)

NASA Astrophysics Data System (ADS)

McLeod, Euan

2016-03-01

The sizing of individual nanoparticles and the recovery of the distributions of sizes from populations of nanoparticles provide valuable information in virology, exosome analysis, air and water quality monitoring, and nanomaterials synthesis. Conventional approaches for nanoparticle sizing include those based on costly or low-throughput laboratory-scale equipment such as transmission electron microscopy or nanoparticle tracking analysis, as well as those approaches that only provide population-averaged quantities, such as dynamic light scattering. Some of these limitations can be overcome using a new family of alternative approaches based on quantitative phase imaging that combines lensfree holographic on-chip microscopy with self-assembled liquid nanolenses. In these approaches, the particles of interest are deposited onto a glass coverslip and the sample is coated with either pure liquid polyethylene glycol (PEG) or aqueous solutions of PEG. Due to surface tension, the PEG self-assembles into nano-scale lenses around the particles of interest. These nanolenses enhance the scattering signatures of the embedded particles such that individual nanoparticles as small as 40 nm are clearly visible in phase images reconstructed from captured holograms. The magnitude of the phase quantitatively corresponds to particle size with an accuracy of +/-11 nm. This family of approaches can individually size more than 10^5 particles in parallel, can handle a large dynamic range of particle sizes (40 nm - 100s of microns), and can accurately size multi-modal distributions of particles. Furthermore, the entire approach has been implemented in a compact and cost-effective device suitable for use in the field or in low-resource settings.

LOG-NORMAL DISTRIBUTION OF COSMIC VOIDS IN SIMULATIONS AND MOCKS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Russell, E.; Pycke, J.-R., E-mail: er111@nyu.edu, E-mail: jrp15@nyu.edu

2017-01-20

Following up on previous studies, we complete here a full analysis of the void size distributions of the Cosmic Void Catalog based on three different simulation and mock catalogs: dark matter (DM), haloes, and galaxies. Based on this analysis, we attempt to answer two questions: Is a three-parameter log-normal distribution a good candidate to satisfy the void size distributions obtained from different types of environments? Is there a direct relation between the shape parameters of the void size distribution and the environmental effects? In an attempt to answer these questions, we find here that all void size distributions of thesemore » data samples satisfy the three-parameter log-normal distribution whether the environment is dominated by DM, haloes, or galaxies. In addition, the shape parameters of the three-parameter log-normal void size distribution seem highly affected by environment, particularly existing substructures. Therefore, we show two quantitative relations given by linear equations between the skewness and the maximum tree depth, and between the variance of the void size distribution and the maximum tree depth, directly from the simulated data. In addition to this, we find that the percentage of voids with nonzero central density in the data sets has a critical importance. If the number of voids with nonzero central density reaches ≥3.84% in a simulation/mock sample, then a second population is observed in the void size distributions. This second population emerges as a second peak in the log-normal void size distribution at larger radius.« less

The effects of landscape modifications on the long-term persistence of animal populations.

PubMed

Nabe-Nielsen, Jacob; Sibly, Richard M; Forchhammer, Mads C; Forbes, Valery E; Topping, Christopher J

2010-01-28

The effects of landscape modifications on the long-term persistence of wild animal populations is of crucial importance to wildlife managers and conservation biologists, but obtaining experimental evidence using real landscapes is usually impossible. To circumvent this problem we used individual-based models (IBMs) of interacting animals in experimental modifications of a real Danish landscape. The models incorporate as much as possible of the behaviour and ecology of four species with contrasting life-history characteristics: skylark (Alauda arvensis), vole (Microtus agrestis), a ground beetle (Bembidion lampros) and a linyphiid spider (Erigone atra). This allows us to quantify the population implications of experimental modifications of landscape configuration and composition. Starting with a real agricultural landscape, we progressively reduced landscape complexity by (i) homogenizing habitat patch shapes, (ii) randomizing the locations of the patches, and (iii) randomizing the size of the patches. The first two steps increased landscape fragmentation. We assessed the effects of these manipulations on the long-term persistence of animal populations by measuring equilibrium population sizes and time to recovery after disturbance. Patch rearrangement and the presence of corridors had a large effect on the population dynamics of species whose local success depends on the surrounding terrain. Landscape modifications that reduced population sizes increased recovery times in the short-dispersing species, making small populations vulnerable to increasing disturbance. The species that were most strongly affected by large disturbances fluctuated little in population sizes in years when no perturbations took place. Traditional approaches to the management and conservation of populations use either classical methods of population analysis, which fail to adequately account for the spatial configurations of landscapes, or landscape ecology, which accounts for landscape structure but has difficulty predicting the dynamics of populations living in them. Here we show how realistic and replicable individual-based models can bridge the gap between non-spatial population theory and non-dynamic landscape ecology. A major strength of the approach is its ability to identify population vulnerabilities not detected by standard population viability analyses.

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.

Mental Health Consequences of Childhood Physical Abuse in Chinese Populations: A Meta-Analysis.

PubMed

Ip, Patrick; Wong, Rosa S; Li, Sophia L; Chan, Ko Ling; Ho, Frederick K; Chow, Chun-Bong

2016-12-01

Childhood physical abuse (CPA) can lead to adverse mental health outcomes in adulthood, but its potential impact on Chinese populations is still unclear. This meta-analysis is the first to examine the association between CPA and mental health outcomes in Chinese populations. Studies published before December 31, 2014 were identified from Embase, CINAHL, Scopus, PsycINFO, PubMed, and Chinese National Knowledge Infrastructure databases. Studies with data on the association between CPA and mental health outcomes from Chinese subjects were included. Twenty-four studies were initially identified but two were excluded because of poor quality. Two reviewers independently extracted data to generate summary effect sizes using a random-effects meta-analytic model. A priori subgroup and sensitivity analyses were performed to evaluate heterogeneity and bias in these studies. Our meta-analysis of 22 studies found a significant positive association between CPA and overall mental health outcomes among all Chinese subjects (pooled effect size: odds ratio [OR] = 2.16, 95% confidence interval [CI] = [1.87, 2.49]) and among community samples (pooled effect size: OR = 2.06, 95% CI [1.71, 2.48]). Based on the Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition, Text Revision, diagnostic criteria, CPA was more strongly associated with Axis II (OR = 2.62, 95% CI [2.13, 3.22]) than Axis I disorders (OR = 1.85, 95% CI [1.58, 2.17]). The detrimental effects of CPA on mental health outcomes in Chinese populations were comparable to, if not more than, the West. Contrary to the Chinese belief that physical punishment is a safe way to discipline children, our findings highlight the potential harm to mental health and the need to change this parenting practice. © The Author(s) 2015.

[Local recurrence based on size after conservative surgery in breast cancer stage T1-T2. A population-based study].

PubMed

Martínez-Ramos, David; Fortea-Sanchis, Carlos; Escrig-Sos, Javier; Prats-de Puig, Miguel; Queralt-Martín, Raquel; Salvador-Sanchis, José Luís

2014-01-01

Conservative surgery can be regarded as the standard treatment for most early stage breast tumors. However, a minority of patients treated with conservative surgery will present local or locoregional recurrence. Therefore, it is of interest to evaluate the possible factors associated with this recurrence. A population-based retrospective study using data from the Tumor Registry of Castellón (Valencia, Spain) of patients operated on for primary nonmetastatic breast cancer between January 2000 and December 2008 was designed. Kaplan-Meier curves and log-rank test to estimate 5-year local recurrence were used. Two groups of patients were defined, one with conservative surgery and another with nonconservative surgery. Cox multivariate analysis was conducted. The total number of patients was 410. Average local recurrence was 6.8%. In univariate analysis, only tumor size and lymph node involvement showed significant differences. On multivariate analysis, independent prognostic factors were conservative surgery (hazard ratio [HR] 4.62; 95% confidence interval [CI]: 1.12-16.82), number of positive lymph nodes (HR 1.07; 95% CI: 1.01-1.17) and tumor size (in mm) (HR 1.02; 95% CI: 1.01-1.06). Local recurrence after breast-conserving surgery is higher in tumors >2 cm. Although tumor size should not be a contraindication for conservative surgery, it should be a risk factor to be considered.

Logistic analysis of shovel and Carabelli's tooth traits in a Caucasoid population.

PubMed

Hsu, J W; Tsai, P; Liu, K; Ferguson, D

1997-09-19

Caucasoid populations differ from Mongoloids by having a high prevalence of Carabelli's trait and a low prevalence of shovel trait. This study was conducted to investigate the association between the shovel and the Carabelli's traits in a Caucasoid population. The research design sought a Caucasoid population at Milwaukee of Wisconsin in United States. The Caucasoid group selected for study was the European descendant. The effects of sex and age on Carabelli's trait were controlled in this investigation, as was the association between tooth size and Carabelli's trait. Results show that males were more likely to have Carabelli's trait expressed on teeth than females. The buccolingual diameter of Carabelli's trait teeth was larger than that of teeth without the trait. After adjusting for sex, age, and tooth size, the existence of the shovel trait decreased the likelihood of having Carabelli's trait which shows an significant effect.

Status and trends of the rainbow trout population in the Lees Ferry reach of the Colorado River downstream from Glen Canyon Dam, Arizona, 1991–2009

USGS Publications Warehouse

Makinster, Andrew S.; Persons, William R.; Avery, Luke A.

2011-01-01

The Lees Ferry reach of the Colorado River, a 25-kilometer segment of river located immediately downstream from Glen Canyon Dam, has contained a nonnative rainbow trout (Oncorhynchus mykiss) sport fishery since it was first stocked in 1964. The fishery has evolved over time in response to changes in dam operations and fish management. Long-term monitoring of the rainbow trout population downstream of Glen Canyon Dam is an essential component of the Glen Canyon Dam Adaptive Management Program. A standardized sampling design was implemented in 1991 and has changed several times in response to independent, external scientific-review recommendations and budget constraints. Population metrics (catch per unit effort, proportional stock density, and relative condition) were estimated from 1991 to 2009 by combining data collected at fixed sampling sites during this time period and at random sampling sites from 2002 to 2009. The validity of combining population metrics for data collected at fixed and random sites was confirmed by a one-way analysis of variance by fish-length class size. Analysis of the rainbow trout population metrics from 1991 to 2009 showed that the abundance of rainbow trout increased from 1991 to 1997, following implementation of a more steady flow regime, but declined from about 2000 to 2007. Abundance in 2008 and 2009 was high compared to previous years, which was likely the result of increased early survival caused by improved habitat conditions following the 2008 high-flow experiment at Glen Canyon Dam. Proportional stock density declined between 1991 and 2006, reflecting increased natural reproduction and large numbers of small fish in samples. Since 2001, the proportional stock density has been relatively stable. Relative condition varied with size class of rainbow trout but has been relatively stable since 1991 for fish smaller than 152 millimeters (mm), except for a substantial decrease in 2009. Relative condition was more variable for larger size classes, and substantial decreases were observed for the 152-304-mm size class in 2009 and 305-405-mm size class in 2008 that persisted into 2009.

Reduced fecundity in small populations of the rare plant Gentianopsis ciliate (Gentianaceae)

USGS Publications Warehouse

Kery, M.; Matthies, D.

2004-01-01

Habitat destruction is the main cause for the biodiversity crisis. Surviving populations are often fragmented, i.e., small and isolated from each other. Reproduction of plants in small populations is often reduced, and this has been attributed to inbreeding depression, reduced attractiveness for pollinators, and reduced habitat quality in small populations. Here we present data on the effects of fragmentation on the rare, self-compatible perennial herb Gentianopsis ciliata (Gentianaceae), a species with very small and presumably well-dispersed seeds. We studied the relationship between population size, plant size, and the number of flowers produced in 63 populations from 1996-1998. In one of the years, leaf and flower size and the number of seeds produced per fruit was studied in a subset of 25 populations. Plant size, flower size, and the number of seeds per fruit and per plant increased with population size, whereas leaf length and the number of flowers per plant did not. The effects of population size on reproduction and on flower size remained significant if the effects were adjusted for differences in plant size, indicating that they could not be explained by differences in habitat quality. The strongly reduced reproduction in small populations may be due to pollination limitation, while the reduced flower size could indicate genetic effects.

Reduced fecundity in small populations of the rare plant Gentianopsis ciliate (Gentianaceae)

USGS Publications Warehouse

Robbins, C.S.

1983-01-01

Habitat destruction is the main cause for the biodiversity crisis. Surviving populations are often fragmented, i.e., small and isolated from each other. Reproduction of plants in small populations is often reduced, and this has been attributed to inbreeding depression, reduced attractiveness for pollinators, and reduced habitat quality in small populations. Here we present data on the effects of fragmentation on the rare, self-compatible perennial herb Gentianopsis ciliata (Gentianaceae), a species with very small and presumably well-dispersed seeds. We studied the relationship between population size, plant size, and the number of flowers produced in 63 populations from 1996-1998. In one of the years, leaf and flower size and the number of seeds produced per fruit was studied in a subset of 25 populations. Plant size, flower size, and the number of seeds per fruit and per plant increased with population size, whereas leaf length and the number of flowers per plant did not. The effects of population size on reproduction and on flower size remained significant if the effects were adjusted for differences in plant size, indicating that they could not be explained by differences in habitat quality. The strongly reduced reproduction in small populations may be due to pollination limitation, while the reduced flower size could indicate genetic effects.

Understanding Crystal Populations; Looking Towards 3D Quantitative Analysis

NASA Astrophysics Data System (ADS)

Jerram, D. A.; Morgan, D. J.

2010-12-01

In order to understand volcanic systems, the potential record held within crystal populations needs to be revealed. It is becoming increasingly clear, however, that the crystal populations that arrive at the surface in volcanic eruptions are commonly mixtures of crystals, which may be representative of simple crystallization, recycling of crystals and incorporation of alien crystals. If we can quantify the true 3D population within a sample then we will be able to separate crystals with different histories and begin to interrogate the true and complex plumbing within the volcanic system. Modeling crystal populations is one area where we can investigate the best methodologies to use when dealing with sections through 3D populations. By producing known 3D shapes and sizes with virtual textures and looking at the statistics of shape and size when such populations are sectioned, we are able to gain confidence about what our 2D information is telling us about the population. We can also use this approach to test the size of population we need to analyze. 3D imaging through serial sectioning or x-ray CT, provides a complete 3D quantification of a rocks texture. Individual phases can be identified and in principle the true 3D statistics of the population can be interrogated. In practice we need to develop strategies (as with 2D-3D transformations), that enable a true characterization of the 3D data, and an understanding of the errors and pitfalls that exist. Ultimately, the reproduction of true 3D textures and the wealth of information they hold, is now within our reach.

Psychosocial risk and protective factors for depression in the dialysis population: a systematic review and meta-regression analysis.

PubMed

Chan, Ramony; Steel, Zachary; Brooks, Robert; Heung, Tracy; Erlich, Jonathan; Chow, Josephine; Suranyi, Michael

2011-11-01

Research into the association between psychosocial factors and depression in End-Stage Renal Disease (ESRD) has expanded considerably in recent years identifying a range of factors that may act as important risk and protective factors of depression for this population. The present study provides the first systematic review and meta-analysis of this body of research. Published studies reporting associations between any psychosocial factor and depression were identified and retrieved from Medline, Embase, and PsycINFO, by applying optimised search strategies. Mean effect sizes were calculated for the associations across five psychosocial constructs (social support, personality attributes, cognitive appraisal, coping process, stress/stressor). Multiple hierarchical meta-regression analysis was applied to examine the moderating effects of methodological and substantive factors on the strength of the observed associations. 57 studies covering 58 independent samples with 5956 participants were identified, resulting in 246 effect sizes of the association between a range of psychosocial factors and depression. The overall mean effect size (Pearsons correlation coefficient) of the association between psychosocial factor and depression was 0.36. The effect sizes between the five psychosocial constructs and depression ranged from medium (0.27) to large levels (0.46) with personality attributes (0.46) and cognitive appraisal (0.46) having the largest effect sizes. In the meta-regression analyses, identified demographic (gender, age, location of study) and treatment (type of dialysis) characteristics moderated the strength of the associations with depression. The current analysis documents a moderate to large association between the presence of psychosocial risk factors and depression in ESRD. 2011. Published by Elsevier Inc. All rights reserved.

Does source population size affect performance in new environments?

PubMed Central

Yates, Matthew C; Fraser, Dylan J

2014-01-01

Small populations are predicted to perform poorly relative to large populations when experiencing environmental change. To explore this prediction in nature, data from reciprocal transplant, common garden, and translocation studies were compared meta-analytically. We contrasted changes in performance resulting from transplantation to new environments among individuals originating from different sized source populations from plants and salmonids. We then evaluated the effect of source population size on performance in natural common garden environments and the relationship between population size and habitat quality. In ‘home-away’ contrasts, large populations exhibited reduced performance in new environments. In common gardens, the effect of source population size on performance was inconsistent across life-history stages (LHS) and environments. When transplanted to the same set of new environments, small populations either performed equally well or better than large populations, depending on life stage. Conversely, large populations outperformed small populations within native environments, but only at later life stages. Population size was not associated with habitat quality. Several factors might explain the negative association between source population size and performance in new environments: (i) stronger local adaptation in large populations and antagonistic pleiotropy, (ii) the maintenance of genetic variation in small populations, and (iii) potential environmental differences between large and small populations. PMID:25469166

Sexual dimorphism in America: geometric morphometric analysis of the craniofacial region.

PubMed

Kimmerle, Erin H; Ross, Ann; Slice, Dennis

2008-01-01

One of the four pillars of the anthropological protocol is the estimation of sex. The protocol generally consists of linear metric analysis or visually assessing individual skeletal traits on the skull and pelvis based on an ordinal scale of 1-5, ranging from very masculine to very feminine. The morphologic traits are then some how averaged by the investigator to estimate sex. Some skulls may be misclassified because of apparent morphologic features that appear more or less robust due to size differences among individuals. The question of misclassification may be further exemplified in light of comparisons across populations that may differ not only in cranial robusticity but also in stature and general physique. The purpose of this study is to further examine the effect of size and sex on craniofacial shape among American populations to better understand the allometric foundation of skeletal traits currently used for sex estimation. Three-dimensional coordinates of 16 standard craniofacial landmarks were collected using a Microscribe-3DX digitizer. Data were collected for 118 American White and Black males and females from the W.M. Bass Donated Collection and the Forensic Data Bank. The MANCOVA procedure tested shape differences as a function of sex and size. Sex had a significant influence on shape for both American Whites (F = 2.90; d.f. = 19, 39; p > F = 0.0024) and Blacks (F = 2.81; d.f. = 19, 37; p > F = 0.0035), whereas size did not have a significant influence on shape in either Whites (F = 1.69; d.f. = 19, 39; p > F = 0.08) or Blacks (F = 1.09; d.f. = 19, 37; p > F = 0.40). Therefore, for each sex, individuals of various sizes were statistically the same shape. In other words, while significant differences were present between the size of males and females (males on average were larger), there was no size effect beyond that accounted for by sex differences in size. Moreover, the consistency between American groups is interesting as it suggests that population differences in sexual dimorphism may result more from human variation in size than allometric variation in craniofacial morphology.

Understanding Crystal Populations: The Role of Textural Analysis in Determining Magmatic Timescales

NASA Astrophysics Data System (ADS)

Jerram, D. A.

2006-12-01

Crystal populations in igneous rocks that erupt at the Earths surface act as records of magma chamber processes at depth, predominantly recording episodes of growth/nucleation and geochemical changes within the host body. Detailed inspection of such crystal populations, however, reveals a complex crystal cargo that comprises crystals which have grown directly from the host, crystals that have spent one or more protracted periods being isolated from the host magma and crystals that originated from a completely different magma body and/or country rock. To further interrogate this crystal cargo we can use textural analysis techniques to fully quantify the crystal population and gather important information about the population, such as crystal morphology, spatial distribution and size relationships. When quantified, such data can be used to better constrain the different components of the resultant crystal population and how they relate to each other. Additionally, by combining textural analysis information with geochemical analysis, a powerful measure of magma timescales and magma chamber processes results. In this contribution the different types of textural analysis techniques in 2D and 3D are introduced with examples from both plutonic and volcanic systems presented to highlight the roll of this approach to quantifying magma timescales.

Using Age-Based Life History Data to Investigate the Life Cycle and Vulnerability of Octopus cyanea

PubMed Central

Herwig, Jade N.; Depczynski, Martial; Roberts, John D.; Semmens, Jayson M.; Gagliano, Monica; Heyward, Andrew J.

2012-01-01

Octopus cyanea is taken as an unregulated, recreationally fished species from the intertidal reefs of Ningaloo, Western Australia. Yet despite its exploitation and importance in many artisanal fisheries throughout the world, little is known about its life history, ecology and vulnerability. We used stylet increment analysis to age a wild O. cyanea population for the first time and gonad histology to examine their reproductive characteristics. O. cyanea conforms to many cephalopod life history generalisations having rapid, non-asymptotic growth, a short life-span and high levels of mortality. Males were found to mature at much younger ages and sizes than females with reproductive activity concentrated in the spring and summer months. The female dominated sex-ratios in association with female brooding behaviours also suggest that larger conspicuous females may be more prone to capture and suggests that this intertidal octopus population has the potential to be negatively impacted in an unregulated fishery. Size at age and maturity comparisons between our temperate bordering population and lower latitude Tanzanian and Hawaiian populations indicated stark differences in growth rates that correlate with water temperatures. The variability in life history traits between global populations suggests that management of O. cyanea populations should be tailored to each unique set of life history characteristics and that stylet increment analysis may provide the integrity needed to accurately assess this. PMID:22912898

The political ecology of disaster: an analysis of factors influencing U.S. tornado fatalities and injuries, 1998-2000.

PubMed

Donner, William R

2007-08-01

This study examines casualties from tornadoes in the United States between the years 1998 and 2000. A political model of human ecology (POET) was used to explore how the environment, technology, and social inequality influence rates of fatalities and injuries in two models. Data were drawn from four sources: John Hart's Severe Plot v2.0, National Weather Service (NWS) Warning Verification data, Storm Prediction Center (SPC) watch data, and tract-level census data. Negative binomial regression was used to analyze the causes of tornado fatalities and injuries. Independent variables (following POET) are classified in the following manner: population, organization, environment, and technology. Rural population, population density, and household size correspond to population; racial minorities and deprivation represent social organization; tornado area represents environment; and tornado watches and warnings, as well as mobile homes, correspond to technology. Findings suggest a strong relationship between the size of a tornado path and both fatalities and injuries, whereas other measures related to technology, population, and organization produce significant yet mixed results. Census tracts having larger populations of rural residents was, of the nonenvironmental factors, the most conclusive regarding its effects across the two models. The outcomes of analysis, although not entirely supportive of the model presented in this study, suggest to some degree that demographic and social factors play a role in vulnerability to tornadoes.

Whole-Genome Resequencing of Experimental Populations Reveals Polygenic Basis of Egg-Size Variation in Drosophila melanogaster

PubMed Central

Jha, Aashish R.; Miles, Cecelia M.; Lippert, Nodia R.; Brown, Christopher D.; White, Kevin P.; Kreitman, Martin

2015-01-01

Complete genome resequencing of populations holds great promise in deconstructing complex polygenic traits to elucidate molecular and developmental mechanisms of adaptation. Egg size is a classic adaptive trait in insects, birds, and other taxa, but its highly polygenic architecture has prevented high-resolution genetic analysis. We used replicated experimental evolution in Drosophila melanogaster and whole-genome sequencing to identify consistent signatures of polygenic egg-size adaptation. A generalized linear-mixed model revealed reproducible allele frequency differences between replicated experimental populations selected for large and small egg volumes at approximately 4,000 single nucleotide polymorphisms (SNPs). Several hundred distinct genomic regions contain clusters of these SNPs and have lower heterozygosity than the genomic background, consistent with selection acting on polymorphisms in these regions. These SNPs are also enriched among genes expressed in Drosophila ovaries and many of these genes have well-defined functions in Drosophila oogenesis. Additional genes regulating egg development, growth, and cell size show evidence of directional selection as genes regulating these biological processes are enriched for highly differentiated SNPs. Genetic crosses performed with a subset of candidate genes demonstrated that these genes influence egg size, at least in the large genetic background. These findings confirm the highly polygenic architecture of this adaptive trait, and suggest the involvement of many novel candidate genes in regulating egg size. PMID:26044351

Logistic analysis of the effects of shovel trait on Carabelli's trait in a Mongoloid population.

PubMed

Tsai, P L; Hsu, J W; Lin, L M; Liu, K M

1996-08-01

Mongoloid populations differ from Caucasoids by having a high prevalence of shovel trait and a low prevalence of Carabelli's trait. This study was conducted to investigate the effects of the shovel trait on Carabelli's trait in a Mongoloid population. The research design sought a population that resides in an isolated area and exhibits low admixture with neighboring populations. The Mongoloid group selected for study was the Bunun tribe of aborigines who inhabit an alpine area in Taiwan. The effects of sex and age on Carabelli's trait were controlled in this investigation, as was the association between tooth size and Carabelli's trait. Results show that males were more likely to have Carabelli's trait expressed on teeth than females. The buccolingual diameter of Carabelli's trait teeth was larger than that of teeth without the trait. After adjusting for sex, age, and tooth size, the existence of the shovel trait increased the likelihood of having Carabelli's trait by a factor of three, an effect that is significant.

Ethnic dental analysis of shovel and Carabelli's traits in a Chinese population.

PubMed

Hsu, J W; Tsai, P L; Hsiao, T H; Chang, H P; Lin, L M; Liu, K M; Yu, H S; Ferguson, D

1999-03-01

Chinese populations differ from Caucasoids by having a high prevalence of shovel trait and a low prevalence of Carabelli's trait. This study was conducted to investigate the association between the shovel and the Carabelli's traits in a Chinese population. The research design investigated a Chinese population that resides in southern Taiwan. The ancestors of this Chinese population migrated to Taiwan from mainland China, mainly from Fukien and Kwangtung. The effects of sex and age on Carabelli's trait were controlled in this investigation, as was the association between tooth size and Carabelli's trait. Results show that males were more likely to have Carabelli's trait expressed on teeth than females. The buccolingual diameter of Carabelli's trait teeth was larger than that of teeth without the trait. After controlling for sex, age, and tooth size, the existence of the shovel trait increased the likelihood of having Carabelli's trait by a factor of five and a half, which is a significant effect.

Analysis of human resources for oral health globally: inequitable distribution.

PubMed

Gallagher, Jennifer E; Hutchinson, Lynn

2018-06-01

Oral diseases affect most of the global population. The aim of this paper was to provide a contemporary analysis of 'human resources for oral health' (HROH) by examining the size and distribution of the dental workforce according to World Health Organization (WHO) region and in the most populous countries. Publically available data on HROH and population size were sourced from the WHO, Central Intelligence Agency, United Nations, World Bank and the UK registration body. Population-to-dentist and dental-workforce ratios were calculated according to WHO region and for the 25 most populous countries globally. Workforce trends over time were examined for one high-income country, the UK. The majority of the world's 1.6 million dentists are based in Europe and the Americas, such that 69% of the world's dentists serve 27% of the global population. Africa has only 1% of the global workforce and thus there are marked inequalities in access to dental personnel, as demonstrated by population to dental-workforce ratios. Gaps exist in dental-workforce data, most notably relating to mid-level clinical providers, such as dental hygienists and therapists, and HROH data are not regularly updated. Workforce expansion and migration may result in rapid changes in dentist numbers. Marked inequalities in the distribution of global HROH exist between regions and countries, with inequalities most apparent in areas of high population growth. Detailed contemporary data on all groups of HROH are required to inform global workforce reform in support of addressing population oral health needs. © 2018 FDI World Dental Federation.

Population demographics and genetic diversity in remnant and translocated populations of sea otters

USGS Publications Warehouse

Bodkin, James L.; Ballachey, Brenda E.; Cronin, M.A.; Scribner, K.T.

1999-01-01

The effects of small population size on genetic diversity and subsequent population recovery are theoretically predicted, but few empirical data are available to describe those relations. We use data from four remnant and three translocated sea otter (Enhydra lutris) populations to examine relations among magnitude and duration of minimum population size, population growth rates, and genetic variation. Metochondrial (mt)DNA haplotype diversity was correlated with the number of years at minimum population size (r = -0.741, p = 0.038) and minimum population size (r = 0.709, p = 0.054). We found no relation between population growth and haplotype diversity, altough growth was significantly greater in translocated than in remnant populations. Haplotype diversity in populations established from two sources was higher than in a population established from a single source and was higher than in the respective source populations. Haplotype frequencies in translocated populations of founding sizes of 4 and 28 differed from expected, indicating genetic drift and differential reproduction between source populations, whereas haplotype frequencies in a translocated population with a founding size of 150 did not. Relations between population demographics and genetic characteristics suggest that genetic sampling of source and translocated populations can provide valuable inferences about translocations.

Evidence for r- and K-selection in a wild bird population: a reciprocal link between ecology and evolution.

PubMed

Sæther, Bernt-Erik; Visser, Marcel E; Grøtan, Vidar; Engen, Steinar

2016-04-27

Understanding the variation in selection pressure on key life-history traits is crucial in our rapidly changing world. Density is rarely considered as a selective agent. To study its importance, we partition phenotypic selection in fluctuating environments into components representing the population growth rate at low densities and the strength of density dependence, using a new stochastic modelling framework. We analysed the number of eggs laid per season in a small song-bird, the great tit, and found balancing selection favouring large clutch sizes at small population densities and smaller clutches in years with large populations. A significant interaction between clutch size and population size in the regression for the Malthusian fitness reveals that those females producing large clutch sizes at small population sizes also are those that show the strongest reduction in fitness when population size is increased. This provides empirical support for ongoing r- and K-selection in this population, favouring phenotypes with large growth rates r at small population sizes and phenotypes with high competitive skills when populations are close to the carrying capacity K This selection causes long-term fluctuations around a stable mean clutch size caused by variation in population size, implying that r- and K-selection is an important mechanism influencing phenotypic evolution in fluctuating environments. This provides a general link between ecological dynamics and evolutionary processes, operating through a joint influence of density dependence and environmental stochasticity on fluctuations in population size. © 2016 The Author(s).

Modelling cell population growth with applications to cancer therapy in human tumour cell lines.

PubMed

Basse, Britta; Baguley, Bruce C; Marshall, Elaine S; Wake, Graeme C; Wall, David J N

2004-01-01

In this paper we present an overview of the work undertaken to model a population of cells and the effects of cancer therapy. We began with a theoretical one compartment size structured cell population model and investigated its asymptotic steady size distributions (SSDs) (On a cell growth model for plankton, MMB JIMA 21 (2004) 49). However these size distributions are not similar to the DNA (size) distributions obtained experimentally via the flow cytometric analysis of human tumour cell lines (data obtained from the Auckland Cancer Society Research Centre, New Zealand). In our one compartment model, size was a generic term, but in order to obtain realistic steady size distributions we chose size to be DNA content and devised a multi-compartment mathematical model for the cell division cycle where each compartment corresponds to a distinct phase of the cell cycle (J. Math. Biol. 47 (2003) 295). We then incorporated another compartment describing the possible induction of apoptosis (cell death) from mitosis phase (Modelling cell death in human tumour cell lines exposed to anticancer drug paclitaxel, J. Math. Biol. 2004, in press). This enabled us to compare our model to flow cytometric data of a melanoma cell line where the anticancer drug, paclitaxel, had been added. The model gives a dynamic picture of the effects of paclitaxel on the cell cycle. We hope to use the model to describe the effects of other cancer therapies on a number of different cell lines. Copyright 2004 Elsevier Ltd.

Community variations in infant and child mortality in Peru.

PubMed Central

Edmonston, B; Andes, N

1983-01-01

Data from the national Peru Fertility Survey are used to estimate infant and childhood mortality ratios, 1968--77, for 124 Peruvian communities, ranging from small Indian hamlets in the Andes to larger cities on the Pacific coast. Significant mortality variations are found: mortality is inversely related to community population size and is higher in the mountains than in the jungle or coast. Multivariate analysis is then used to assess the influence of community population size, average female education, medical facilities, and altitude on community mortality. Finally, this study concludes that large-scale sample surveys, which include maternal birth history, add useful data for epidemiological studies of childhood mortality. PMID:6886581

The Relative Impacts of Disease on Health Status and Capability Wellbeing: A Multi-Country Study

PubMed Central

Mitchell, Paul Mark; Al-Janabi, Hareth; Richardson, Jeff; Iezzi, Angelo; Coast, Joanna

2015-01-01

Background Evaluations of the impact of interventions for resource allocation purposes commonly focus on health status. There is, however, also concern about broader impacts on wellbeing and, increasingly, on a person's capability. This study aims to compare the impact on health status and capability of seven major health conditions, and highlight differences in treatment priorities when outcomes are measured by capability as opposed to health status. Methods The study was a cross-sectional four country survey (n = 6650) of eight population groups: seven disease groups with: arthritis, asthma, cancer, depression, diabetes, hearing loss, and heart disease and one health population ‘comparator’ group. Two simple self-complete questionnaires were used to measure health status (EQ-5D-5L) and capability (ICECAP-A). Individuals were classified by illness severity using condition-specific questionnaires. Effect sizes were used to estimate: (i) the difference in health status and capability for those with conditions, relative to a healthy population; and (ii) the impact of the severity of the condition on health status and capability within each disease group. Findings 5248 individuals were included in the analysis. Individuals with depression have the greatest mean reduction in both health (effect size, 1.26) and capability (1.22) compared to the healthy population. The effect sizes for capability for depression are much greater than for all other conditions, which is not the case for health. For example, the arthritis group effect size for health (1.24) is also high and similar to that of depression, whereas for the same arthritis group, the effect size for capability is much lower than that for depression (0.55). In terms of severity within disease groups, individuals categorised as 'mild' have similar capability levels to the healthy population (effect sizes <0.2, excluding depression) but lower health status than the healthy population (≥0.4). Conclusion Significant differences exist in the relative effect sizes across diseases when measured by health status and capability. In terms of treating morbidity, a shift in focus from health gain to capability gain would increase funding priorities for patients with depression specifically and severe illnesses more generally. PMID:26630131

Monte Carlo simulations on marker grouping and ordering.

PubMed

Wu, J; Jenkins, J; Zhu, J; McCarty, J; Watson, C

2003-08-01

Four global algorithms, maximum likelihood (ML), sum of adjacent LOD score (SALOD), sum of adjacent recombinant fractions (SARF) and product of adjacent recombinant fraction (PARF), and one approximation algorithm, seriation (SER), were used to compare the marker ordering efficiencies for correctly given linkage groups based on doubled haploid (DH) populations. The Monte Carlo simulation results indicated the marker ordering powers for the five methods were almost identical. High correlation coefficients were greater than 0.99 between grouping power and ordering power, indicating that all these methods for marker ordering were reliable. Therefore, the main problem for linkage analysis was how to improve the grouping power. Since the SER approach provided the advantage of speed without losing ordering power, this approach was used for detailed simulations. For more generality, multiple linkage groups were employed, and population size, linkage cutoff criterion, marker spacing pattern (even or uneven), and marker spacing distance (close or loose) were considered for obtaining acceptable grouping powers. Simulation results indicated that the grouping power was related to population size, marker spacing distance, and cutoff criterion. Generally, a large population size provided higher grouping power than small population size, and closely linked markers provided higher grouping power than loosely linked markers. The cutoff criterion range for achieving acceptable grouping power and ordering power differed for varying cases; however, combining all situations in this study, a cutoff criterion ranging from 50 cM to 60 cM was recommended for achieving acceptable grouping power and ordering power for different cases.

Spatially explicit dynamic N-mixture models

USGS Publications Warehouse

Zhao, Qing; Royle, Andy; Boomer, G. Scott

2017-01-01

Knowledge of demographic parameters such as survival, reproduction, emigration, and immigration is essential to understand metapopulation dynamics. Traditionally the estimation of these demographic parameters requires intensive data from marked animals. The development of dynamic N-mixture models makes it possible to estimate demographic parameters from count data of unmarked animals, but the original dynamic N-mixture model does not distinguish emigration and immigration from survival and reproduction, limiting its ability to explain important metapopulation processes such as movement among local populations. In this study we developed a spatially explicit dynamic N-mixture model that estimates survival, reproduction, emigration, local population size, and detection probability from count data under the assumption that movement only occurs among adjacent habitat patches. Simulation studies showed that the inference of our model depends on detection probability, local population size, and the implementation of robust sampling design. Our model provides reliable estimates of survival, reproduction, and emigration when detection probability is high, regardless of local population size or the type of sampling design. When detection probability is low, however, our model only provides reliable estimates of survival, reproduction, and emigration when local population size is moderate to high and robust sampling design is used. A sensitivity analysis showed that our model is robust against the violation of the assumption that movement only occurs among adjacent habitat patches, suggesting wide applications of this model. Our model can be used to improve our understanding of metapopulation dynamics based on count data that are relatively easy to collect in many systems.

Association Studies and Legume Synteny Reveal Haplotypes Determining Seed Size in Vigna unguiculata.

PubMed

Lucas, Mitchell R; Huynh, Bao-Lam; da Silva Vinholes, Patricia; Cisse, Ndiaga; Drabo, Issa; Ehlers, Jeffrey D; Roberts, Philip A; Close, Timothy J

2013-01-01

Highly specific seed market classes for cowpea and other grain legumes exist because grain is most commonly cooked and consumed whole. Size, shape, color, and texture are critical features of these market classes and breeders target development of cultivars for market acceptance. Resistance to biotic and abiotic stresses that are absent from elite breeding material are often introgressed through crosses to landraces or wild relatives. When crosses are made between parents with different grain quality characteristics, recovery of progeny with acceptable or enhanced grain quality is problematic. Thus genetic markers for grain quality traits can help in pyramiding genes needed for specific market classes. Allelic variation dictating the inheritance of seed size can be tagged and used to assist the selection of large seeded lines. In this work we applied 1,536-plex SNP genotyping and knowledge of legume synteny to characterize regions of the cowpea genome associated with seed size. These marker-trait associations will enable breeders to use marker-based selection approaches to increase the frequency of progeny with large seed. For 804 individuals derived from eight bi-parental populations, QTL analysis was used to identify markers linked to 10 trait determinants. In addition, the population structure of 171 samples from the USDA core collection was identified and incorporated into a genome-wide association study which supported more than half of the trait-associated regions important in the bi-parental populations. Seven of the total 10 QTLs were supported based on synteny to seed size associated regions identified in the related legume soybean. In addition to delivering markers linked to major trait determinants in the context of modern breeding, we provide an analysis of the diversity of the USDA core collection of cowpea to identify genepools, migrants, admixture, and duplicates.

Reduced body size and cub recruitment in polar bears associated with sea ice decline.

PubMed

Rode, Karyn D; Amstrup, Steven C; Regehr, Eric V

2010-04-01

Rates of reproduction and survival are dependent upon adequate body size and condition of individuals. Declines in size and condition have provided early indicators of population decline in polar bears (Ursus maritimus) near the southern extreme of their range. We tested whether patterns in body size, condition, and cub recruitment of polar bears in the southern Beaufort Sea of Alaska were related to the availability of preferred sea ice habitats and whether these measures and habitat availability exhibited trends over time, between 1982 and 2006. The mean skull size and body length of all polar bears over three years of age declined over time, corresponding with long-term declines in the spatial and temporal availability of sea ice habitat. Body size of young, growing bears declined over time and was smaller after years when sea ice availability was reduced. Reduced litter mass and numbers of yearlings per female following years with lower availability of optimal sea ice habitat, suggest reduced reproductive output and juvenile survival. These results, based on analysis of a long-term data set, suggest that declining sea ice is associated with nutritional limitations that reduced body size and reproduction in this population.

Reduced body size and cub recruitment in polar bears associated with sea ice decline

USGS Publications Warehouse

Rode, Karyn D.; Amstrup, Steven C.; Regehr, Eric V.

2010-01-01

Rates of reproduction and survival are dependent upon adequate body size and condition of individuals. Declines in size and condition have provided early indicators of population decline in polar bears (Ursus maritimus) near the southern extreme of their range. We tested whether patterns in body size, condition, and cub recruitment of polar bears in the southern Beaufort Sea of Alaska were related to the availability of preferred sea ice habitats and whether these measures and habitat availability exhibited trends over time, between 1982 and 2006. The mean skull size and body length of all polar bears over three years of age declined over time, corresponding with long‐term declines in the spatial and temporal availability of sea ice habitat. Body size of young, growing bears declined over time and was smaller after years when sea ice availability was reduced. Reduced litter mass and numbers of yearlings per female following years with lower availability of optimal sea ice habitat, suggest reduced reproductive output and juvenile survival. These results, based on analysis of a long‐term data set, suggest that declining sea ice is associated with nutritional limitations that reduced body size and reproduction in this population.

A preliminary study of variation of Trapa in Japan

USGS Publications Warehouse

Kadono, Yasuro; Rybicki, Nancy B.; Lai, Vincent

2018-05-31

SummaryFrequent occurrence of intermediate forms and poor knowledge on the variability of characters have caused some difficulties in the taxonomy of Trapa in Japan. Thus I made a preliminary analysis on the variation of nuts collected from 21 populations in Southwestern Japan. Attention was paid to some morphometrical characters of the nut and development of lower spines or “pseudohorns.” Each population usually contained different forms of nuts. Among them, however, several entities could be recognized based on the shape of nut as follows. 1) Two-spined form: This included nuts of middle size (width 30–50 mm) and ones of big size (width over 45 mm). In case of the former ones, the nuts with pseudohorns of varying degree of development usually occurred together within one population and even on a single plant. I propose to treat them as one taxon, Trapa japonica, sensu OHWI (1965), without inventing varieties. But at the same time, it was remarkable that the tendency of development of pseudohorns was apparently different from population to population. The bigger ones included two types, that is, one without pseudohorns and the other with pseudohorns. The former one may be identified as T. bispinosa ROXB., but the latter one has not been described in literature. 2) Four-spined form: The nuts of small size (width of about 20 mm) were well definable and thought to be T. incisa SIEB. et ZUCC. The nuts of bigger size showed some variations with respect to their size and/or stoutness of lower spines. The big ones (width over 45 mm) may be treated as one taxon, T. natans or its variety. The nuts of middle size have been named T. natans var. pumila NAKANO. But so far as present materials were concerned, its entity seemed dubious. They might be immature nuts of bigger ones. The different patterns of variation among populations were ascribed to genetic differentiation. Predominance of self-pollination and isolation of habitats were thought to promote genetic isolation and preservation of genetic variations which occurred in each population. But the possibility of hybridization cannot be excluded.

Analysis of multinomial models with unknown index using data augmentation

USGS Publications Warehouse

Royle, J. Andrew; Dorazio, R.M.; Link, W.A.

2007-01-01

Multinomial models with unknown index ('sample size') arise in many practical settings. In practice, Bayesian analysis of such models has proved difficult because the dimension of the parameter space is not fixed, being in some cases a function of the unknown index. We describe a data augmentation approach to the analysis of this class of models that provides for a generic and efficient Bayesian implementation. Under this approach, the data are augmented with all-zero detection histories. The resulting augmented dataset is modeled as a zero-inflated version of the complete-data model where an estimable zero-inflation parameter takes the place of the unknown multinomial index. Interestingly, data augmentation can be justified as being equivalent to imposing a discrete uniform prior on the multinomial index. We provide three examples involving estimating the size of an animal population, estimating the number of diabetes cases in a population using the Rasch model, and the motivating example of estimating the number of species in an animal community with latent probabilities of species occurrence and detection.

Guidance for the utility of linear models in meta-analysis of genetic association studies of binary phenotypes.

PubMed

Cook, James P; Mahajan, Anubha; Morris, Andrew P

2017-02-01

Linear mixed models are increasingly used for the analysis of genome-wide association studies (GWAS) of binary phenotypes because they can efficiently and robustly account for population stratification and relatedness through inclusion of random effects for a genetic relationship matrix. However, the utility of linear (mixed) models in the context of meta-analysis of GWAS of binary phenotypes has not been previously explored. In this investigation, we present simulations to compare the performance of linear and logistic regression models under alternative weighting schemes in a fixed-effects meta-analysis framework, considering designs that incorporate variable case-control imbalance, confounding factors and population stratification. Our results demonstrate that linear models can be used for meta-analysis of GWAS of binary phenotypes, without loss of power, even in the presence of extreme case-control imbalance, provided that one of the following schemes is used: (i) effective sample size weighting of Z-scores or (ii) inverse-variance weighting of allelic effect sizes after conversion onto the log-odds scale. Our conclusions thus provide essential recommendations for the development of robust protocols for meta-analysis of binary phenotypes with linear models.

Analysis options for estimating status and trends in long-term monitoring

USGS Publications Warehouse

Bart, Jonathan; Beyer, Hawthorne L.

2012-01-01

This chapter describes methods for estimating long-term trends in ecological parameters. Other chapters in this volume discuss more advanced methods for analyzing monitoring data, but these methods may be relatively inaccessible to some readers. Therefore, this chapter provides an introduction to trend analysis for managers and biologists while also discussing general issues relevant to trend assessment in any long-term monitoring program. For simplicity, we focus on temporal trends in population size across years. We refer to the survey results for each year as the “annual means” (e.g. mean per transect, per plot, per time period). The methods apply with little or no modification, however, to formal estimates of population size, other temporal units (e.g. a month), to spatial or other dimensions such as elevation or a north–south gradient, and to other quantities such as chemical or geological parameters. The chapter primarily discusses methods for estimating population-wide parameters rather than studying variation in trend within the population, which can be examined using methods presented in other chapters (e.g. Chapters 7, 12, 20). We begin by reviewing key concepts related to trend analysis. We then describe how to evaluate potential bias in trend estimates. An overview of the statistical models used to quantify trends is then presented. We conclude by showing ways to estimate trends using simple methods that can be implemented with spreadsheets.

Recurrent jellyfish blooms are a consequence of global oscillations.

PubMed

Condon, Robert H; Duarte, Carlos M; Pitt, Kylie A; Robinson, Kelly L; Lucas, Cathy H; Sutherland, Kelly R; Mianzan, Hermes W; Bogeberg, Molly; Purcell, Jennifer E; Decker, Mary Beth; Uye, Shin-ichi; Madin, Laurence P; Brodeur, Richard D; Haddock, Steven H D; Malej, Alenka; Parry, Gregory D; Eriksen, Elena; Quiñones, Javier; Acha, Marcelo; Harvey, Michel; Arthur, James M; Graham, William M

2013-01-15

A perceived recent increase in global jellyfish abundance has been portrayed as a symptom of degraded oceans. This perception is based primarily on a few case studies and anecdotal evidence, but a formal analysis of global temporal trends in jellyfish populations has been missing. Here, we analyze all available long-term datasets on changes in jellyfish abundance across multiple coastal stations, using linear and logistic mixed models and effect-size analysis to show that there is no robust evidence for a global increase in jellyfish. Although there has been a small linear increase in jellyfish since the 1970s, this trend was unsubstantiated by effect-size analysis that showed no difference in the proportion of increasing vs. decreasing jellyfish populations over all time periods examined. Rather, the strongest nonrandom trend indicated jellyfish populations undergo larger, worldwide oscillations with an approximate 20-y periodicity, including a rising phase during the 1990s that contributed to the perception of a global increase in jellyfish abundance. Sustained monitoring is required over the next decade to elucidate with statistical confidence whether the weak increasing linear trend in jellyfish after 1970 is an actual shift in the baseline or part of an oscillation. Irrespective of the nature of increase, given the potential damage posed by jellyfish blooms to fisheries, tourism, and other human industries, our findings foretell recurrent phases of rise and fall in jellyfish populations that society should be prepared to face.

Associations of ACE I/D, AGT M235T gene polymorphisms with pregnancy induced hypertension in Chinese population: a meta-analysis.

PubMed

Zhu, Ming; Zhang, Jie; Nie, Shaofa; Yan, Weirong

2012-09-01

There have been many studies concerning the associations of angiotensin-converting enzyme (ACE) I/D, angiotensinogen (AGT) M235T polymorphisms with pregnancy induced hypertension (PIH) among Chinese populations. However, the results were inconsistent, prompting the necessity of meta-analysis. Studies published in English and Chinese were mainly searched in EMbase, PubMed and CBM up to January 2012. Twenty-three studies with 3,551 subjects for ACE I/D and seven studies with 1,296 subjects for AGT M235T were included. Significant associations were found between ACE I/D and PIH under dominant, recessive and allelic models. A separate analysis confined to preeclampsia suggested that ACE I/D was associated with preeclampsia under recessive model and allelic model, but not dominant model. Stratified analyses were conducted as meta-regression analysis indicated that the sample size of case group was a significant source of heterogeneity, which suggested no significant association between ACE I/D and PIH in the subgroup of more than 100 cases. Associations were found between AGT M235T and PIH under dominant genetic model (OR = 1.59; 95 %CI: 1.04-2.42), recessive genetic model (OR = 1.60; 95 %CI: 1.07-2.40), and allelic model (OR = 1.40; 95 %CI: 1.17-1.68). No publication bias was found in either meta-analysis. The present meta-analysis suggested significant associations between ACE I/D, AGT M235T and PIH in Chinese populations. However, no significant association was found between ACE I/D and PIH in the subgroup of more than 100 cases. Studies with larger sample sizes are necessary to investigate the associations between gene polymorphisms and PIH in Chinese populations.

An exploratory analysis on how geographic, socioeconomic, and environmental drivers affect the diversity of livestock breeds worldwide.

PubMed

Leroy, G; Boettcher, P; Hoffmann, I; Mottet, A; Teillard, F; Baumung, R

2016-12-01

This study investigates the relationships between various environmental and geographic, demographic, and socioeconomic factors with the diversity of livestock breeds reported within countries across the world. Statistical analyses were performed considering the numbers of breeds reported by 158 countries for 4 livestock mammalian species (cattle, sheep, goats, and pigs). Organization for Economic Cooperation and Development (OECD) countries reported more breeds than non-OECD countries in general. Strong and positive correlations were found between agricultural area, human population size, species population size, and number of breeds per country. When considering regression models, the species population size was found as the most important explanatory factor for the number of breeds reported by countries in the 4 species. Diversity of production systems in the country had a significant association with the number of breeds reported for sheep, goats, and pigs. The number of ruminant breeds was positively associated with the size of agricultural area and the diversity of land cover in the country. While demographic and cultural importance of a given species is a major factor associated with the number of livestock breeds within countries, this diversity is also connected to the variability in environmental and production conditions.

Muddled or mixed? Inferring palaeoclimate from size distributions of deep-sea clastics

NASA Astrophysics Data System (ADS)

Weltje, G. J.; Prins, M. A.

2003-04-01

One of the outstanding problems of palaeoclimate reconstruction from physico-chemical properties of terrigenous deep-sea sediments is the fact that most basin fills are mixtures of sediment populations derived from different sources and transported to the site of deposition by different mechanisms. Conventional approaches to palaeoclimate reconstruction from deep-sea sediments, which ignore this common fact, often fail to recognise the true significance of variations in sediment properties. We formulate a set of requirements that each proposed palaeoenvironmental indicator should fulfil, and focus on the intrinsic coupling between grain size and chemical composition. A critical review of past achievements in grain-size analysis is given to provide a starting point for a conceptual model of spatio-temporal grain-size variation in terms of dynamic populations. Each dynamic population results from a characteristic combination of production and transport mechanisms that corresponds to a distinct subpopulation in the data analysed. The mathematical-statistical equivalent of the conceptual model may be solved by means of the end-member modelling algorithm EMMA. Applications of the model to several ocean basins are discussed, as well as methods to examine the validity of the palaeoclimate reconstructions.

The effects of isolation on the demography and genetic diversity of long-lived species: Implications for conservation and management of the gopher tortoise (Gopherus polyphemus)

USGS Publications Warehouse

Ennen, J.R.; Birkhead, R.D.; Kreiser, B.R.; Gaillard, D.L.; Qualls, C.P.; Lovich, J.E.

2011-01-01

In the southeastern United States, habitat loss has fragmented the landscape and isolated many populations of this region's flora and fauna, which has presumably resulted in smaller population sizes and reduced levels of genetic diversity. For example, forestry practices and anthropogenic disturbances are both cited as factors fragmenting the once extensive range of Gopherus polyphemus. One localized, but extreme, source of fragmentation was the impoundment of the Chattahoochee River in 1963 to form Walter F. George Reservoir along the border of Georgia and Alabama. The formation of this reservoir isolated populations of G. polyphemus on two newly created islands providing a natural laboratory to explore the demographics and genetic effects of fragmentation on a long-lived species. These populations were first surveyed in 1984 and, 21 years later, we revisited them to collect demographic data and tissue samples for genetic analysis. We genotyped all individuals for 10 microsatellite loci, and we tested these data for bottlenecks and compared them to levels of genetic diversity for populations from other portions of the range. We found 45 and two individuals on the larger and smaller islands, respectively. On the large island, however, the population size was identical to the 1984 survey. Only the population structure based on estimated age differed between the 1984 and 2004 surveys, while population size structure based on carapace length, sex ratio, and sex-specific growth rates did not differ. The population of the large island showed genetic evidence of a past bottleneck. The genetic diversity indices from the population of the large island, however, were comparable to or greater than those found at mainland sites, in particular from western populations.

On the absence of a correlation between population size and 'toolkit size' in ethnographic hunter-gatherers.

PubMed

Aoki, Kenichi

2018-04-05

In apparent contradiction to the theoretically predicted effect of population size on the quality/quantity of material culture, statistical analyses on ethnographic hunter-gatherers have shown an absence of correlation between population size and toolkit size. This has sparked a heated, if sometimes tangential, debate as to the usefulness of the theoretical models and as to what modes of cultural transmission humans are capable of and hunter-gatherers rely on. I review the directly relevant theoretical literature and argue that much of the confusion is caused by a mismatch between the theoretical variable and the empirical observable. I then confirm that a model incorporating the appropriate variable does predict a positive association between population size and toolkit size for random oblique, vertical, best-of- K , conformist, anticonformist, success bias and one-to-many cultural transmission, with the caveat that for all populations sampled, the population size has remained constant and toolkit size has reached the equilibrium for this population size. Finally, I suggest three theoretical scenarios, two of them involving variable population size, that would attenuate or eliminate this association and hence help to explain the empirical absence of correlation.This article is part of the theme issue 'Bridging cultural gaps: interdisciplinary studies in human cultural evolution'. © 2018 The Author(s).

Population size is weakly related to quantitative genetic variation and trait differentiation in a stream fish.

PubMed

Wood, Jacquelyn L A; Tezel, Defne; Joyal, Destin; Fraser, Dylan J

2015-09-01

How population size influences quantitative genetic variation and differentiation among natural, fragmented populations remains unresolved. Small, isolated populations might occupy poor quality habitats and lose genetic variation more rapidly due to genetic drift than large populations. Genetic drift might furthermore overcome selection as population size decreases. Collectively, this might result in directional changes in additive genetic variation (VA ) and trait differentiation (QST ) from small to large population size. Alternatively, small populations might exhibit larger variation in VA and QST if habitat fragmentation increases variability in habitat types. We explored these alternatives by investigating VA and QST using nine fragmented populations of brook trout varying 50-fold in census size N (179-8416) and 10-fold in effective number of breeders, Nb (18-135). Across 15 traits, no evidence was found for consistent differences in VA and QST with population size and almost no evidence for increased variability of VA or QST estimates at small population size. This suggests that (i) small populations of some species may retain adaptive potential according to commonly adopted quantitative genetic measures and (ii) populations of varying sizes experience a variety of environmental conditions in nature, however extremely large studies are likely required before any firm conclusions can be made. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

Exact Interval Estimation, Power Calculation, and Sample Size Determination in Normal Correlation Analysis

ERIC Educational Resources Information Center

Shieh, Gwowen

2006-01-01

This paper considers the problem of analysis of correlation coefficients from a multivariate normal population. A unified theorem is derived for the regression model with normally distributed explanatory variables and the general results are employed to provide useful expressions for the distributions of simple, multiple, and partial-multiple…

Incorporating Quality Scores in Meta-Analysis

ERIC Educational Resources Information Center

Ahn, Soyeon; Becker, Betsy Jane

2011-01-01

This paper examines the impact of quality-score weights in meta-analysis. A simulation examines the roles of study characteristics such as population effect size (ES) and its variance on the bias and mean square errors (MSEs) of the estimators for several patterns of relationship between quality and ES, and for specific patterns of systematic…

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.

Population dynamics of American horseshoe crabs-historic climatic events and recent anthropogenic pressures

USGS Publications Warehouse

Faurby, S.; King, T.L.; Obst, M.; Hallerman, E.M.; Pertoldi, C.; Funch, P.

2010-01-01

Populations of the American horseshoe crab, Limulus polyphemus, have declined, but neither the causes nor the magnitude are fully understood. In order to evaluate historic demography, variation at 12 microsatellite DNA loci surveyed in 1218 L. polyphemus sampled from 28 localities was analysed with Bayesian coalescent-based methods. The analysis showed strong declines in population sizes throughout the species' distribution except in the geographically isolated southern-most population in Mexico, where a strong increase in population size was inferred. Analyses suggested that demographic changes in the core of the distribution occurred in association with the recolonization after the Ice Age and also by anthropogenic effects, such as the past overharvest of the species for fertilizer or the current use of the animals as bait for American eel (Anguilla rostrata) and whelk (Busycon spp.) fisheries. This study highlights the importance of considering both climatic changes and anthropogenic effects in efforts to understand population dynamics-a topic which is highly relevant in the ongoing assessments of the effects of climate change and overharvest. ?? 2010 Blackwell Publishing Ltd.

Population dynamics of American horseshoe crabs--historic climatic events and recent anthropogenic pressures.

PubMed

Faurby, Søren; King, Tim L; Obst, Matthias; Hallerman, Eric M; Pertoldi, Cino; Funch, Peter

2010-08-01

Populations of the American horseshoe crab, Limulus polyphemus, have declined, but neither the causes nor the magnitude are fully understood. In order to evaluate historic demography, variation at 12 microsatellite DNA loci surveyed in 1218 L. polyphemus sampled from 28 localities was analysed with Bayesian coalescent-based methods. The analysis showed strong declines in population sizes throughout the species' distribution except in the geographically isolated southern-most population in Mexico, where a strong increase in population size was inferred. Analyses suggested that demographic changes in the core of the distribution occurred in association with the recolonization after the Ice Age and also by anthropogenic effects, such as the past overharvest of the species for fertilizer or the current use of the animals as bait for American eel (Anguilla rostrata) and whelk (Busycon spp.) fisheries. This study highlights the importance of considering both climatic changes and anthropogenic effects in efforts to understand population dynamics--a topic which is highly relevant in the ongoing assessments of the effects of climate change and overharvest.

Accounting for randomness in measurement and sampling in studying cancer cell population dynamics.

PubMed

Ghavami, Siavash; Wolkenhauer, Olaf; Lahouti, Farshad; Ullah, Mukhtar; Linnebacher, Michael

2014-10-01

Knowing the expected temporal evolution of the proportion of different cell types in sample tissues gives an indication about the progression of the disease and its possible response to drugs. Such systems have been modelled using Markov processes. We here consider an experimentally realistic scenario in which transition probabilities are estimated from noisy cell population size measurements. Using aggregated data of FACS measurements, we develop MMSE and ML estimators and formulate two problems to find the minimum number of required samples and measurements to guarantee the accuracy of predicted population sizes. Our numerical results show that the convergence mechanism of transition probabilities and steady states differ widely from the real values if one uses the standard deterministic approach for noisy measurements. This provides support for our argument that for the analysis of FACS data one should consider the observed state as a random variable. The second problem we address is about the consequences of estimating the probability of a cell being in a particular state from measurements of small population of cells. We show how the uncertainty arising from small sample sizes can be captured by a distribution for the state probability.

Spatiotemporal variation in reproductive parameters of yellow-bellied marmots.

PubMed

Ozgul, Arpat; Oli, Madan K; Olson, Lucretia E; Blumstein, Daniel T; Armitage, Kenneth B

2007-11-01

Spatiotemporal variation in reproductive rates is a common phenomenon in many wildlife populations, but the population dynamic consequences of spatial and temporal variability in different components of reproduction remain poorly understood. We used 43 years (1962-2004) of data from 17 locations and a capture-mark-recapture (CMR) modeling framework to investigate the spatiotemporal variation in reproductive parameters of yellow-bellied marmots (Marmota flaviventris), and its influence on the realized population growth rate. Specifically, we estimated and modeled breeding probabilities of two-year-old females (earliest age of first reproduction), >2-year-old females that have not reproduced before (subadults), and >2-year-old females that have reproduced before (adults), as well as the litter sizes of two-year old and >2-year-old females. Most reproductive parameters exhibited spatial and/or temporal variation. However, reproductive parameters differed with respect to their relative influence on the realized population growth rate (lambda). Litter size had a stronger influence than did breeding probabilities on both spatial and temporal variations in lambda. Our analysis indicated that lambda was proportionately more sensitive to survival than recruitment. However, the annual fluctuation in litter size, abetted by the breeding probabilities, accounted for most of the temporal variation in lambda.

Line transect estimation of population size: the exponential case with grouped data

USGS Publications Warehouse

Anderson, D.R.; Burnham, K.P.; Crain, B.R.

1979-01-01

Gates, Marshall, and Olson (1968) investigated the line transect method of estimating grouse population densities in the case where sighting probabilities are exponential. This work is followed by a simulation study in Gates (1969). A general overview of line transect analysis is presented by Burnham and Anderson (1976). These articles all deal with the ungrouped data case. In the present article, an analysis of line transect data is formulated under the Gates framework of exponential sighting probabilities and in the context of grouped data.

Community characteristics that attract physicians in Japan: a cross-sectional analysis of community demographic and economic factors.

PubMed

Matsumoto, Masatoshi; Inoue, Kazuo; Noguchi, Satomi; Toyokawa, Satoshi; Kajii, Eiji

2009-02-18

In many countries, there is a surplus of physicians in some communities and a shortage in others. Population size is known to be correlated with the number of physicians in a community, and is conventionally considered to represent the power of communities to attract physicians. However, associations between other demographic/economic variables and the number of physicians in a community have not been fully evaluated. This study seeks other parameters that correlate with the physician population and show which characteristics of a community determine its "attractiveness" to physicians. Associations between the number of physicians and selected demographic/economic/life-related variables of all of Japan's 3132 municipalities were examined. In order to exclude the confounding effect of community size, correlations between the physician-to-population ratio and other variable-to-population ratios or variable-to-area ratios were evaluated with simple correlation and multiple regression analyses. The equity of physician distribution against each variable was evaluated by the orenz curve and Gini index. Among the 21 variables selected, the service industry workers-to-population ratio (0.543), commercial land price (0.527), sales of goods per person (0.472), and daytime population density (0.451) were better correlated with the physician-to-population ratio than was population density (0.409). Multiple regression analysis showed that the service industry worker-to-population ratio, the daytime population density, and the elderly rate were each independently correlated with the physician-to-population ratio (standardized regression coefficient 0.393, 0.355, 0.089 respectively; each p<0.001). Equity of physician distribution was higher against service industry population (Gini index=0.26) and daytime population (0.28) than against population (0.33). Daytime population and service industry population in a municipality are better parameters of community attractiveness to physicians than population. Because attractiveness is supposed to consist of medical demand and the amenities of urban life, the two parameters may represent the amount of medical demand and/or the extent of urban amenities of the community more precisely than population does. The conventional demand-supply analysis based solely on population as the demand parameter may overestimate the inequity of the physician distribution among communities.

The effects of atomoxetine on emotional control in adults with ADHD: An integrated analysis of multicenter studies.

PubMed

Asherson, P; Stes, S; Nilsson Markhed, M; Berggren, L; Svanborg, P; Kutzelnigg, A; Deberdt, W

2015-06-01

To investigate the effects of atomoxetine on emotional control in adults with ADHD. We performed an integrated analysis using individual patient data pooled from three Eli Lilly-sponsored studies. An integrated analysis can be viewed as a meta-analysis of individual patient-level data, rather than study-level summary data. Two populations were identified: a large sample of patients with pre-treatment baseline data (the "overall population"; n=2846); and a subset of these patients with placebo-controlled efficacy data from baseline to 10 or 12 weeks after initiating treatment (the "placebo-controlled population"; n=829). At baseline, in the overall population, ∼50% of ADHD patients had BRIEF-AS (Behavior Rating Inventory of Executive Function-Adult Version Self-Report) Emotional control subscores between 21 and 30, compared with ∼10% of normative subjects in the BRIEF-A manual. At endpoint, in the placebo-controlled population, atomoxetine led to a small (effect size 0.19) but significant (P=0.013) treatment effect for emotional control. The effect size was 0.32 in patients with BRIEF-AS Emotional control scores>20 at baseline. Improvements in emotional control correlated with improvements in the core ADHD symptoms and quality-of-life. As deficient emotional control is associated with impaired social, educational and occupational functioning over and above that explained by core ADHD symptoms alone, improvements in emotional control may be clinically relevant. At baseline, adults with ADHD were more likely to have impaired emotional control than normative subjects. In the adult ADHD patients, atomoxetine treatment was associated with improvements in emotional control, as well as in core ADHD symptoms and quality-of-life. Copyright © 2015. Published by Elsevier Masson SAS.

Detecting concerted demographic response across community assemblages using hierarchical approximate Bayesian computation.

PubMed

Chan, Yvonne L; Schanzenbach, David; Hickerson, Michael J

2014-09-01

Methods that integrate population-level sampling from multiple taxa into a single community-level analysis are an essential addition to the comparative phylogeographic toolkit. Detecting how species within communities have demographically tracked each other in space and time is important for understanding the effects of future climate and landscape changes and the resulting acceleration of extinctions, biological invasions, and potential surges in adaptive evolution. Here, we present a statistical framework for such an analysis based on hierarchical approximate Bayesian computation (hABC) with the goal of detecting concerted demographic histories across an ecological assemblage. Our method combines population genetic data sets from multiple taxa into a single analysis to estimate: 1) the proportion of a community sample that demographically expanded in a temporally clustered pulse and 2) when the pulse occurred. To validate the accuracy and utility of this new approach, we use simulation cross-validation experiments and subsequently analyze an empirical data set of 32 avian populations from Australia that are hypothesized to have expanded from smaller refugia populations in the late Pleistocene. The method can accommodate data set heterogeneity such as variability in effective population size, mutation rates, and sample sizes across species and exploits the statistical strength from the simultaneous analysis of multiple species. This hABC framework used in a multitaxa demographic context can increase our understanding of the impact of historical climate change by determining what proportion of the community responded in concert or independently and can be used with a wide variety of comparative phylogeographic data sets as biota-wide DNA barcoding data sets accumulate. © The Author 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Estimate of the size and demographic structure of the owned dog and cat population living in Veneto region (north-eastern Italy).

PubMed

Capello, Katia; Bortolotti, Laura; Lanari, Manuela; Baioni, Elisa; Mutinelli, Franco; Vascellari, Marta

2015-01-01

The knowledge of the size and demographic structure of animal populations is a necessary prerequisite for any population-based epidemiological study, especially to ascertain and interpret prevalence data, to implement surveillance plans in controlling zoonotic diseases and, moreover, to provide accurate estimates of tumours incidence data obtained by population-based registries. The main purpose of this study was to provide an accurate estimate of the size and structure of the canine population in Veneto region (north-eastern Italy), using the Lincoln-Petersen version of the capture-recapture methodology. The Regional Canine Demographic Registry (BAC) and a sample survey of households of Veneto Region were the capture and recapture sources, respectively. The secondary purpose was to estimate the size and structure of the feline population in the same region, using the same survey applied for dog population. A sample of 2465 randomly selected households was drawn and submitted to a questionnaire using the CATI technique, in order to obtain information about the ownership of dogs and cats. If the dog was declared to be identified, owner's information was used to recapture the dog in the BAC. The study was conducted in Veneto Region during 2011, when the dog population recorded in the BAC was 605,537. Overall, 616 households declared to possess at least one dog (25%), with a total of 805 dogs and an average per household of 1.3. The capture-recapture analysis showed that 574 dogs (71.3%, 95% CI: 68.04-74.40%) had been recaptured in both sources, providing a dog population estimate of 849,229 (95% CI: 814,747-889,394), 40% higher than that registered in the BAC. Concerning cats, 455 of 2465 (18%, 95% CI: 17-20%) households declared to possess at least one cat at the time of the telephone interview, with a total of 816 cats. The mean number of cats per household was equal to 1.8, providing an estimate of the cat population in Veneto region equal to 663,433 (95% CI: 626,585-737,159). The estimate of the size and structure of owned canine and feline populations in Veneto region provide useful data to perform epidemiological studies and monitoring plans in this area. Copyright © 2014 Elsevier B.V. All rights reserved.

Modeling of the Orbital Debris Population of RORSAT Sodium-Potassium Droplets

NASA Technical Reports Server (NTRS)

Xu, Y.-L.; Krisko, P. H.; Matney, Mark; Stansbery, E. G.

2010-01-01

A large population resident in the orbital debris environment is composed of eutectic sodium-potassium (NaK) droplets, released during the reactor core ejection of 16 nuclear-powered Radar Ocean Reconnaissance Satellites (RORSATs) launched in the 1980s by the former Soviet Union. These electrically conducting RORSAT debris objects are spherical in shape, generating highly polarized radar returns. Their diameters are mostly in the centimeter and millimeter size regimes. Since the Space Surveillance Network catalog is limited to objects greater than 5 cm in low Earth orbit, our current knowledge about this special class of orbital debris relies largely on the analysis of Haystack radar data. This paper elaborates the simulation of the RORSAT debris populations in the new NASA Orbital Debris Engineering Model ORDEM2010, which replaces ORDEM2000. The estimation of the NaK populations uses the NASA NaK-module as a benchmark. It follows the general statistical approach to developing all other ORDEM2010-required LEO populations (for various types of debris and across a wide range of object sizes). This paper describes, in detail, each major step in the NaK-population derivation, including a specific discussion on the conversion between Haystack-measured radar-cross-sections and object-size distribution for the NaK droplets. Modeling results show that the RORSAT debris population is stable for the time period under study and that Haystack data sets are fairly consistent over the observations of multiple years.

Two-strain competition in quasineutral stochastic disease dynamics.

PubMed

Kogan, Oleg; Khasin, Michael; Meerson, Baruch; Schneider, David; Myers, Christopher R

2014-10-01

We develop a perturbation method for studying quasineutral competition in a broad class of stochastic competition models and apply it to the analysis of fixation of competing strains in two epidemic models. The first model is a two-strain generalization of the stochastic susceptible-infected-susceptible (SIS) model. Here we extend previous results due to Parsons and Quince [Theor. Popul. Biol. 72, 468 (2007)], Parsons et al. [Theor. Popul. Biol. 74, 302 (2008)], and Lin, Kim, and Doering [J. Stat. Phys. 148, 646 (2012)]. The second model, a two-strain generalization of the stochastic susceptible-infected-recovered (SIR) model with population turnover, has not been studied previously. In each of the two models, when the basic reproduction numbers of the two strains are identical, a system with an infinite population size approaches a point on the deterministic coexistence line (CL): a straight line of fixed points in the phase space of subpopulation sizes. Shot noise drives one of the strain populations to fixation, and the other to extinction, on a time scale proportional to the total population size. Our perturbation method explicitly tracks the dynamics of the probability distribution of the subpopulations in the vicinity of the CL. We argue that, whereas the slow strain has a competitive advantage for mathematically "typical" initial conditions, it is the fast strain that is more likely to win in the important situation when a few infectives of both strains are introduced into a susceptible population.

Demographic History of a Recent Invasion of House Mice on the Isolated Island of Gough

PubMed Central

Gray, Melissa M.; Wegmann, Daniel; Haasl, Ryan J.; White, Michael A.; Gabriel, Sofia I.; Searle, Jeremy B.; Cuthbert, Richard J.; Ryan, Peter G.; Payseur, Bret A.

2014-01-01

Island populations provide natural laboratories for studying key contributors to evolutionary change, including natural selection, population size, and the colonization of new environments. The demographic histories of island populations can be reconstructed from patterns of genetic diversity. House mice (Mus musculus) inhabit islands throughout the globe, making them an attractive system for studying island colonization from a genetic perspective. Gough Island, in the central South Atlantic Ocean, is one of the remotest islands in the world. House mice were introduced to Gough Island by sealers during the 19th century, and display unusual phenotypes, including exceptionally large body size and carnivorous feeding behavior. We describe genetic variation in Gough Island mice using mitochondrial sequences, nuclear sequences, and microsatellites. Phylogenetic analysis of mitochondrial sequences suggested that Gough Island mice belong to Mus musculus domesticus, with the maternal lineage possibly originating in England or France. Cluster analyses of microsatellites revealed genetic membership for Gough Island mice in multiple coastal populations in Western Europe, suggesting admixed ancestry. Gough Island mice showed substantial reductions in mitochondrial and nuclear sequence variation and weak reductions in microsatellite diversity compared with Western European populations, consistent with a population bottleneck. Approximate Bayesian Computation (ABC) estimated that mice recently colonized Gough Island (~100 years ago) and experienced a 98% reduction in population size followed by a rapid expansion. Our results indicate that the unusual phenotypes of Gough Island mice evolved rapidly, positioning these mice as useful models for understanding rapid phenotypic evolution. PMID:24617968

An ecological analysis of prison overcrowding and suicide rates in England and Wales, 2000-2014.

PubMed

van Ginneken, Esther F J C; Sutherland, Alex; Molleman, Toon

Prisoners are at a greatly increased risk of suicides compared to the general population. Differences in suicide risk can be partly explained by individual risk factors, but the contribution of prison characteristics remains unclear. Overcrowded prisons have higher suicide rates, but this may be related to prison function, security level, population size and turnover. The aim of the current study was to investigate the contribution of each of these prison characteristics to suicide rates, using data from the Ministry of Justice for adult prisons in England and Wales from 2000 to 2014. Negative binomial regression analysis showed that larger population size, higher turnover, higher security and public management were associated with higher suicide rates. When controlling for these factors, overcrowding was not found to be related to suicide rates. Questions remain about the causal mechanisms underlying variation in prison suicides and the impact of the lived experience of overcrowding. Further research is needed to examine the relative contribution of prison and prisoner characteristics to suicides. Copyright © 2016 Elsevier Ltd. All rights reserved.

Violation of the Sphericity Assumption and Its Effect on Type-I Error Rates in Repeated Measures ANOVA and Multi-Level Linear Models (MLM).

PubMed

Haverkamp, Nicolas; Beauducel, André

2017-01-01

We investigated the effects of violations of the sphericity assumption on Type I error rates for different methodical approaches of repeated measures analysis using a simulation approach. In contrast to previous simulation studies on this topic, up to nine measurement occasions were considered. Effects of the level of inter-correlations between measurement occasions on Type I error rates were considered for the first time. Two populations with non-violation of the sphericity assumption, one with uncorrelated measurement occasions and one with moderately correlated measurement occasions, were generated. One population with violation of the sphericity assumption combines uncorrelated with highly correlated measurement occasions. A second population with violation of the sphericity assumption combines moderately correlated and highly correlated measurement occasions. From these four populations without any between-group effect or within-subject effect 5,000 random samples were drawn. Finally, the mean Type I error rates for Multilevel linear models (MLM) with an unstructured covariance matrix (MLM-UN), MLM with compound-symmetry (MLM-CS) and for repeated measures analysis of variance (rANOVA) models (without correction, with Greenhouse-Geisser-correction, and Huynh-Feldt-correction) were computed. To examine the effect of both the sample size and the number of measurement occasions, sample sizes of n = 20, 40, 60, 80, and 100 were considered as well as measurement occasions of m = 3, 6, and 9. With respect to rANOVA, the results plead for a use of rANOVA with Huynh-Feldt-correction, especially when the sphericity assumption is violated, the sample size is rather small and the number of measurement occasions is large. For MLM-UN, the results illustrate a massive progressive bias for small sample sizes ( n = 20) and m = 6 or more measurement occasions. This effect could not be found in previous simulation studies with a smaller number of measurement occasions. The proportionality of bias and number of measurement occasions should be considered when MLM-UN is used. The good news is that this proportionality can be compensated by means of large sample sizes. Accordingly, MLM-UN can be recommended even for small sample sizes for about three measurement occasions and for large sample sizes for about nine measurement occasions.

Spatial and temporal dynamics of fucoid populations (Ascophyllum nodosum and Fucus serratus): a comparison between central and range edge populations.

PubMed

Araújo, Rita M; Serrão, Ester A; Sousa-Pinto, Isabel; Åberg, Per

2014-01-01

Persistence of populations at range edges relies on local population dynamics and fitness, in the case of geographically isolated populations of species with low dispersal potential. Focusing on spatial variations in demography helps to predict the long-term capability for persistence of populations across the geographical range of species' distribution. The demography of two ecological and phylogenetically close macroalgal species with different life history characteristics was investigated by using stochastic, stage-based matrix models. Populations of Ascophyllum nodosum and Fucus serratus were sampled for up to 4 years at central locations in France and at their southern range limits in Portugal. The stochastic population growth rate (λ(s)) of A. nodosum was lower and more variable in central than in southern sites whilst for F. serratus this trend was reversed with λ(s) much lower and more variable in southern than in central populations. Individuals were larger in central than in southern populations for both species, which was reflected in the lower transition probabilities of individuals to larger size classes and higher probability of shrinkage in the southern populations. In both central and southern populations elasticity analysis (proportional sensitivity) of population growth rate showed that fertility elements had a small contribution to λ(s) that was more sensitive to changes in matrix transitions corresponding to survival. The highest elasticities were found for loop transitions in A. nodosum and for growth to larger size classes in F. serratus. Sensitivity analysis showed high selective pressure on individual growth for both species at both locations. The results of this study highlight the deterministic role of species-specific life-history traits in population demography across the geographical range of species. Additionally, this study demonstrates that individuals' life-transitions differ in vulnerability to environmental variability and shows the importance of vegetative compared to reproductive stages for the long-term persistence of populations.

Density, distribution, and genetic structure of grizzly bears in the Cabinet-Yaak Ecosystem

USGS Publications Warehouse

Macleod, Amy C.; Boyd, Kristina L.; Boulanger, John; Royle, J. Andrew; Kasworm, Wayne F.; Paetkau, David; Proctor, Michael F.; Annis, Kim; Graves, Tabitha A.

2016-01-01

The conservation status of the 2 threatened grizzly bear (Ursus arctos) populations in the Cabinet-Yaak Ecosystem (CYE) of northern Montana and Idaho had remained unchanged since designation in 1975; however, the current demographic status of these populations was uncertain. No rigorous data on population density and distribution or analysis of recent population genetic structure were available to measure the effectiveness of conservation efforts. We used genetic detection data from hair corral, bear rub, and opportunistic sampling in traditional and spatial capture–recapture models to generate estimates of abundance and density of grizzly bears in the CYE. We calculated mean bear residency on our sampling grid from telemetry data using Huggins and Pledger models to estimate the average number of bears present and to correct our superpopulation estimates for lack of geographic closure. Estimated grizzly bear abundance (all sex and age classes) in the CYE in 2012 was 48–50 bears, approximately half the population recovery goal. Grizzly bear density in the CYE (4.3–4.5 grizzly bears/1,000 km2) was among the lowest of interior North American populations. The sizes of the Cabinet (n = 22–24) and Yaak (n = 18–22) populations were similar. Spatial models produced similar estimates of abundance and density with comparable precision without requiring radio-telemetry data to address assumptions of geographic closure. The 2 populations in the CYE were demographically and reproductively isolated from each other and the Cabinet population was highly inbred. With parentage analysis, we documented natural migrants to the Cabinet and Yaak populations by bears born to parents in the Selkirk and Northern Continental Divide populations. These events supported data from other sources suggesting that the expansion of neighboring populations may eventually help sustain the CYE populations. However, the small size, isolation, and inbreeding documented by this study demonstrate the need for comprehensive management designed to support CYE population growth and increased connectivity and gene flow with other populations.

Complex interaction of dendritic connectivity and hierarchical patch size on biodiversity in river-like landscapes.

PubMed

Carrara, Francesco; Rinaldo, Andrea; Giometto, Andrea; Altermatt, Florian

2014-01-01

Habitat fragmentation and land use changes are causing major biodiversity losses. Connectivity of the landscape or environmental conditions alone can shape biodiversity patterns. In nature, however, local habitat characteristics are often intrinsically linked to a specific connectivity. Such a link is evident in riverine ecosystems, where hierarchical dendritic structures command related scaling on habitat capacity. We experimentally disentangled the effect of local habitat capacity (i.e., the patch size) and dendritic connectivity on biodiversity in aquatic microcosm metacommunities by suitably arranging patch sizes within river-like networks. Overall, more connected communities that occupy a central position in the network exhibited higher species richness, irrespective of patch size arrangement. High regional evenness in community composition was found only in landscapes preserving geomorphological scaling properties of patch sizes. In these landscapes, some of the rarer species sustained regionally more abundant populations better tracking their own niche requirements compared to landscapes with homogeneous patch size or landscapes with spatially uncorrelated patch size. Our analysis suggests that altering the natural link between dendritic connectivity and patch size strongly affects community composition and population persistence at multiple scales. The experimental results are demonstrating a principle that can be tested in theoretical metacommunity models and eventually be projected to real riverine ecosystems.

Temperature-dependent body size effects determine population responses to climate warming.

PubMed

Lindmark, Max; Huss, Magnus; Ohlberger, Jan; Gårdmark, Anna

2018-02-01

Current understanding of animal population responses to rising temperatures is based on the assumption that biological rates such as metabolism, which governs fundamental ecological processes, scale independently with body size and temperature, despite empirical evidence for interactive effects. Here, we investigate the consequences of interactive temperature- and size scaling of vital rates for the dynamics of populations experiencing warming using a stage-structured consumer-resource model. We show that interactive scaling alters population and stage-specific responses to rising temperatures, such that warming can induce shifts in population regulation and stage-structure, influence community structure and govern population responses to mortality. Analysing experimental data for 20 fish species, we found size-temperature interactions in intraspecific scaling of metabolic rate to be common. Given the evidence for size-temperature interactions and the ubiquity of size structure in animal populations, we argue that accounting for size-specific temperature effects is pivotal for understanding how warming affects animal populations and communities. © 2017 The Authors. Ecology Letters published by CNRS and John Wiley & Sons Ltd.

Altitudinal variation in age and body size in Yunnan pond frog (Pelophylax pleuraden).

PubMed

Lou, Shang Ling; Jin, Long; Liu, Yan Hong; Mi, Zhi Ping; Tao, Gang; Tang, Yu Mei; Liao, Wen Bo

2012-08-01

Large-scale systematic patterns of body size are a basic concern of evolutionary biology. Identifying body size variation along altitudinal gradients may help us to understand the evolution of life history of animals. In this study, we investigated altitudinal variation in body size, age and growth rate in Chinese endemic frog, Pelophylax pleuraden. Data sampled from five populations covering an altitudinal span of 1413 to 1935 m in Sichuan province revealed that body size from five populations did not co-vary with altitudes, not following Bergmann's rule. Average adult SVL differed significantly among populations in males, but not in females. For both sexes, average adult age differed significantly among populations. Post-metamorphic growth rate did not co-vary with altitude, and females grew faster than males in all populations. When controlling the effect of age, body size did not differ among populations in both sexes, suggesting that age did not affect variation in body size among populations. For females, there may be other factors, such as the allocation of energy between growth and reproduction, that eliminated the effect of age on body size. To our minds, the major reason of body size variation among populations in male frogs may be related to individual longevity. Our findings also suggest that factors other than age and growth rate may contribute to size differences among populations.

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.

Understanding Past Population Dynamics: Bayesian Coalescent-Based Modeling with Covariates

PubMed Central

Gill, Mandev S.; Lemey, Philippe; Bennett, Shannon N.; Biek, Roman; Suchard, Marc A.

2016-01-01

Effective population size characterizes the genetic variability in a population and is a parameter of paramount importance in population genetics and evolutionary biology. Kingman’s coalescent process enables inference of past population dynamics directly from molecular sequence data, and researchers have developed a number of flexible coalescent-based models for Bayesian nonparametric estimation of the effective population size as a function of time. Major goals of demographic reconstruction include identifying driving factors of effective population size, and understanding the association between the effective population size and such factors. Building upon Bayesian nonparametric coalescent-based approaches, we introduce a flexible framework that incorporates time-varying covariates that exploit Gaussian Markov random fields to achieve temporal smoothing of effective population size trajectories. To approximate the posterior distribution, we adapt efficient Markov chain Monte Carlo algorithms designed for highly structured Gaussian models. Incorporating covariates into the demographic inference framework enables the modeling of associations between the effective population size and covariates while accounting for uncertainty in population histories. Furthermore, it can lead to more precise estimates of population dynamics. We apply our model to four examples. We reconstruct the demographic history of raccoon rabies in North America and find a significant association with the spatiotemporal spread of the outbreak. Next, we examine the effective population size trajectory of the DENV-4 virus in Puerto Rico along with viral isolate count data and find similar cyclic patterns. We compare the population history of the HIV-1 CRF02_AG clade in Cameroon with HIV incidence and prevalence data and find that the effective population size is more reflective of incidence rate. Finally, we explore the hypothesis that the population dynamics of musk ox during the Late Quaternary period were related to climate change. [Coalescent; effective population size; Gaussian Markov random fields; phylodynamics; phylogenetics; population genetics. PMID:27368344

Effects of constant immigration on the dynamics and persistence of stable and unstable Drosophila populations

PubMed Central

Dey, Snigdhadip; Joshi, Amitabh

2013-01-01

Constant immigration can stabilize population size fluctuations but its effects on extinction remain unexplored. We show that constant immigration significantly reduced extinction in fruitfly populations with relatively stable or unstable dynamics. In unstable populations with oscillations of amplitude around 1.5 times the mean population size, persistence and constancy were unrelated. Low immigration enhanced persistence without affecting constancy whereas high immigration increased constancy without enhancing persistence. In relatively stable populations with erratic fluctuations of amplitude close to the mean population size, both low and high immigration enhanced persistence. In these populations, the amplitude of fluctuations relative to mean population size went down due to immigration, and their dynamics were altered to low-period cycles. The effects of immigration on the population size distribution and intrinsic dynamics of stable versus unstable populations differed considerably, suggesting that the mechanisms by which immigration reduced extinction risk depended on underlying dynamics in complex ways. PMID:23470546

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 divergence between the populations, which are likely cryptic species. Genome size variation is known to occur in other diatom genera; we hypothesize that genome duplication may be an active and important mechanism of genetic and physiological diversification and speciation in diatoms. PMID:20044934

Devastating decline of forest elephants in central Africa.

PubMed

Maisels, Fiona; Strindberg, Samantha; Blake, Stephen; Wittemyer, George; Hart, John; Williamson, Elizabeth A; Aba'a, Rostand; Abitsi, Gaspard; Ambahe, Ruffin D; Amsini, Fidèl; Bakabana, Parfait C; Hicks, Thurston Cleveland; Bayogo, Rosine E; Bechem, Martha; Beyers, Rene L; Bezangoye, Anicet N; Boundja, Patrick; Bout, Nicolas; Akou, Marc Ella; Bene, Lambert Bene; Fosso, Bernard; Greengrass, Elizabeth; Grossmann, Falk; Ikamba-Nkulu, Clement; Ilambu, Omari; Inogwabini, Bila-Isia; Iyenguet, Fortune; Kiminou, Franck; Kokangoye, Max; Kujirakwinja, Deo; Latour, Stephanie; Liengola, Innocent; Mackaya, Quevain; Madidi, Jacob; Madzoke, Bola; Makoumbou, Calixte; Malanda, Guy-Aimé; Malonga, Richard; Mbani, Olivier; Mbendzo, Valentin A; Ambassa, Edgar; Ekinde, Albert; Mihindou, Yves; Morgan, Bethan J; Motsaba, Prosper; Moukala, Gabin; Mounguengui, Anselme; Mowawa, Brice S; Ndzai, Christian; Nixon, Stuart; Nkumu, Pele; Nzolani, Fabian; Pintea, Lilian; Plumptre, Andrew; Rainey, Hugo; de Semboli, Bruno Bokoto; Serckx, Adeline; Stokes, Emma; Turkalo, Andrea; Vanleeuwe, Hilde; Vosper, Ashley; Warren, Ymke

2013-01-01

African forest elephants- taxonomically and functionally unique-are being poached at accelerating rates, but we lack range-wide information on the repercussions. Analysis of the largest survey dataset ever assembled for forest elephants (80 foot-surveys; covering 13,000 km; 91,600 person-days of fieldwork) revealed that population size declined by ca. 62% between 2002-2011, and the taxon lost 30% of its geographical range. The population is now less than 10% of its potential size, occupying less than 25% of its potential range. High human population density, hunting intensity, absence of law enforcement, poor governance, and proximity to expanding infrastructure are the strongest predictors of decline. To save the remaining African forest elephants, illegal poaching for ivory and encroachment into core elephant habitat must be stopped. In addition, the international demand for ivory, which fuels illegal trade, must be dramatically reduced.

Shifting latitudinal clines in avian body size correlate with global warming in Australian passerines.

PubMed

Gardner, Janet L; Heinsohn, Robert; Joseph, Leo

2009-11-07

Intraspecific latitudinal clines in the body size of terrestrial vertebrates, where members of the same species are larger at higher latitudes, are widely interpreted as evidence for natural selection and adaptation to local climate. These clines are predicted to shift in response to climate change. We used museum specimens to measure changes in the body size of eight passerine bird species from south-eastern Australia over approximately the last 100 years. Four species showed significant decreases in body size (1.8-3.6% of wing length) and a shift in latitudinal cline over that period, and a meta-analysis demonstrated a consistent trend across all eight species. Southern high-latitude populations now display the body sizes typical of more northern populations pre-1950, equivalent to a 7 degrees shift in latitude. Using ptilochronology, we found no evidence that these morphological changes were a plastic response to changes in nutrition, a likely non-genetic mechanism for the pattern observed. Our results demonstrate a generalized response by eight avian species to some major environmental change over the last 100 years or so, probably global warming.

Population characteristics and assessment of overfishing for an exploited paddlefish population in the lower Tennessee River

USGS Publications Warehouse

Scholten, G.D.; Bettoli, P.W.

2005-01-01

Paddlefish Polyodon spathula (n = 576) were collected from Kentucky Lake, Kentucky-Tennessee, with experimental gill nets in 2003-2004 to assess population characteristics and the potential for commercial overfishing. Additional data were collected from 1,039 paddlefish caught by commercial gillnetters in this impoundment. Since the most recent study in 1991, size and age structure have been reduced and annual mortality has tripled. In the 1991 study, 37% of the fish collected were older than the maximum age we observed (age 11), and in 2003 annual mortality for paddlefish age 7 and older was high (A = 68%). Natural mortality is presumably low (<10%) for paddlefish; therefore, exploitation in recent years is high. Estimates of total annual mortality were negatively related to river discharge in the years preceding each estimate. The number of paddlefish harvested since 1999 was also negatively related to river discharge because gill nets cannot be easily deployed when discharge exceeds approximately 850 m3/s. Large females spawn annually because all females longer than 1,034 mm eye-fork length (EFL) were gravid. No mature females were protected by the current 864-mm minimum EFL limit. At a low natural mortality rate, higher size limits when exploitation was high (40-70%) increased simulated flesh yields by 10-20%. Even at low levels of exploitation (21%), spawning potential ratios (SPRs) under the current 864-mm minimum EFL size limit fell below 20%. If the size limit was raised to 1,016 mm EFL, the population could withstand up to 62% exploitation before the SPR falls below 20%. An analysis of annual mortality caps indicated that the best way to increase the average size of harvested fish is to increase the minimum size limit. Recruitment overfishing probably occurs during drought years; however, variation in river discharge has prevented the population from being exploited at unsustainable rates in the past. ?? Copyright by the American Fisheries Society 2005.

A Carefully Characterized and Tracked Trans-Neptunian Survey: The Size distribution of the Plutinos and the Number of Neptunian Trojans

NASA Astrophysics Data System (ADS)

Alexandersen, Mike; Gladman, Brett; Kavelaars, J. J.; Petit, Jean-Marc; Gwyn, Stephen D. J.; Shankman, Cory J.; Pike, Rosemary E.

2016-11-01

The trans-Neptunian objects (TNOs) preserve evidence of planet building processes in their orbital and size distributions. While all populations show steep size distributions for large objects, a relative deficit of Neptunian trojans and scattering objects with diameters of D < 100 km has been detected. We investigated this deficit with a 32 square degree survey, in which we detected 77 TNOs that are brighter than a limiting r-band magnitude of 24.6. Our plutino sample (18 objects in 3:2 mean-motion resonance with Neptune) shows a deficit of D < 100 km objects, rejecting a single power-law size distribution at >99% confidence. Combining our survey with the Canada-France Ecliptic Plane Survey, we perform a detailed analysis of the allowable parameters for the plutino size distribution, including knees and divots. We surmise the existence of 9000 ± 3000 plutinos with an absolute magnitude of H r ≤ 8.66 and {37000}-10000+12000 with H r ≤ 10.0 (95% confidence). Our survey also discovered one temporary Uranian trojan, one temporary Neptunian trojan, and one stable Neptunian trojan, for which we estimate populations of {110}-100+500, {210}-200+900, and {150}-140+600 with H r ≤ 10.0, respectively. All three populations are thus less numerous than the main belt asteroids (592 asteroids with H r ≤ 10.0). With such population sizes, the temporary Neptunian trojans cannot be previously stable trojans diffusing out of the resonance now; they must be recently captured Centaurs or scattering objects. As the bias against the detection of objects grows with larger semimajor axes, our discovery of three 3:1 resonators and one 4:1 resonator adds to the growing evidence that the high-order resonances are far more populated than is typically predicted.

Hydrodynamic fractionation of finite size gold nanoparticle clusters.

PubMed

Tsai, De-Hao; Cho, Tae Joon; DelRio, Frank W; Taurozzi, Julian; Zachariah, Michael R; Hackley, Vincent A

2011-06-15

We demonstrate a high-resolution in situ experimental method for performing simultaneous size classification and characterization of functional gold nanoparticle clusters (GNCs) based on asymmetric-flow field flow fractionation (AFFF). Field emission scanning electron microscopy, atomic force microscopy, multi-angle light scattering (MALS), and in situ ultraviolet-visible optical spectroscopy provide complementary data and imagery confirming the cluster state (e.g., dimer, trimer, tetramer), packing structure, and purity of fractionated populations. An orthogonal analysis of GNC size distributions is obtained using electrospray-differential mobility analysis (ES-DMA). We find a linear correlation between the normalized MALS intensity (measured during AFFF elution) and the corresponding number concentration (measured by ES-DMA), establishing the capacity for AFFF to quantify the absolute number concentration of GNCs. The results and corresponding methodology summarized here provide the proof of concept for general applications involving the formation, isolation, and in situ analysis of both functional and adventitious nanoparticle clusters of finite size. © 2011 American Chemical Society

Trapped within the city: integrating demography, time since isolation and population-specific traits to assess the genetic effects of urbanization.

PubMed

Lourenço, André; Álvarez, David; Wang, Ian J; Velo-Antón, Guillermo

2017-03-01

Urbanization is a severe form of habitat fragmentation that can cause many species to be locally extirpated and many others to become trapped and isolated within an urban matrix. The role of drift in reducing genetic diversity and increasing genetic differentiation is well recognized in urban populations. However, explicit incorporation and analysis of the demographic and temporal factors promoting drift in urban environments are poorly studied. Here, we genotyped 15 microsatellites in 320 fire salamanders from the historical city of Oviedo (Est. 8th century) to assess the effects of time since isolation, demographic history (historical effective population size; N e ) and patch size on genetic diversity, population structure and contemporary N e . Our results indicate that urban populations of fire salamanders are highly differentiated, most likely due to the recent N e declines, as calculated in coalescence analyses, concomitant with the urban development of Oviedo. However, urbanization only caused a small loss of genetic diversity. Regression modelling showed that patch size was positively associated with contemporary N e , while we found only moderate support for the effects of demographic history when excluding populations with unresolved history. This highlights the interplay between different factors in determining current genetic diversity and structure. Overall, the results of our study on urban populations of fire salamanders provide some of the very first insights into the mechanisms affecting changes in genetic diversity and population differentiation via drift in urban environments, a crucial subject in a world where increasing urbanization is forecasted. © 2017 John Wiley & Sons Ltd.

A Statistical Analysis of the Economic Drivers of Battery Energy Storage in Commercial Buildings: Preprint

DOE Office of Scientific and Technical Information (OSTI.GOV)

Long, Matthew; Simpkins, Travis; Cutler, Dylan

There is significant interest in using battery energy storage systems (BESS) to reduce peak demand charges, and therefore the life cycle cost of electricity, in commercial buildings. This paper explores the drivers of economic viability of BESS in commercial buildings through statistical analysis. A sample population of buildings was generated, a techno-economic optimization model was used to size and dispatch the BESS, and the resulting optimal BESS sizes were analyzed for relevant predictor variables. Explanatory regression analyses were used to demonstrate that peak demand charges are the most significant predictor of an economically viable battery, and that the shape ofmore » the load profile is the most significant predictor of the size of the battery.« less

A Statistical Analysis of the Economic Drivers of Battery Energy Storage in Commercial Buildings

DOE Office of Scientific and Technical Information (OSTI.GOV)

Long, Matthew; Simpkins, Travis; Cutler, Dylan

There is significant interest in using battery energy storage systems (BESS) to reduce peak demand charges, and therefore the life cycle cost of electricity, in commercial buildings. This paper explores the drivers of economic viability of BESS in commercial buildings through statistical analysis. A sample population of buildings was generated, a techno-economic optimization model was used to size and dispatch the BESS, and the resulting optimal BESS sizes were analyzed for relevant predictor variables. Explanatory regression analyses were used to demonstrate that peak demand charges are the most significant predictor of an economically viable battery, and that the shape ofmore » the load profile is the most significant predictor of the size of the battery.« less

Psychotic experiences and risk of self-injurious behaviour in the general population: a systematic review and meta-analysis.

PubMed

Honings, S; Drukker, M; Groen, R; van Os, J

2016-01-01

Recent studies suggest that psychotic experiences (PE) in the general population are associated with an increased risk of self-injurious behaviour. Both the magnitude of this association and the level of adjustment for confounders vary among studies. A meta-analysis was performed to integrate the available evidence. The influence of possible confounders, including variably defined depression, was assessed. A systematic review and meta-analysis was conducted including general population studies reporting on the risk of self-injurious behaviour in individuals with PE. Studies were identified by a systematic search strategy in Pubmed, PsycINFO and Embase. Reported effect sizes were extracted and meta-analytically pooled. The risk of self-injurious behaviour was 3.20 times higher in individuals with PE compared with those without. Subanalyses showed that PE were associated with self-harm, suicidal ideation as well as suicidal attempts. All studies had scope for considerable residual confounding; effect sizes adjusted for depression were significantly smaller than effect sizes unadjusted for depression. In the longitudinal studies, adjustment for psychopathology resulted in a 74% reduction in excess risk. PE are associated with self-injurious behaviour, suggesting they have potential as passive markers of suicidality. However, the association is confounded and several methodological issues remain, particularly how to separate PE from the full range of connected psychopathology in determining any specific association with self-injurious behaviour. Given evidence that PE represent an indicator of severity of non-psychotic psychopathology, the association between PE and self-injurious behaviour probably reflects a greater likelihood of self-injurious behaviour in more severe states of mental distress.

Challenges in the size analysis of a silica nanoparticle mixture as candidate certified reference material

NASA Astrophysics Data System (ADS)

Kestens, Vikram; Roebben, Gert; Herrmann, Jan; Jämting, Åsa; Coleman, Victoria; Minelli, Caterina; Clifford, Charles; De Temmerman, Pieter-Jan; Mast, Jan; Junjie, Liu; Babick, Frank; Cölfen, Helmut; Emons, Hendrik

2016-06-01

A new certified reference material for quality control of nanoparticle size analysis methods has been developed and produced by the Institute for Reference Materials and Measurements of the European Commission's Joint Research Centre. The material, ERM-FD102, consists of an aqueous suspension of a mixture of silica nanoparticle populations of distinct particle size and origin. The characterisation relied on an interlaboratory comparison study in which 30 laboratories of demonstrated competence participated with a variety of techniques for particle size analysis. After scrutinising the received datasets, certified and indicative values for different method-defined equivalent diameters that are specific for dynamic light scattering (DLS), centrifugal liquid sedimentation (CLS), scanning and transmission electron microscopy (SEM and TEM), atomic force microscopy (AFM), particle tracking analysis (PTA) and asymmetrical-flow field-flow fractionation (AF4) were assigned. The value assignment was a particular challenge because metrological concepts were not always interpreted uniformly across all participating laboratories. This paper presents the main elements and results of the ERM-FD102 characterisation study and discusses in particular the key issues of measurand definition and the estimation of measurement uncertainty.

Rapid population divergence in thermal reaction norms for an invading species: breaking the temperature-size rule.

PubMed

Kingsolver, J G; Massie, K R; Ragland, G J; Smith, M H

2007-05-01

The temperature-size rule is a common pattern of phenotypic plasticity in which higher temperature during development results in a smaller adult body size (i.e. a thermal reaction norm with negative slope). Examples and exceptions to the rule are known in multiple groups of organisms, but rapid population differentiation in the temperature-size rule has not been explored. Here we examine the genetic and parental contributions to population differentiation in thermal reaction norms for size, development time and survival in the Cabbage White Butterfly Pieris rapae, for two geographical populations that have likely diverged within the past 150 years. We used split-sibship experiments with two temperature treatments (warm and cool) for P. rapae from Chapel Hill, NC, and from Seattle, WA. Mixed-effect model analyses demonstrate significant genetic differences between NC and WA populations for adult size and for thermal reaction norms for size. Mean adult mass was 12-24% greater in NC than in WA populations for both temperature treatments; mean size was unaffected or decreased with temperature (the temperature-size rule) for the WA population, but size increased with temperature for the NC population. Our study shows that the temperature-size rule and related thermal reaction norms can evolve rapidly within species in natural field conditions. Rapid evolutionary divergence argues against the existence of a simple, general mechanistic constraint as the underlying cause of the temperature-size rule.

Phenotypic characterization and genealogical tracing in an Afrikaner schizophrenia database.

PubMed

Karayiorgou, Maria; Torrington, Marie; Abecasis, Gonçalo R; Pretorius, Herman; Robertson, Brian; Kaliski, Sean; Lay, Stephen; Sobin, Christina; Möller, Natalie; Lundy, S Laura; Blundell, Maude L; Gogos, Joseph A; Roos, J Louw

2004-01-01

Founder populations hold tremendous promise for mapping genes for complex traits, as they offer less genetic and environmental heterogeneity and greater potential for genealogical research. Not all founder populations are equally valuable, however. The Afrikaner population meets several criteria that make it an ideal population for mapping complex traits, including founding by a small number of initial founders that likely allowed for a relatively restricted set of mutations and a large current population size that allows identification of a sufficient number of cases. Here, we examine the potential to conduct genealogical research in this population and present initial results indicating that accurate genealogical tracing for up to 17 generations is feasible. We also examine the clinical similarities of schizophrenia cases diagnosed in South Africa and those diagnosed in other, heterogeneous populations, specifically the US. We find that, with regard to basic sample descriptors and cardinal symptoms of disease, the two populations are equivalent. It is, therefore, likely that results from our genetic study of schizophrenia will be applicable to other populations. Based on the results presented here, the history and current size of the population, as well as our previous analysis addressing the extent of background linkage disequilibrium (LD) in the Afrikaners, we conclude that the Afrikaner population is likely an appropriate founder population to map genes for schizophrenia using both linkage and LD approaches. Copyright 2003 Wiley-Liss, Inc.

Mitochondrial Variation among the Aymara and the Signatures of Population Expansion in the Central Andes

PubMed Central

BATAI, KEN; WILLIAMS, SLOAN R.

2015-01-01

Objectives The exploitation of marine resources and intensive agriculture led to a marked population increase early in central Andean prehistory. Constant historic and prehistoric population movements also characterize this region. These features undoubtedly affected regional genetic variation, but the exact nature of these effects remains uncertain. Methods Mitochondrial DNA (mtDNA) hypervariable region I sequence variation in 61 Aymara individuals from La Paz, Bolivia, was analyzed and compared to sequences from 47 other South American populations to test hypotheses of whether increased female effective population size and gene flow influenced the mtDNA variation among central Andean populations. Results The Aymara and Quechua were genetically diverse showing evidence of population expansion and large effective population size, and a demographic expansion model fits the mtDNA variation found among central Andean populations well. Estimated migration rates and the results of AMOVA and multidimensional scaling analysis suggest that female gene flow was also an important factor, influencing genetic variation among the central Andeans as well as lowland populations from western South America. mtDNA variation in south central Andes correlated better with geographic proximity than with language, and fit a population continuity model. Conclusion The mtDNA data suggests that the central Andeans experienced population expansion, most likely because of rapid demographic expansion after introduction of intensive agriculture, but roles of female gene flow need to be further explored. PMID:24449040

Association of computed tomography-derived left ventricular size with major cardiovascular events in the general population: the Heinz Nixdorf recall study.

PubMed

Dykun, Iryna; Geisel, Marie H; Kälsch, Hagen; Lehmann, Nils; Bauer, Marcus; Moebus, Susanne; Jöckel, Karl-Heinz; Möhlenkamp, Stefan; Erbel, Raimund; Mahabadi, Amir A

2015-05-01

To investigate the relationship between LV size as determined by non-contrast enhanced cardiac CT with incident cardiovascular disease in the general population free of clinical cardiovascular disease. LV axial area was quantified from non-contrast CT in axial, end-diastolic images at a mid-ventricular slice in participants from the population-based Heinz Nixdorf recall study, free of cardiovascular disease (n=3926, 59±8years, 53%female). LV size index (LVI) was defined as the quotient of LV area and body surface area. Major CV events (coronary events, stroke, CV death) were assessed during follow-up. Association of LVI with events was assessed using Cox regression analysis in unadjusted and multivariable adjusted models. During 8.0±1.5years of follow-up, 219 subjects developed a major CV event. Those with events had larger LVI at baseline (2258±352 vs. 2149±276 mm2/m2, p<0.0001). In univariate analysis, increase of LVI by 1 standard deviation was associated with 40% higher risk of events (HR(95%CI):1.41(1.26-1.59), p<0.0001). Associations remained statistically significant after adjustment for CV risk factors (1.24(1.10-1.40), p=0.0007) and when further adjusting for CAC (1.21(1.07-1.37), p=0.003). There was a trend towards stronger association for subjects with low CAC-score (CAC<100:1.41(1.16-1.71), p=0.0005, CAC≥100:1.24(1.06-1.44), p=0.006) in univariate analysis which persisted after multivariable adjustment (CAC<100: 1.41(1.14-1.73), p=0.001, CAC≥100: 1.12(0.96-1.31), p=0.16). CT-derived LV size is associated with incident major CV events independent of traditional risk factors and CAC-score in a population-based cohort and may improve the prediction of hard events especially in subjects with low CAC-scores. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Plasminogen activator inhibitor-1 4G/5G gene polymorphism and coronary artery disease in the Chinese Han population: a meta-analysis.

PubMed

Li, Yan-yan

2012-01-01

The polymorphism of plasminogen activator inhibitor-1 (PAI-1) 4G/5G gene has been indicated to be correlated with coronary artery disease (CAD) susceptibility, but study results are still debatable. The present meta-analysis was performed to investigate the association between PAI-1 4G/5G gene polymorphism and CAD in the Chinese Han population. A total of 879 CAD patients and 628 controls from eight separate studies were involved. The pooled odds ratio (OR) for the distribution of the 4G allele frequency of PAI-1 4G/5G gene and its corresponding 95% confidence interval (CI) was assessed by the random effect model. The distribution of the 4 G allele frequency was 0.61 for the CAD group and 0.51 for the control group. The association between PAI-1 4G/5G gene polymorphism and CAD in the Chinese Han population was significant under an allelic genetic model (OR = 1.70, 95% CI = 1.18 to 2.44, P = 0.004). The heterogeneity test was also significant (P<0.0001). Meta-regression was performed to explore the heterogeneity source. Among the confounding factors, the heterogeneity could be explained by the publication year (P = 0.017), study region (P = 0.014), control group sample size (P = 0.011), total sample size (P = 0.011), and ratio of the case to the control group sample size (RR) (P = 0.019). In a stratified analysis by the total sample size, significantly increased risk was only detected in subgroup 2 under an allelic genetic model (OR = 1.93, 95% CI = 1.09 to 3.35, P = 0.02). In the Chinese Han population, PAI-1 4G/5G gene polymorphism was implied to be associated with increased CAD risk. Carriers of the 4G allele of the PAI-1 4G/5G gene might predispose to CAD.

Plasminogen Activator Inhibitor-1 4G/5G Gene Polymorphism and Coronary Artery Disease in the Chinese Han Population: A Meta-Analysis

PubMed Central

Li, Yan-yan

2012-01-01

Background The polymorphism of plasminogen activator inhibitor-1 (PAI-1) 4G/5G gene has been indicated to be correlated with coronary artery disease (CAD) susceptibility, but study results are still debatable. Objective and Methods The present meta-analysis was performed to investigate the association between PAI-1 4G/5G gene polymorphism and CAD in the Chinese Han population. A total of 879 CAD patients and 628 controls from eight separate studies were involved. The pooled odds ratio (OR) for the distribution of the 4G allele frequency of PAI-1 4G/5G gene and its corresponding 95% confidence interval (CI) was assessed by the random effect model. Results The distribution of the 4 G allele frequency was 0.61 for the CAD group and 0.51 for the control group. The association between PAI-1 4G/5G gene polymorphism and CAD in the Chinese Han population was significant under an allelic genetic model (OR = 1.70, 95% CI = 1.18 to 2.44, P = 0.004). The heterogeneity test was also significant (P<0.0001). Meta-regression was performed to explore the heterogeneity source. Among the confounding factors, the heterogeneity could be explained by the publication year (P = 0.017), study region (P = 0.014), control group sample size (P = 0.011), total sample size (P = 0.011), and ratio of the case to the control group sample size (RR) (P = 0.019). In a stratified analysis by the total sample size, significantly increased risk was only detected in subgroup 2 under an allelic genetic model (OR = 1.93, 95% CI = 1.09 to 3.35, P = 0.02). Conclusions In the Chinese Han population, PAI-1 4G/5G gene polymorphism was implied to be associated with increased CAD risk. Carriers of the 4G allele of the PAI-1 4G/5G gene might predispose to CAD. PMID:22496752

Investigating the effect of chemical stress and resource ...

EPA Pesticide Factsheets

Modeling exposure and recovery of fish and wildlife populations after stressor mitigation serves as a basis for evaluating population status and remediation success. The Atlantic killifish (Fundulus heteroclitus) is an important and well-studied model organism for understanding the effects of pollutants and other stressors in estuarine and marine ecosystems. Herein, we develop a density dependent matrix population model for Atlantic killifish that analyzes both size-structure and age class-structure of the population so that we could readily incorporate output from a dynamic energy budget (DEB) model currently under development. This population modeling approach emphasizes application in conjunction with field monitoring efforts (e.g., through effects-based monitoring programs) and/or laboratory analysis to link effects due to chemical stress to adverse outcomes in whole organisms and populations. We applied the model using data for killifish exposed to dioxin-like compounds, taken from a previously published study. Specifically, the model was used to investigate population trajectories for Atlantic killifish with dietary exposures to 112, 296, and 875 pg/g of dioxin with effects on fertility and survival rates. All effects were expressed relative to control fish. Further, the population model was employed to examine age and size distributions of a population exposed to resource limitation in addition to chemical stress. For each dietary exposure concentration o

Geostatistical analysis of disease data: accounting for spatial support and population density in the isopleth mapping of cancer mortality risk using area-to-point Poisson kriging

PubMed Central

Goovaerts, Pierre

2006-01-01

Background Geostatistical techniques that account for spatially varying population sizes and spatial patterns in the filtering of choropleth maps of cancer mortality were recently developed. Their implementation was facilitated by the initial assumption that all geographical units are the same size and shape, which allowed the use of geographic centroids in semivariogram estimation and kriging. Another implicit assumption was that the population at risk is uniformly distributed within each unit. This paper presents a generalization of Poisson kriging whereby the size and shape of administrative units, as well as the population density, is incorporated into the filtering of noisy mortality rates and the creation of isopleth risk maps. An innovative procedure to infer the point-support semivariogram of the risk from aggregated rates (i.e. areal data) is also proposed. Results The novel methodology is applied to age-adjusted lung and cervix cancer mortality rates recorded for white females in two contrasted county geographies: 1) state of Indiana that consists of 92 counties of fairly similar size and shape, and 2) four states in the Western US (Arizona, California, Nevada and Utah) forming a set of 118 counties that are vastly different geographical units. Area-to-point (ATP) Poisson kriging produces risk surfaces that are less smooth than the maps created by a naïve point kriging of empirical Bayesian smoothed rates. The coherence constraint of ATP kriging also ensures that the population-weighted average of risk estimates within each geographical unit equals the areal data for this unit. Simulation studies showed that the new approach yields more accurate predictions and confidence intervals than point kriging of areal data where all counties are simply collapsed into their respective polygon centroids. Its benefit over point kriging increases as the county geography becomes more heterogeneous. Conclusion A major limitation of choropleth maps is the common biased visual perception that larger rural and sparsely populated areas are of greater importance. The approach presented in this paper allows the continuous mapping of mortality risk, while accounting locally for population density and areal data through the coherence constraint. This form of Poisson kriging will facilitate the analysis of relationships between health data and putative covariates that are typically measured over different spatial supports. PMID:17137504

Whole-Genome Resequencing of Experimental Populations Reveals Polygenic Basis of Egg-Size Variation in Drosophila melanogaster.

PubMed

Jha, Aashish R; Miles, Cecelia M; Lippert, Nodia R; Brown, Christopher D; White, Kevin P; Kreitman, Martin

2015-10-01

Complete genome resequencing of populations holds great promise in deconstructing complex polygenic traits to elucidate molecular and developmental mechanisms of adaptation. Egg size is a classic adaptive trait in insects, birds, and other taxa, but its highly polygenic architecture has prevented high-resolution genetic analysis. We used replicated experimental evolution in Drosophila melanogaster and whole-genome sequencing to identify consistent signatures of polygenic egg-size adaptation. A generalized linear-mixed model revealed reproducible allele frequency differences between replicated experimental populations selected for large and small egg volumes at approximately 4,000 single nucleotide polymorphisms (SNPs). Several hundred distinct genomic regions contain clusters of these SNPs and have lower heterozygosity than the genomic background, consistent with selection acting on polymorphisms in these regions. These SNPs are also enriched among genes expressed in Drosophila ovaries and many of these genes have well-defined functions in Drosophila oogenesis. Additional genes regulating egg development, growth, and cell size show evidence of directional selection as genes regulating these biological processes are enriched for highly differentiated SNPs. Genetic crosses performed with a subset of candidate genes demonstrated that these genes influence egg size, at least in the large genetic background. These findings confirm the highly polygenic architecture of this adaptive trait, and suggest the involvement of many novel candidate genes in regulating egg size. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Household demographic determinants of Ebola epidemic risk.

PubMed

Adams, Ben

2016-03-07

A salient characteristic of Ebola, and some other infectious diseases such as Tuberculosis, is intense transmission among small groups of cohabitants and relatively limited indiscriminate transmission in the wider population. Here we consider a mathematical model for an Ebola epidemic in a population structured into households of equal size. We show that household size, a fundamental demographic unit, is a critical factor that determines the vulnerability of a community to epidemics, and the effort required to control them. Our analysis is based on the household reproduction number, but we also consider the basic reproduction number, intrinsic growth rate and final epidemic size. We show that, when other epidemiological parameters are kept the same, all of these quantifications of epidemic growth and size are increased by larger households and more intense within-household transmission. We go on to model epidemic control by case detection and isolation followed by household quarantine. We show that, if household quarantine is ineffective, the critical probability with which cases must be detected to halt an epidemic increases significantly with each increment in household size and may be a very challenging target for communities composed of large households. Effective quarantine may, however, mitigate the detrimental impact of large household sizes. We conclude that communities composed of large households are fundamentally more vulnerable to epidemics of infectious diseases primarily transmitted by close contact, and any assessment of control strategies for these epidemics should take into account the demographic structure of the population. Copyright © 2015 Elsevier Ltd. All rights reserved.

Localised estimates and spatial mapping of poverty incidence in the state of Bihar in India—An application of small area estimation techniques

PubMed Central

Aditya, Kaustav; Sud, U. C.

2018-01-01

Poverty affects many people, but the ramifications and impacts affect all aspects of society. Information about the incidence of poverty is therefore an important parameter of the population for policy analysis and decision making. In order to provide specific, targeted solutions when addressing poverty disadvantage small area statistics are needed. Surveys are typically designed and planned to produce reliable estimates of population characteristics of interest mainly at higher geographic area such as national and state level. Sample sizes are usually not large enough to provide reliable estimates for disaggregated analysis. In many instances estimates are required for areas of the population for which the survey providing the data was unplanned. Then, for areas with small sample sizes, direct survey estimation of population characteristics based only on the data available from the particular area tends to be unreliable. This paper describes an application of small area estimation (SAE) approach to improve the precision of estimates of poverty incidence at district level in the State of Bihar in India by linking data from the Household Consumer Expenditure Survey 2011–12 of NSSO and the Population Census 2011. The results show that the district level estimates generated by SAE method are more precise and representative. In contrast, the direct survey estimates based on survey data alone are less stable. PMID:29879202

Localised estimates and spatial mapping of poverty incidence in the state of Bihar in India-An application of small area estimation techniques.

PubMed

Chandra, Hukum; Aditya, Kaustav; Sud, U C

2018-01-01

Poverty affects many people, but the ramifications and impacts affect all aspects of society. Information about the incidence of poverty is therefore an important parameter of the population for policy analysis and decision making. In order to provide specific, targeted solutions when addressing poverty disadvantage small area statistics are needed. Surveys are typically designed and planned to produce reliable estimates of population characteristics of interest mainly at higher geographic area such as national and state level. Sample sizes are usually not large enough to provide reliable estimates for disaggregated analysis. In many instances estimates are required for areas of the population for which the survey providing the data was unplanned. Then, for areas with small sample sizes, direct survey estimation of population characteristics based only on the data available from the particular area tends to be unreliable. This paper describes an application of small area estimation (SAE) approach to improve the precision of estimates of poverty incidence at district level in the State of Bihar in India by linking data from the Household Consumer Expenditure Survey 2011-12 of NSSO and the Population Census 2011. The results show that the district level estimates generated by SAE method are more precise and representative. In contrast, the direct survey estimates based on survey data alone are less stable.

Dietary assessment in minority ethnic groups: a systematic review of instruments for portion-size estimation in the United Kingdom

PubMed Central

Almiron-Roig, Eva; Aitken, Amanda; Galloway, Catherine

2017-01-01

Context: Dietary assessment in minority ethnic groups is critical for surveillance programs and for implementing effective interventions. A major challenge is the accurate estimation of portion sizes for traditional foods and dishes. Objective: The aim of this systematic review was to assess records published up to 2014 describing a portion-size estimation element (PSEE) applicable to the dietary assessment of UK-residing ethnic minorities. Data sources, selection, and extraction: Electronic databases, internet sites, and theses repositories were searched, generating 5683 titles, from which 57 eligible full-text records were reviewed. Data analysis: Forty-two publications about minority ethnic groups (n = 20) or autochthonous populations (n = 22) were included. The most common PSEEs (47%) were combination tools (eg, food models and portion-size lists), followed by portion-size lists in questionnaires/guides (19%) and image-based and volumetric tools (17% each). Only 17% of PSEEs had been validated against weighed data. Conclusions: When developing ethnic-specific dietary assessment tools, it is important to consider customary portion sizes by sex and age, traditional household utensil usage, and population literacy levels. Combining multiple PSEEs may increase accuracy, but such methods require validation. PMID:28340101

Statistical power and effect sizes of depression research in Japan.

PubMed

Okumura, Yasuyuki; Sakamoto, Shinji

2011-06-01

Few studies have been conducted on the rationales for using interpretive guidelines for effect size, and most of the previous statistical power surveys have covered broad research domains. The present study aimed to estimate the statistical power and to obtain realistic target effect sizes of depression research in Japan. We systematically reviewed 18 leading journals of psychiatry and psychology in Japan and identified 974 depression studies that were mentioned in 935 articles published between 1990 and 2006. In 392 studies, logistic regression analyses revealed that using clinical populations was independently associated with being a statistical power of <0.80 (odds ratio 5.9, 95% confidence interval 2.9-12.0) and of <0.50 (odds ratio 4.9, 95% confidence interval 2.3-10.5). Of the studies using clinical populations, 80% did not achieve a power of 0.80 or more, and 44% did not achieve a power of 0.50 or more to detect the medium population effect sizes. A predictive model for the proportion of variance explained was developed using a linear mixed-effects model. The model was then used to obtain realistic target effect sizes in defined study characteristics. In the face of a real difference or correlation in population, many depression researchers are less likely to give a valid result than simply tossing a coin. It is important to educate depression researchers in order to enable them to conduct an a priori power analysis. © 2011 The Authors. Psychiatry and Clinical Neurosciences © 2011 Japanese Society of Psychiatry and Neurology.

Estimating population sizes for elusive animals: the forest elephants of Kakum National Park, Ghana.

PubMed

Eggert, L S; Eggert, J A; Woodruff, D S

2003-06-01

African forest elephants are difficult to observe in the dense vegetation, and previous studies have relied upon indirect methods to estimate population sizes. Using multilocus genotyping of noninvasively collected samples, we performed a genetic survey of the forest elephant population at Kakum National Park, Ghana. We estimated population size, sex ratio and genetic variability from our data, then combined this information with field observations to divide the population into age groups. Our population size estimate was very close to that obtained using dung counts, the most commonly used indirect method of estimating the population sizes of forest elephant populations. As their habitat is fragmented by expanding human populations, management will be increasingly important to the persistence of forest elephant populations. The data that can be obtained from noninvasively collected samples will help managers plan for the conservation of this keystone species.

Imputation-Based Meta-Analysis of Severe Malaria in Three African Populations

PubMed Central

Band, Gavin; Le, Quang Si; Jostins, Luke; Pirinen, Matti; Kivinen, Katja; Jallow, Muminatou; Sisay-Joof, Fatoumatta; Bojang, Kalifa; Pinder, Margaret; Sirugo, Giorgio; Conway, David J.; Nyirongo, Vysaul; Kachala, David; Molyneux, Malcolm; Taylor, Terrie; Ndila, Carolyne; Peshu, Norbert; Marsh, Kevin; Williams, Thomas N.; Alcock, Daniel; Andrews, Robert; Edkins, Sarah; Gray, Emma; Hubbart, Christina; Jeffreys, Anna; Rowlands, Kate; Schuldt, Kathrin; Clark, Taane G.; Small, Kerrin S.; Teo, Yik Ying; Kwiatkowski, Dominic P.; Rockett, Kirk A.; Barrett, Jeffrey C.; Spencer, Chris C. A.

2013-01-01

Combining data from genome-wide association studies (GWAS) conducted at different locations, using genotype imputation and fixed-effects meta-analysis, has been a powerful approach for dissecting complex disease genetics in populations of European ancestry. Here we investigate the feasibility of applying the same approach in Africa, where genetic diversity, both within and between populations, is far more extensive. We analyse genome-wide data from approximately 5,000 individuals with severe malaria and 7,000 population controls from three different locations in Africa. Our results show that the standard approach is well powered to detect known malaria susceptibility loci when sample sizes are large, and that modern methods for association analysis can control the potential confounding effects of population structure. We show that pattern of association around the haemoglobin S allele differs substantially across populations due to differences in haplotype structure. Motivated by these observations we consider new approaches to association analysis that might prove valuable for multicentre GWAS in Africa: we relax the assumptions of SNP–based fixed effect analysis; we apply Bayesian approaches to allow for heterogeneity in the effect of an allele on risk across studies; and we introduce a region-based test to allow for heterogeneity in the location of causal alleles. PMID:23717212

Noninvasive methods for monitoring bear population trends

USGS Publications Warehouse

Kendall, Katherine

2010-01-01

The U.S. Geological Survey began a grizzly bear research project in 2009 in the Northern Continental Divide Ecosystem (NCDE) of northwestern Montana. This work uses hair collection and DNA analysis methods similar to those used in the 2004 Northern Divide Grizzly Bear Project. However, instead of producing a snapshot of population size, the objectives of this new work are to estimate population growth rates by collecting hair at natural bear rubs along trails, roads, and fence and power lines. This approach holds promise of providing reliable estimates of population trends in an efficient, cost-effective, and unobtrusive way.

East Greenland and Barents Sea polar bears (Ursus maritimus): adaptive variation between two populations using skull morphometrics as an indicator of environmental and genetic differences.

PubMed

Pertoldi, Cino; Sonne, Christian; Wiig, Øystein; Baagøe, Hans J; Loeschcke, Volker; Bechshøft, Thea Østergaard

2012-06-01

A morphometric study was conducted on four skull traits of 37 male and 18 female adult East Greenland polar bears (Ursus maritimus) collected 1892-1968, and on 54 male and 44 female adult Barents Sea polar bears collected 1950-1969. The aim was to compare differences in size and shape of the bear skulls using a multivariate approach, characterizing the variation between the two populations using morphometric traits as an indicator of environmental and genetic differences. Mixture analysis testing for geographic differentiation within each population revealed three clusters for Barents Sea males and three clusters for Barents Sea females. East Greenland consisted of one female and one male cluster. A principal component analysis (PCA) conducted on the clusters defined by the mixture analysis, showed that East Greenland and Barents Sea polar bear populations overlapped to a large degree, especially with regards to females. Multivariate analyses of variance (MANOVA) showed no significant differences in morphometric means between the two populations, but differences were detected between clusters from each respective geographic locality. To estimate the importance of genetics and environment in the morphometric differences between the bears, a PCA was performed on the covariance matrix derived from the skull measurements. Skull trait size (PC1) explained approx. 80% of the morphometric variation, whereas shape (PC2) defined approx. 15%, indicating some genetic differentiation. Hence, both environmental and genetic factors seem to have contributed to the observed skull differences between the two populations. Overall, results indicate that many Barents Sea polar bears are morphometrically similar to the East Greenland ones, suggesting an exchange of individuals between the two populations. Furthermore, a subpopulation structure in the Barents Sea population was also indicated from the present analyses, which should be considered with regards to future management decisions. © 2012 The Authors.

Determination of the optimal sample size for a clinical trial accounting for the population size.

PubMed

Stallard, Nigel; Miller, Frank; Day, Simon; Hee, Siew Wan; Madan, Jason; Zohar, Sarah; Posch, Martin

2017-07-01

The problem of choosing a sample size for a clinical trial is a very common one. In some settings, such as rare diseases or other small populations, the large sample sizes usually associated with the standard frequentist approach may be infeasible, suggesting that the sample size chosen should reflect the size of the population under consideration. Incorporation of the population size is possible in a decision-theoretic approach either explicitly by assuming that the population size is fixed and known, or implicitly through geometric discounting of the gain from future patients reflecting the expected population size. This paper develops such approaches. Building on previous work, an asymptotic expression is derived for the sample size for single and two-arm clinical trials in the general case of a clinical trial with a primary endpoint with a distribution of one parameter exponential family form that optimizes a utility function that quantifies the cost and gain per patient as a continuous function of this parameter. It is shown that as the size of the population, N, or expected size, N∗ in the case of geometric discounting, becomes large, the optimal trial size is O(N1/2) or O(N∗1/2). The sample size obtained from the asymptotic expression is also compared with the exact optimal sample size in examples with responses with Bernoulli and Poisson distributions, showing that the asymptotic approximations can also be reasonable in relatively small sample sizes. © 2016 The Author. Biometrical Journal published by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Rapid Increase in Genome Size as a Consequence of Transposable Element Hyperactivity in Wood-White (Leptidea) Butterflies

PubMed Central

Talla, Venkat; Suh, Alexander; Kalsoom, Faheema; Dincă, Vlad; Vila, Roger; Friberg, Magne; Wiklund, Christer

2017-01-01

Abstract Characterizing and quantifying genome size variation among organisms and understanding if genome size evolves as a consequence of adaptive or stochastic processes have been long-standing goals in evolutionary biology. Here, we investigate genome size variation and association with transposable elements (TEs) across lepidopteran lineages using a novel genome assembly of the common wood-white (Leptidea sinapis) and population re-sequencing data from both L. sinapis and the closely related L. reali and L. juvernica together with 12 previously available lepidopteran genome assemblies. A phylogenetic analysis confirms established relationships among species, but identifies previously unknown intraspecific structure within Leptidea lineages. The genome assembly of L. sinapis is one of the largest of any lepidopteran taxon so far (643 Mb) and genome size is correlated with abundance of TEs, both in Lepidoptera in general and within Leptidea where L. juvernica from Kazakhstan has considerably larger genome size than any other Leptidea population. Specific TE subclasses have been active in different Lepidoptera lineages with a pronounced expansion of predominantly LINEs, DNA elements, and unclassified TEs in the Leptidea lineage after the split from other Pieridae. The rate of genome expansion in Leptidea in general has been in the range of four Mb/Million year (My), with an increase in a particular L. juvernica population to 72 Mb/My. The considerable differences in accumulation rates of specific TE classes in different lineages indicate that TE activity plays a major role in genome size evolution in butterflies and moths. PMID:28981642

Phenotypic plasticity in clutch size regulation among populations of a potential invasive fruit fly from environments that vary in host heterogeneity and isolation.

PubMed

Aluja, M; Birke, A; Díaz-Fleischer, F; Rull, J

2018-05-21

Phenotypic plasticity is thought to evolve in response to environmental unpredictability and can shield genotypes from selection. However, selection can also act on plastic traits. Egg-laying behaviour, including clutch size regulation, is a plastic behavioural trait among tephritid fruit flies. We compared plasticity in clutch size regulation among females of Anastrepha ludens populations stemming from environments that differed in the degree of predictability in egg-laying opportunities. Clutch size regulation in response to hosts of different sizes was compared among flies from (a) a wild, highly isolated population, (b) a wild population that switches seasonally from a small wild host fruit that varies greatly in abundance to an abundant large-sized commercial host, and (c) a laboratory population. Flies from all three populations adjusted clutch number and size according to host size. However, flies from the heterogeneous wild environment were more plastic in adjusting clutch size than flies from agricultural settings that also laid fewer eggs; yet both populations were more plastic in adjusting clutch size in line with host size when compared with laboratory females. When wild and orchard females encountered the largest host, clutch size was extremely variable and egg regulation did not follow the same trend. Heterogeneity in host availability in space and time appears to be as important as seasonal variation in host size in maintaining plastic clutch size regulation behaviour. In stable environments, there was a clear reduction in the plasticity of these traits.

A Class of Population Covariance Matrices in the Bootstrap Approach to Covariance Structure Analysis

ERIC Educational Resources Information Center

Yuan, Ke-Hai; Hayashi, Kentaro; Yanagihara, Hirokazu

2007-01-01

Model evaluation in covariance structure analysis is critical before the results can be trusted. Due to finite sample sizes and unknown distributions of real data, existing conclusions regarding a particular statistic may not be applicable in practice. The bootstrap procedure automatically takes care of the unknown distribution and, for a given…

Lipoprotein lipase S447X variant associated with VLDL, LDL and HDL diameter clustering in the MetS

USDA-ARS?s Scientific Manuscript database

Previous analysis clustered 1,238 individuals from the general population Genetics of Lipid Lowering Drugs Network (GOLDN) study by the size of their fasting very low-density, low-density and high-density lipoproteins (VLDL, LDL, HDL) using latent class analysis. From two of the eight identified gro...

Random-growth urban model with geographical fitness

NASA Astrophysics Data System (ADS)

Kii, Masanobu; Akimoto, Keigo; Doi, Kenji

2012-12-01

This paper formulates a random-growth urban model with a notion of geographical fitness. Using techniques of complex-network theory, we study our system as a type of preferential-attachment model with fitness, and we analyze its macro behavior to clarify the properties of the city-size distributions it predicts. First, restricting the geographical fitness to take positive values and using a continuum approach, we show that the city-size distributions predicted by our model asymptotically approach Pareto distributions with coefficients greater than unity. Then, allowing the geographical fitness to take negative values, we perform local coefficient analysis to show that the predicted city-size distributions can deviate from Pareto distributions, as is often observed in actual city-size distributions. As a result, the model we propose can generate a generic class of city-size distributions, including but not limited to Pareto distributions. For applications to city-population projections, our simple model requires randomness only when new cities are created, not during their subsequent growth. This property leads to smooth trajectories of city population growth, in contrast to other models using Gibrat’s law. In addition, a discrete form of our dynamical equations can be used to estimate past city populations based on present-day data; this fact allows quantitative assessment of the performance of our model. Further study is needed to determine appropriate formulas for the geographical fitness.

Analysis of intraspecific seed diversity in Astragalus aquilanus (Fabaceae), an endemic species of Central Apennine.

PubMed

Di Cecco, V; Di Musciano, M; D'Archivio, A A; Frattaroli, A R; Di Martino, L

2018-05-20

This work aims to study seeds of the endemic species Astragalus aquilanus from four different populations of central Italy. We investigated seed morpho-colorimetric features (shape and size) and chemical differences (through infrared spectroscopy) among populations and between dark and light seeds. Seed morpho-colorimetric quantitative variables, describing shape, size and colour traits, were measured using image analysis techniques. Fourier transform infrared (FT-IR) spectroscopy was used to attempt seed chemical characterisation. The measured data were analysed by step-wise linear discriminant analysis (LDA). Moreover, we analysed the correlation between the four most important traits and six climatic variables extracted from WorldClim 2.0. The LDA on seeds traits shows clear differentiation of the four populations, which can be attributed to different chemical composition, as confirmed by Wilk's lambda test (P < 0.001). A strong correlation between morphometric traits and temperature (annual mean temperature, mean temperature of the warmest and coolest quarter), colorimetric traits and precipitation (annual precipitation, precipitation of wettest and driest quarter) was observed. The characterisation of A. aquilanus seeds shows large intraspecific plasticity both in morpho-colorimetric and chemical composition. These results confirm the strong relationship between the type of seed produced and the climatic variables. © 2018 German Society for Plant Sciences and The Royal Botanical Society of the Netherlands.

Spatial extent of analysis influences observed patterns of population genetic structure in a widespread darter species (Percidae)

USGS Publications Warehouse

Argentina, Jane E.; Angermeier, Paul L.; Hallerman, Eric M.; Welsh, Stuart A.

2018-01-01

Connectivity among stream fish populations allows for exchange of genetic material and helps maintain genetic diversity, adaptive potential and population stability over time. Changes in species demographics and population connectivity have the potential to permanently alter the genetic patterns of stream fish, although these changes through space and time are variable and understudied in small‐bodied freshwater fish.As a spatially widespread, common species of benthic freshwater fish, the variegate darter (Etheostoma variatum) is a model species for documenting how patterns of genetic structure and diversity respond to increasing isolation due to large dams and how scale of study may shape our understanding of these patterns. We sampled variegate darters from 34 sites across their range in the North American Ohio River basin and examined how patterns of genetic structure and diversity within and between populations responded to historical population changes and dams within and between populations.Spatial scale and configuration of genetic structure varied across the eight identified populations, from tributaries within a watershed, to a single watershed, to multiple watersheds that encompass Ohio River mainstem habitats. This multiwatershed pattern of population structuring suggests genetic dispersal across large distances was and may continue to be common, although some populations remain isolated despite no apparent structural dispersal barriers. Populations with low effective population sizes and evidence of past population bottlenecks showed low allelic richness, but diversity patterns were not related to watershed size, a surrogate for habitat availability. Pairwise genetic differentiation (FST) increased with fluvial distance and was related to both historic and contemporary processes. Genetic diversity changes were influenced by underlying population size and stability, and while instream barriers were not strong determinants of genetic structuring or loss of genetic diversity, they reduce population connectivity and may impact long‐term population persistence.The broad spatial scale of this study demonstrated the large spatial extent of some variegate darter populations and indicated that dispersal is more extensive than expected given the movement patterns typically observed for small‐bodied, benthic fish. Dam impacts depended on underlying population size and stability, with larger populations more resilient to genetic drift and allelic richness loss than smaller populations.Other darters that inhabit large river habitats may show similar patterns in landscape‐scale studies, and large river barriers may impact populations of small‐bodied fish more than previously expected. Estimation of dispersal rates and behaviours is critical to conservation of imperilled riverine species such as darters.

Shape variation in the human pelvis and limb skeleton: Implications for obstetric adaptation.

PubMed

Kurki, Helen K; Decrausaz, Sarah-Louise

2016-04-01

Under the obstetrical dilemma (OD) hypothesis, selection acts on the human female pelvis to ensure a sufficiently sized obstetric canal for birthing a large-brained, broad shouldered neonate, while bipedal locomotion selects for a narrower and smaller pelvis. Despite this female-specific stabilizing selection, variability of linear dimensions of the pelvic canal and overall size are not reduced in females, suggesting shape may instead be variable among females of a population. Female canal shape has been shown to vary among populations, while male canal shape does not. Within this context, we examine within-population canal shape variation in comparison with that of noncanal aspects of the pelvis and the limbs. Nine skeletal samples (total female n = 101, male n = 117) representing diverse body sizes and shapes were included. Principal components analysis was applied to size-adjusted variables of each skeletal region. A multivariate variance was calculated using the weighted PC scores for all components in each model and F-ratios used to assess differences in within-population variances between sexes and skeletal regions. Within both sexes, multivariate canal shape variance is significantly greater than noncanal pelvis and limb variances, while limb variance is greater than noncanal pelvis variance in some populations. Multivariate shape variation is not consistently different between the sexes in any of the skeletal regions. Diverse selective pressures, including obstetrics, locomotion, load carrying, and others may act on canal shape, as well as genetic drift and plasticity, thus increasing variation in morphospace while protecting obstetric sufficiency. © 2015 Wiley Periodicals, Inc.

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.

The minimum area requirements (MAR) for giant panda: an empirical study.

PubMed

Qing, Jing; Yang, Zhisong; He, Ke; Zhang, Zejun; Gu, Xiaodong; Yang, Xuyu; Zhang, Wen; Yang, Biao; Qi, Dunwu; Dai, Qiang

2016-12-08

Habitat fragmentation can reduce population viability, especially for area-sensitive species. The Minimum Area Requirements (MAR) of a population is the area required for the population's long-term persistence. In this study, the response of occupancy probability of giant pandas against habitat patch size was studied in five of the six mountain ranges inhabited by giant panda, which cover over 78% of the global distribution of giant panda habitat. The probability of giant panda occurrence was positively associated with habitat patch area, and the observed increase in occupancy probability with patch size was higher than that due to passive sampling alone. These results suggest that the giant panda is an area-sensitive species. The MAR for giant panda was estimated to be 114.7 km 2 based on analysis of its occupancy probability. Giant panda habitats appear more fragmented in the three southern mountain ranges, while they are large and more continuous in the other two. Establishing corridors among habitat patches can mitigate habitat fragmentation, but expanding habitat patch sizes is necessary in mountain ranges where fragmentation is most intensive.

Naming game with biased assimilation over adaptive networks

NASA Astrophysics Data System (ADS)

Fu, Guiyuan; Zhang, Weidong

2018-01-01

The dynamics of two-word naming game incorporating the influence of biased assimilation over adaptive network is investigated in this paper. Firstly an extended naming game with biased assimilation (NGBA) is proposed. The hearer in NGBA accepts the received information in a biased manner, where he may refuse to accept the conveyed word from the speaker with a predefined probability, if the conveyed word is different from his current memory. Secondly, the adaptive network is formulated by rewiring the links. Theoretical analysis is developed to show that the population in NGBA will eventually reach global consensus on either A or B. Numerical simulation results show that the larger strength of biased assimilation on both words, the slower convergence speed, while larger strength of biased assimilation on only one word can slightly accelerate the convergence; larger population size can make the rate of convergence slower to a large extent when it increases from a relatively small size, while such effect becomes minor when the population size is large; the behavior of adaptively reconnecting the existing links can greatly accelerate the rate of convergence especially on the sparse connected network.

Estimating effective population size from linkage disequilibrium between unlinked loci: theory and application to fruit fly outbreak populations.

PubMed

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

2013-01-01

There is a substantial literature on the use of linkage disequilibrium (LD) to estimate effective population size using unlinked loci. The Ne estimates are extremely sensitive to the sampling process, and there is currently no theory to cope with the possible biases. We derive formulae for the analysis of idealised populations mating at random with multi-allelic (microsatellite) loci. The 'Burrows composite index' is introduced in a novel way with a 'composite haplotype table'. We show that in a sample of diploid size S, the mean value of x2 or r2 from the composite haplotype table is biased by a factor of 1-1/(2S-1)2, rather than the usual factor 1+1/(2S-1) for a conventional haplotype table. But analysis of population data using these formulae leads to Ne estimates that are unrealistically low. We provide theory and simulation to show that this bias towards low Ne estimates is due to null alleles, and introduce a randomised permutation correction to compensate for the bias. We also consider the effect of introducing a within-locus disequilibrium factor to r2, and find that this factor leads to a bias in the Ne estimate. However this bias can be overcome using the same randomised permutation correction, to yield an altered r2 with lower variance than the original r2, and one that is also insensitive to null alleles. The resulting formulae are used to provide Ne estimates on 40 samples of the Queensland fruit fly, Bactrocera tryoni, from populations with widely divergent Ne expectations. Linkage relationships are known for most of the microsatellite loci in this species. We find that there is little difference in the estimated Ne values from using known unlinked loci as compared to using all loci, which is important for conservation studies where linkage relationships are unknown.

Genome-wide population structure and evolutionary history of the Frizarta dairy sheep.

PubMed

Kominakis, A; Hager-Theodorides, A L; Saridaki, A; Antonakos, G; Tsiamis, G

2017-10-01

In the present study, we used genomic data, generated with a medium density single nucleotide polymorphisms (SNP) array, to acquire more information on the population structure and evolutionary history of the synthetic Frizarta dairy sheep. First, two typical measures of linkage disequilibrium (LD) were estimated at various physical distances that were then used to make inferences on the effective population size at key past time points. Population structure was also assessed by both multidimensional scaling analysis and k-means clustering on the distance matrix obtained from the animals' genomic relationships. The Wright's fixation F ST index was also employed to assess herds' genetic homogeneity and to indirectly estimate past migration rates. The Wright's fixation F IS index and genomic inbreeding coefficients based on the genomic relationship matrix as well as on runs of homozygosity were also estimated. The Frizarta breed displays relatively low LD levels with r 2 and |D'| equal to 0.18 and 0.50, respectively, at an average inter-marker distance of 31 kb. Linkage disequilibrium decayed rapidly by distance and persisted over just a few thousand base pairs. Rate of LD decay (β) varied widely among the 26 autosomes with larger values estimated for shorter chromosomes (e.g. β=0.057, for OAR6) and smaller values for longer ones (e.g. β=0.022, for OAR2). The inferred effective population size at the beginning of the breed's formation was as high as 549, was then reduced to 463 in 1981 (end of the breed's formation) and further declined to 187, one generation ago. Multidimensional scaling analysis and k-means clustering suggested a genetically homogenous population, F ST estimates indicated relatively low genetic differentiation between herds, whereas a heat map of the animals' genomic kinship relationships revealed a stratified population, at a herd level. Estimates of genomic inbreeding coefficients suggested that most recent parental relatedness may have been a major determinant of the current effective population size. A denser than the 50k SNP panel may be more beneficial when performing genome wide association studies in the breed.

Reproductive Declines in an Endangered Seabird: Cause for Concern or Signs of Conservation Success?

PubMed Central

Schuetz, Justin

2011-01-01

Collection and analysis of demographic data play a critical role in monitoring and management of endangered taxa. I analyzed long-term clutch size and fledgling productivity data for California least tern (Sternula antillarum browni), a federally endangered subspecies that has recently become a candidate for down-listing. While the breeding population grew from approximately 1,253 to 7,241 pairs (578%) during the study period (1988–2009) both clutch size and fledgling productivity declined. Clutch size decreased by approximately 0.27 eggs (14%) from 1990–2004 then showed a moderate increase of 0.11 eggs from 2004–2009. Estimates of fledgling productivity showed a similar pattern of decline and moderate increase even after controlling for clutch size. Sea surface temperature anomalies, an index of El Niño-Southern Oscillation activity, did not influence clutch size but were associated with fledgling productivity through a non-linear relationship. Both clutch size and fledgling productivity increased with latitude, potentially indicating a gradient of life-history trade-offs. Random site effects explained little of the overall variation in clutch size (3%) or fledgling productivity (<1%) suggesting that site characteristics beyond those associated with latitude had little bearing on either measure of reproduction. Despite intensive monitoring and management, causes of variation in key demographic parameters remain poorly understood. Long-term declines in clutch size and fledgling productivity may reflect: 1) reduced food availability, 2) increased density-dependent competition, and/or 3) age-dependent reproduction coupled with a shifting population age-structure. Until the mechanisms shaping demographic parameters and population change are better understood, the success of past management and the probability of ongoing recovery will remain difficult to characterize. PMID:21559287

The Nation's Report Card: Mega-States--An Analysis of Student Performance in the Five Most Heavily Populated States in the Nation. NCES 2013-450

ERIC Educational Resources Information Center

National Center for Education Statistics, 2013

2013-01-01

California, Florida, Illinois, New York, and Texas enroll close to 40 percent of the nation's public school students. The importance of these "Mega-States" goes beyond the sheer size of their population. They now serve more than half of the nation's English language learners (ELL), as well as some of the largest concentrations of…

Models for Threat Assessment in Networks

DTIC Science & Technology

2006-09-01

Software International and Command AntiVirus . [Online]. Available: http://www.commandsoftware.com/virus/newlove.html [38] C. Ng and P. Ferrie. (2000...28 2.3 False positive trends across all population sizes for r=0.7 and m=0.1 . . . . 33 2.4 False negative trends across all population...benefits analysis is often performed to determine the list of mitigation procedures. Traditionally, risk assessment has been done in part with software

Evolutionary behaviour, trade-offs and cyclic and chaotic population dynamics.

PubMed

Hoyle, Andy; Bowers, Roger G; White, Andy

2011-05-01

Many studies of the evolution of life-history traits assume that the underlying population dynamical attractor is stable point equilibrium. However, evolutionary outcomes can change significantly in different circumstances. We present an analysis based on adaptive dynamics of a discrete-time demographic model involving a trade-off whose shape is also an important determinant of evolutionary behaviour. We derive an explicit expression for the fitness in the cyclic region and consequently present an adaptive dynamic analysis which is algebraic. We do this fully in the region of 2-cycles and (using a symbolic package) almost fully for 4-cycles. Simulations illustrate and verify our results. With equilibrium population dynamics, trade-offs with accelerating costs produce a continuously stable strategy (CSS) whereas trade-offs with decelerating costs produce a non-ES repellor. The transition to 2-cycles produces a discontinuous change: the appearance of an intermediate region in which branching points occur. The size of this region decreases as we move through the region of 2-cycles. There is a further discontinuous fall in the size of the branching region during the transition to 4-cycles. We extend our results numerically and with simulations to higher-period cycles and chaos. Simulations show that chaotic population dynamics can evolve from equilibrium and vice-versa.

Measuring selected PPCPs in wastewater to estimate the population in different cities in China.

PubMed

Gao, Jianfa; O'Brien, Jake; Du, Peng; Li, Xiqing; Ort, Christoph; Mueller, Jochen F; Thai, Phong K

2016-10-15

Sampling and analysis of wastewater from municipal wastewater treatment plants (WWTPs) has become a useful tool for understanding exposure to chemicals. Both wastewater based studies and management and planning of the catchment require information on catchment population in the time of monitoring. Recently, a model has been developed and calibrated using selected pharmaceutical and personal care products (PPCPs) measured in influent wastewater for estimating population in different catchments in Australia. The present study aimed at evaluating the feasibility of utilizing this population estimation approach in China. Twenty-four hour composite influent samples were collected from 31 WWTPs in 17 cities with catchment sizes from 200,000-3,450,000 people representing all seven regions of China. The samples were analyzed for 19 PPCPs using liquid chromatography coupled to tandem mass spectrometry in direct injection mode. Eight chemicals were detected in more than 50% of the samples. Significant positive correlations were found between individual PPCP mass loads and population estimates provided by WWTP operators. Using the PPCP mass load modeling approach calibrated with WWTP operator data, we estimated the population size of each catchment with good agreement with WWTP operator values (between 50-200% for all sites and 75-125% for 23 of the 31 sites). Overall, despite much lower detection and relatively high heterogeneity in PPCP consumption across China the model provided a good estimate of the population contributing to a given wastewater sample. Wastewater analysis could also provide objective PPCP consumption status in China. Copyright © 2016 Elsevier B.V. All rights reserved.

Molecular insights into the historic demography of bowhead whales: understanding the evolutionary basis of contemporary management practices

PubMed Central

Phillips, C D; Hoffman, J I; George, J C; Suydam, R S; Huebinger, R M; Patton, J C; Bickham, J W

2013-01-01

Patterns of genetic variation observed within species reflect evolutionary histories that include signatures of past demography. Understanding the demographic component of species' history is fundamental to informed management because changes in effective population size affect response to environmental change and evolvability, the strength of genetic drift, and maintenance of genetic variability. Species experiencing anthropogenic population reductions provide valuable case studies for understanding the genetic response to demographic change because historic changes in the census size are often well documented. A classic example is the bowhead whale, Balaena mysticetus, which experienced dramatic population depletion due to commercial whaling in the late 19th and early 20th centuries. Consequently, we analyzed a large multi-marker dataset of bowhead whales using a variety of analytical methods, including extended Bayesian skyline analysis and approximate Bayesian computation, to characterize genetic signatures of both ancient and contemporary demographic histories. No genetic signature of recent population depletion was recovered through any analysis incorporating realistic mutation assumptions, probably due to the combined influences of long generation time, short bottleneck duration, and the magnitude of population depletion. In contrast, a robust signal of population expansion was detected around 70,000 years ago, followed by a population decline around 15,000 years ago. The timing of these events coincides to a historic glacial period and the onset of warming at the end of the last glacial maximum, respectively. By implication, climate driven long-term variation in Arctic Ocean productivity, rather than recent anthropogenic disturbance, appears to have been the primary driver of historic bowhead whale demography. PMID:23403722

Mapping by admixture linkage disequilibrium in human populations: Limits and guidelines

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stephens, J.C.; Briscoe, D.; O`Brien, S.J.

1994-10-01

Certain human hereditary conditions, notably those with low penetrance and those which require an environmental event such as infectious disease exposure, are difficult to localize in pedigree analysis, because of uncertainty in the phenotype of an affected patient`s relatives. An approach to locating these genes in human cohort studies would be to use association analysis, which depends on linkage disequilibrium of flanking polymorphic DNA markers. In theory, a high degree of linkage disequilibrium between genes separated by 10-20 cM will be generated and persist in populations that have a history of recent (3-20 generations ago) admixture between genetically differentiated racialmore » groups, such as has occurred in African Americans and Hispanic populations. We have conducted analytic and computer simulations to quantify the effect of genetic, genomic, and population parameters that affect the amount and ascertainment of linkage disequilibrium in populations with a history of genetic admixture. Our goal is to thoroughly explore the ranges of all relevant parameters or factors (e.g., sample size and degree of genetic differentiation between populations) that may be involved in gene localization studies, in hopes of prescribing guidelines for an efficient mapping strategy. The results provide reasonable limits on sample size (200-300 patients), marker number (200-300 in 20-cM intervals), and allele differentiation (loci with allele frequency difference of {ge}.3 between admixed parent populations) to produce an efficient approach (>95% ascertainment) for locating genes not easily tracked in human pedigrees. 321 refs., 8 figs., 7 tabs.« less

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

PubMed

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.

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

Sediment transport processes in the Pearl River Estuary as revealed by grain-size end-member modeling and sediment trend analysis

NASA Astrophysics Data System (ADS)

Li, Tao; Li, Tuan-Jie

2018-04-01

The analysis of grain-size distribution enables us to decipher sediment transport processes and understand the causal relations between dynamic processes and grain-size distributions. In the present study, grain sizes were measured from surface sediments collected in the Pearl River Estuary and its adjacent coastal areas. End-member modeling analysis attempts to unmix the grain sizes into geologically meaningful populations. Six grain-size end-members were identified. Their dominant modes are 0 Φ, 1.5 Φ, 2.75 Φ, 4.5 Φ, 7 Φ, and 8 Φ, corresponding to coarse sand, medium sand, fine sand, very coarse silt, silt, and clay, respectively. The spatial distributions of the six end-members are influenced by sediment transport and depositional processes. The two coarsest end-members (coarse sand and medium sand) may reflect relict sediments deposited during the last glacial period. The fine sand end-member would be difficult to transport under fair weather conditions, and likely indicates storm deposits. The three remaining fine-grained end-members (very coarse silt, silt, and clay) are recognized as suspended particles transported by saltwater intrusion via the flood tidal current, the Guangdong Coastal Current, and riverine outflow. The grain-size trend analysis shows distinct transport patterns for the three fine-grained end-members. The landward transport of the very coarse silt end-member occurs in the eastern part of the estuary, the seaward transport of the silt end-member occurs in the western part, and the east-west transport of the clay end-member occurs in the coastal areas. The results show that grain-size end-member modeling analysis in combination with sediment trend analysis help to better understand sediment transport patterns and the associated transport mechanisms.

Weber's law implies neural discharge more regular than a Poisson process.

PubMed

Kang, Jing; Wu, Jianhua; Smerieri, Anteo; Feng, Jianfeng

2010-03-01

Weber's law is one of the basic laws in psychophysics, but the link between this psychophysical behavior and the neuronal response has not yet been established. In this paper, we carried out an analysis on the spike train statistics when Weber's law holds, and found that the efferent spike train of a single neuron is less variable than a Poisson process. For population neurons, Weber's law is satisfied only when the population size is small (< 10 neurons). However, if the population neurons share a weak correlation in their discharges and individual neuronal spike train is more regular than a Poisson process, Weber's law is true without any restriction on the population size. Biased competition attractor network also demonstrates that the coefficient of variation of interspike interval in the winning pool should be less than one for the validity of Weber's law. Our work links Weber's law with neural firing property quantitatively, shedding light on the relation between psychophysical behavior and neuronal responses.

StrAuto: automation and parallelization of STRUCTURE analysis.

PubMed

Chhatre, Vikram E; Emerson, Kevin J

2017-03-24

Population structure inference using the software STRUCTURE has become an integral part of population genetic studies covering a broad spectrum of taxa including humans. The ever-expanding size of genetic data sets poses computational challenges for this analysis. Although at least one tool currently implements parallel computing to reduce computational overload of this analysis, it does not fully automate the use of replicate STRUCTURE analysis runs required for downstream inference of optimal K. There is pressing need for a tool that can deploy population structure analysis on high performance computing clusters. We present an updated version of the popular Python program StrAuto, to streamline population structure analysis using parallel computing. StrAuto implements a pipeline that combines STRUCTURE analysis with the Evanno Δ K analysis and visualization of results using STRUCTURE HARVESTER. Using benchmarking tests, we demonstrate that StrAuto significantly reduces the computational time needed to perform iterative STRUCTURE analysis by distributing runs over two or more processors. StrAuto is the first tool to integrate STRUCTURE analysis with post-processing using a pipeline approach in addition to implementing parallel computation - a set up ideal for deployment on computing clusters. StrAuto is distributed under the GNU GPL (General Public License) and available to download from http://strauto.popgen.org .

Population growth enhances the mean fixation time of neutral mutations and the persistence of neutral variation.

PubMed

Waxman, D

2012-06-01

A fundamental result of population genetics states that a new mutation, at an unlinked neutral locus in a randomly mating diploid population, has a mean time of fixation of ∼4N(e) generations, where N(e) is the effective population size. This result is based on an assumption of fixed population size, which does not universally hold in natural populations. Here, we analyze such neutral fixations in populations of changing size within the framework of the diffusion approximation. General expressions are derived for the mean and variance of the fixation time in changing populations. Some explicit results are given for two cases: (i) the effective population size undergoes a sudden change, representing a sudden population expansion or a sudden bottleneck; (ii) the effective population changes linearly for a limited period of time and then remains constant. Additionally, a lower bound for the mean time of fixation is obtained for an effective population size that increases with time, and this is applied to exponentially growing populations. The results obtained in this work show, among other things, that for populations that increase in size, the mean time of fixation can be enhanced, sometimes substantially so, over 4N(e,0) generations, where N(e,0) is the effective population size at the time the mutation arises. Such an enhancement is associated with (i) an increased probability of neutral polymorphism in a population and (ii) an enhanced persistence of high-frequency neutral variation, which is the variation most likely to be observed.

Retrieval of phytoplankton cell size from chlorophyll a specific absorption and scattering spectra of phytoplankton.

PubMed

Zhou, Wen; Wang, Guifen; Li, Cai; Xu, Zhantang; Cao, Wenxi; Shen, Fang

2017-10-20

Phytoplankton cell size is an important property that affects diverse ecological and biogeochemical processes, and analysis of the absorption and scattering spectra of phytoplankton can provide important information about phytoplankton size. In this study, an inversion method for extracting quantitative phytoplankton cell size data from these spectra was developed. This inversion method requires two inputs: chlorophyll a specific absorption and scattering spectra of phytoplankton. The average equivalent-volume spherical diameter (ESD v ) was calculated as the single size approximation for the log-normal particle size distribution (PSD) of the algal suspension. The performance of this method for retrieving cell size was assessed using the datasets from cultures of 12 phytoplankton species. The estimations of a(λ) and b(λ) for the phytoplankton population using ESD v had mean error values of 5.8%-6.9% and 7.0%-10.6%, respectively, compared to the a(λ) and b(λ) for the phytoplankton populations using the log-normal PSD. The estimated values of C i ESD v were in good agreement with the measurements, with r 2 =0.88 and relative root mean square error (NRMSE)=25.3%, and relatively good performances were also found for the retrieval of ESD v with r 2 =0.78 and NRMSE=23.9%.

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

NASA Astrophysics Data System (ADS)

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

2012-08-01

We introduce a population model for species under cyclic competition. This model allows individuals to coexist and interact on single cells while migration takes place between adjacent cells. In contrast to the model introduced by Reichenbach, Mobilia, and Frey [Reichenbach, Mobilia, and Frey, Nature (London)NATUAS0028-083610.1038/nature06095 448, 1046 (2007)], we find that the emergence of spirals results in an ambiguous behavior regarding the stability of coexistence. The typical time until extinction exhibits, however, a qualitatively opposite dependence on the newly introduced nonunit carrying capacity in the spiraling and the nonspiraling regimes. This allows us to determine a critical mobility that marks the onset of this spiraling state sharply. In contrast, we demonstrate that the conventional finite size stability analysis with respect to spatial size is of limited use for identifying the onset of the spiraling regime.

Generalization and dilution of association results from European GWAS in populations of non-European ancestry: the PAGE study.

PubMed

Carlson, Christopher S; Matise, Tara C; North, Kari E; Haiman, Christopher A; Fesinmeyer, Megan D; Buyske, Steven; Schumacher, Fredrick R; Peters, Ulrike; Franceschini, Nora; Ritchie, Marylyn D; Duggan, David J; Spencer, Kylee L; Dumitrescu, Logan; Eaton, Charles B; Thomas, Fridtjof; Young, Alicia; Carty, Cara; Heiss, Gerardo; Le Marchand, Loic; Crawford, Dana C; Hindorff, Lucia A; Kooperberg, Charles L

2013-09-01

The vast majority of genome-wide association study (GWAS) findings reported to date are from populations with European Ancestry (EA), and it is not yet clear how broadly the genetic associations described will generalize to populations of diverse ancestry. The Population Architecture Using Genomics and Epidemiology (PAGE) study is a consortium of multi-ancestry, population-based studies formed with the objective of refining our understanding of the genetic architecture of common traits emerging from GWAS. In the present analysis of five common diseases and traits, including body mass index, type 2 diabetes, and lipid levels, we compare direction and magnitude of effects for GWAS-identified variants in multiple non-EA populations against EA findings. We demonstrate that, in all populations analyzed, a significant majority of GWAS-identified variants have allelic associations in the same direction as in EA, with none showing a statistically significant effect in the opposite direction, after adjustment for multiple testing. However, 25% of tagSNPs identified in EA GWAS have significantly different effect sizes in at least one non-EA population, and these differential effects were most frequent in African Americans where all differential effects were diluted toward the null. We demonstrate that differential LD between tagSNPs and functional variants within populations contributes significantly to dilute effect sizes in this population. Although most variants identified from GWAS in EA populations generalize to all non-EA populations assessed, genetic models derived from GWAS findings in EA may generate spurious results in non-EA populations due to differential effect sizes. Regardless of the origin of the differential effects, caution should be exercised in applying any genetic risk prediction model based on tagSNPs outside of the ancestry group in which it was derived. Models based directly on functional variation may generalize more robustly, but the identification of functional variants remains challenging.

Generalization and Dilution of Association Results from European GWAS in Populations of Non-European Ancestry: The PAGE Study

PubMed Central

Carlson, Christopher S.; Matise, Tara C.; North, Kari E.; Haiman, Christopher A.; Fesinmeyer, Megan D.; Buyske, Steven; Schumacher, Fredrick R.; Peters, Ulrike; Franceschini, Nora; Ritchie, Marylyn D.; Duggan, David J.; Spencer, Kylee L.; Dumitrescu, Logan; Eaton, Charles B.; Thomas, Fridtjof; Young, Alicia; Carty, Cara; Heiss, Gerardo; Le Marchand, Loic; Crawford, Dana C.; Hindorff, Lucia A.; Kooperberg, Charles L.

2013-01-01

The vast majority of genome-wide association study (GWAS) findings reported to date are from populations with European Ancestry (EA), and it is not yet clear how broadly the genetic associations described will generalize to populations of diverse ancestry. The Population Architecture Using Genomics and Epidemiology (PAGE) study is a consortium of multi-ancestry, population-based studies formed with the objective of refining our understanding of the genetic architecture of common traits emerging from GWAS. In the present analysis of five common diseases and traits, including body mass index, type 2 diabetes, and lipid levels, we compare direction and magnitude of effects for GWAS-identified variants in multiple non-EA populations against EA findings. We demonstrate that, in all populations analyzed, a significant majority of GWAS-identified variants have allelic associations in the same direction as in EA, with none showing a statistically significant effect in the opposite direction, after adjustment for multiple testing. However, 25% of tagSNPs identified in EA GWAS have significantly different effect sizes in at least one non-EA population, and these differential effects were most frequent in African Americans where all differential effects were diluted toward the null. We demonstrate that differential LD between tagSNPs and functional variants within populations contributes significantly to dilute effect sizes in this population. Although most variants identified from GWAS in EA populations generalize to all non-EA populations assessed, genetic models derived from GWAS findings in EA may generate spurious results in non-EA populations due to differential effect sizes. Regardless of the origin of the differential effects, caution should be exercised in applying any genetic risk prediction model based on tagSNPs outside of the ancestry group in which it was derived. Models based directly on functional variation may generalize more robustly, but the identification of functional variants remains challenging. PMID:24068893

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.

Placing College Graduation Rates in Context: How 4-Year College Graduation Rates Vary with Selectivity and the Size of Low-Income Enrollment. Postsecondary Education Descriptive Analysis Report. NCES 2007-161

ERIC Educational Resources Information Center

Horn, Laura

2006-01-01

This report uses data primarily from the 2004 Graduation Rate Survey (GRS), a component of the Integrated Postsecondary Education Data System (IPEDS), to provide a systemwide overview of how graduation rates of comparable 4-year institutions vary with institution selectivity and the size of the low-income population enrolled. The report clearly…

Recurrent jellyfish blooms are a consequence of global oscillations

PubMed Central

Condon, Robert H.; Duarte, Carlos M.; Pitt, Kylie A.; Robinson, Kelly L.; Lucas, Cathy H.; Sutherland, Kelly R.; Mianzan, Hermes W.; Bogeberg, Molly; Purcell, Jennifer E.; Decker, Mary Beth; Uye, Shin-ichi; Madin, Laurence P.; Brodeur, Richard D.; Haddock, Steven H. D.; Malej, Alenka; Parry, Gregory D.; Eriksen, Elena; Quiñones, Javier; Acha, Marcelo; Harvey, Michel; Arthur, James M.; Graham, William M.

2013-01-01

A perceived recent increase in global jellyfish abundance has been portrayed as a symptom of degraded oceans. This perception is based primarily on a few case studies and anecdotal evidence, but a formal analysis of global temporal trends in jellyfish populations has been missing. Here, we analyze all available long-term datasets on changes in jellyfish abundance across multiple coastal stations, using linear and logistic mixed models and effect-size analysis to show that there is no robust evidence for a global increase in jellyfish. Although there has been a small linear increase in jellyfish since the 1970s, this trend was unsubstantiated by effect-size analysis that showed no difference in the proportion of increasing vs. decreasing jellyfish populations over all time periods examined. Rather, the strongest nonrandom trend indicated jellyfish populations undergo larger, worldwide oscillations with an approximate 20-y periodicity, including a rising phase during the 1990s that contributed to the perception of a global increase in jellyfish abundance. Sustained monitoring is required over the next decade to elucidate with statistical confidence whether the weak increasing linear trend in jellyfish after 1970 is an actual shift in the baseline or part of an oscillation. Irrespective of the nature of increase, given the potential damage posed by jellyfish blooms to fisheries, tourism, and other human industries, our findings foretell recurrent phases of rise and fall in jellyfish populations that society should be prepared to face. PMID:23277544

The Population Structure of Glossina palpalis gambiensis from Island and Continental Locations in Coastal Guinea

PubMed Central

Solano, Philippe; Ravel, Sophie; Bouyer, Jeremy; Camara, Mamadou; Kagbadouno, Moise S.; Dyer, Naomi; Gardes, Laetitia; Herault, Damien; Donnelly, Martin J.; De Meeûs, Thierry

2009-01-01

Background We undertook a population genetics analysis of the tsetse fly Glossina palpalis gambiensis, a major vector of sleeping sickness in West Africa, using microsatellite and mitochondrial DNA markers. Our aims were to estimate effective population size and the degree of isolation between coastal sites on the mainland of Guinea and Loos Islands. The sampling locations encompassed Dubréka, the area with the highest Human African Trypanosomosis (HAT) prevalence in West Africa, mangrove and savannah sites on the mainland, and two islands, Fotoba and Kassa, within the Loos archipelago. These data are discussed with respect to the feasibility and sustainability of control strategies in those sites currently experiencing, or at risk of, sleeping sickness. Principal Findings We found very low migration rates between sites except between those sampled around the Dubréka area that seems to contain a widely dispersed and panmictic population. In the Kassa island samples, various effective population size estimates all converged on surprisingly small values (10

Do food availability, parasitism, and stress have synergistic effects on red colobus populations living in forest fragments?

PubMed

Chapman, Colin A; Wasserman, Michael D; Gillespie, Thomas R; Speirs, Michaela L; Lawes, Michael J; Saj, Tania L; Ziegler, Toni E

2006-12-01

Identifying factors that influence animal density is a fundamental goal in ecology that has taken on new importance with the need to develop informed management plans. This is particularly the case for primates as the tropical forest that supports many species is being rapidly converted. We use a system of forest fragments adjacent to Kibale National Park, Uganda, to examine if food availability and parasite infections have synergistic affects on red colobus (Piliocolobus tephrosceles) abundance. Given that the size of primate populations can often respond slowly to environmental changes, we also examined how these factors influenced cortisol levels. To meet these objectives, we monitored gastrointestinal parasites, evaluated fecal cortisol levels, and determined changes in food availability by conducting complete tree inventories in eight fragments in 2000 and 2003. Red colobus populations declined by an average of 21% among the fragments; however, population change ranged from a 25% increase to a 57% decline. The cumulative basal area of food trees declined by an average of 29.5%; however, forest change was highly variable (a 2% gain to a 71% decline). We found that nematode prevalence averaged 58% among fragments (range 29-83%). The change in colobus population size was correlated both with food availability and a number of indices of parasite infections. A path analysis suggests that change in food availability has a strong direct effect on population size, but it also has an indirect effect via parasite infections. 2006 Wiley-Liss, Inc.

Repeated Habitat Disturbances by Fire Decrease Local Effective Population Size

PubMed Central

Ragsdale, Alexandria K.; McCoy, Earl D.; Mushinsky, Henry R.

2016-01-01

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. PMID:26976940

Bribery games on interdependent complex networks.

PubMed

Verma, Prateek; Nandi, Anjan K; Sengupta, Supratim

2018-08-07

Bribe demands present a social conflict scenario where decisions have wide-ranging economic and ethical consequences. Nevertheless, such incidents occur daily in many countries across the globe. Harassment bribery constitute a significant sub-set of such bribery incidents where a government official demands a bribe for providing a service to a citizen legally entitled to it. We employ an evolutionary game-theoretic framework to analyse the evolution of corrupt and honest strategies in structured populations characterized by an interdependent complex network. The effects of changing network topology, average number of links and asymmetry in size of the citizen and officer population on the proliferation of incidents of bribery are explored. A complex network topology is found to be beneficial for the dominance of corrupt strategies over a larger region of phase space when compared with the outcome for a regular network, for equal citizen and officer population sizes. However, the extent of the advantage depends critically on the network degree and topology. A different trend is observed when there is a difference between the citizen and officer population sizes. Under those circumstances, increasing randomness of the underlying citizen network can be beneficial to the fixation of honest officers up to a certain value of the network degree. Our analysis reveals how the interplay between network topology, connectivity and strategy update rules can affect population level outcomes in such asymmetric games. Copyright © 2018 Elsevier Ltd. All rights reserved.

Workplace health promotion: a meta-analysis of effectiveness.

PubMed

Rongen, Anne; Robroek, Suzan J W; van Lenthe, Frank J; Burdorf, Alex

2013-04-01

An unhealthy lifestyle may contribute to ill health, absence due to sickness, productivity loss at work, and reduced ability to work. Workplace health promotion programs (WHPPs) aim to improve lifestyle and consequently improve health, work ability, and work productivity. However, systematic reviews on intervention studies have reported small effects, and the overall evaluation of effectiveness of WHPPs is hampered by a large heterogeneity in interventions and study populations. This systematic review aims to investigate the influence of population, study and intervention characteristics, and study quality on the effectiveness of workplace health promotion programs. A systematic literature search was conducted identifying RCTs, published before June 2012, evaluating the effect of a WHPP aimed at smoking cessation, physical activity, healthy nutrition, and/or obesity on self-perceived health, work absence due to sickness, work productivity, or work ability. Studies were included in the meta-analyses if quantitative information was present to calculate an effect size (ES). A meta-analysis, stratified meta-analyses, and meta-regression analyses were performed in Spring 2012 using Comprehensive Meta-analysis software 2.0 and PAWS 17.0.2. In 18 studies describing 21 interventions, the overall effect of a WHPP was small (ES=0.24, 95% CI=0.14, 0.34). The effectiveness of a WHPP was larger in younger populations, in interventions with weekly contacts, and in studies in which the control group received no health promotion. A 2.6-fold lower effectiveness was observed for studies performing an intention-to-treat analysis and a 1.7-fold lower effectiveness for studies controlling for confounders. Studies of poor methodologic quality reported a 2.9-fold higher effect size of the WHPP. The effectiveness of a WHPP is partly determined by intervention characteristics and statistical analysis. High-quality RCTs reported lower effect sizes. It is important to determine the effectiveness of WHPPs in RCTs of high quality. Copyright © 2013 American Journal of Preventive Medicine. Published by Elsevier Inc. All rights reserved.

Projecting pest population dynamics under global warming: the combined effect of inter- and intra-annual variations.

PubMed

Zidon, Royi; Tsueda, Hirotsugu; Morin, Efrat; Morin, Shai

2016-06-01

The typical short generation length of insects makes their population dynamics highly sensitive not only to mean annual temperatures but also to their intra-annual variations. To consider the combined effect of both thermal factors under global warming, we propose a modeling framework that links general circulation models (GCMs) with a stochastic weather generator and population dynamics models to predict species population responses to inter- and intra-annual temperature changes. This framework was utilized to explore future changes in populations of Bemisia tabaci, an invasive insect pest-species that affects multiple agricultural systems in the Mediterranean region. We considered three locations representing different pest status and climatic conditions: Montpellier (France), Seville (Spain), and Beit-Jamal (Israel). We produced ensembles of local daily temperature realizations representing current and future (mid-21st century) climatic conditions under two emission scenarios for the three locations. Our simulations predicted a significant increase in the average number of annual generations and in population size, and a significant lengthening of the growing season in all three locations. A negative effect was found only in Seville for the summer season, where future temperatures lead to a reduction in population size. High variability in population size was observed between years with similar annual mean temperatures, suggesting a strong effect of intra-annual temperature variation. Critical periods were from late spring to late summer in Montpellier and from late winter to early summer in Seville and Beit-Jamal. Although our analysis suggested that earlier seasonal activity does not necessarily lead to increased populations load unless an additional generation is produced, it is highly likely that the insect will become a significant pest of open-fields at Mediterranean latitudes above 40° during the next 50 years. Our simulations also implied that current predictions based on mean temperature anomalies are relatively conservative and it is better to apply stochastic tools to resolve complex responses to climate change while taking natural variability into account. In summary, we propose a modeling framework capable of determining distinct intra-annual temperature patterns leading to large or small population sizes, for pest risk assessment and management planning of both natural and agricultural ecosystems.

Determinants of genetic structure in a nonequilibrium metapopulation of the plant Silene latifolia.

PubMed

Fields, Peter D; Taylor, Douglas R

2014-01-01

Population genetic differentiation will be influenced by the demographic history of populations, opportunities for migration among neighboring demes and founder effects associated with repeated extinction and recolonization. In natural populations, these factors are expected to interact with each other and their magnitudes will vary depending on the spatial distribution and age structure of local demes. Although each of these effects has been individually identified as important in structuring genetic variance, their relative magnitude is seldom estimated in nature. We conducted a population genetic analysis in a metapopulation of the angiosperm, Silene latifolia, from which we had more than 20 years of data on the spatial distribution, demographic history, and extinction and colonization of demes. We used hierarchical Bayesian methods to disentangle which features of the populations contributed to among population variation in allele frequencies, including the magnitude and direction of their effects. We show that population age, long-term size and degree of connectivity all combine to affect the distribution of genetic variance; small, recently-founded, isolated populations contributed most to increase FST in the metapopulation. However, the effects of population size and population age are best understood as being modulated through the effects of connectivity to other extant populations, i.e. FST diminishes as populations age, but at a rate that depends how isolated the population is. These spatial and temporal correlates of population structure give insight into how migration, founder effect and within-deme genetic drift have combined to enhance and restrict genetic divergence in a natural metapopulation.

MRI-based assessment of the pineal gland in a large population of children aged 0-5 years and comparison with pineoblastoma: part II, the cystic gland.

PubMed

Sirin, Selma; de Jong, Marcus C; Galluzzi, Paolo; Maeder, Philippe; Brisse, Hervé J; Castelijns, Jonas A; de Graaf, Pim; Goericke, Sophia L

2016-07-01

Pineal cysts are a common incidental finding on brain MRI with resulting difficulties in differentiation between normal glands and pineal pathologies. The aim of this study was to assess the size and morphology of the cystic pineal gland in children (0-5 years) and compare the findings with published pineoblastoma cases. In this retrospective multicenter study, 257 MR examinations (232 children, 0-5 years) were evaluated regarding pineal gland size (width, height, planimetric area, maximal cyst(s) size) and morphology. We performed linear regression analysis with 99 % prediction intervals of gland size versus age for the size parameters. Results were compared with a recent meta-analysis of pineoblastoma by de Jong et al. Follow-up was available in 25 children showing stable cystic findings in 48 %, cyst size increase in 36 %, and decrease in 16 %. Linear regression analysis gave 99 % upper prediction bounds of 10.8 mm, 10.9 mm, 7.7 mm and 66.9 mm(2), respectively, for cyst size, width, height, and area. The slopes (size increase per month) of each parameter were 0.030, 0.046, 0.021, and 0.25, respectively. Most of the pineoblastomas showed a size larger than the 99 % upper prediction margin, but with considerable overlap between the groups. We presented age-adapted normal values for size and morphology of the cystic pineal gland in children aged 0 to 5 years. Analysis of size is helpful in discriminating normal glands from cystic pineal pathologies such as pineoblastoma. We also presented guidelines for the approach of a solid or cystic pineal gland in hereditary retinoblastoma patients.

Hierarchical nuclear and cytoplasmic genetic architectures for plant growth and defense within Arabidopsis.

PubMed

Joseph, Bindu; Corwin, Jason A; Züst, Tobias; Li, Baohua; Iravani, Majid; Schaepman-Strub, Gabriela; Turnbull, Lindsay A; Kliebenstein, Daniel J

2013-06-01

To understand how genetic architecture translates between phenotypic levels, we mapped the genetic architecture of growth and defense within the Arabidopsis thaliana Kas × Tsu recombinant inbred line population. We measured plant growth using traditional size measurements and size-corrected growth rates. This population contains genetic variation in both the nuclear and cytoplasmic genomes, allowing us to separate their contributions. The cytoplasmic genome regulated a significant variance in growth but not defense, which was due to cytonuclear epistasis. Furthermore, growth adhered to an infinitesimal model of genetic architecture, while defense metabolism was more of a moderate-effect model. We found a lack of concordance between quantitative trait loci (QTL) regulating defense and those regulating growth. Given the published evidence proving the link between glucosinolates and growth, this is likely a false negative result caused by the limited population size. This size limitation creates an inability to test the entire potential genetic landscape possible between these two parents. We uncovered a significant effect of glucosinolates on growth once we accounted for allelic differences in growth QTLs. Therefore, other growth QTLs can mask the effects of defense upon growth. Investigating direct links across phenotypic hierarchies is fraught with difficulty; we identify issues complicating this analysis.

Hierarchical Nuclear and Cytoplasmic Genetic Architectures for Plant Growth and Defense within Arabidopsis[C][W

PubMed Central

Joseph, Bindu; Corwin, Jason A.; Züst, Tobias; Li, Baohua; Iravani, Majid; Schaepman-Strub, Gabriela; Turnbull, Lindsay A.; Kliebenstein, Daniel J.

2013-01-01

To understand how genetic architecture translates between phenotypic levels, we mapped the genetic architecture of growth and defense within the Arabidopsis thaliana Kas × Tsu recombinant inbred line population. We measured plant growth using traditional size measurements and size-corrected growth rates. This population contains genetic variation in both the nuclear and cytoplasmic genomes, allowing us to separate their contributions. The cytoplasmic genome regulated a significant variance in growth but not defense, which was due to cytonuclear epistasis. Furthermore, growth adhered to an infinitesimal model of genetic architecture, while defense metabolism was more of a moderate-effect model. We found a lack of concordance between quantitative trait loci (QTL) regulating defense and those regulating growth. Given the published evidence proving the link between glucosinolates and growth, this is likely a false negative result caused by the limited population size. This size limitation creates an inability to test the entire potential genetic landscape possible between these two parents. We uncovered a significant effect of glucosinolates on growth once we accounted for allelic differences in growth QTLs. Therefore, other growth QTLs can mask the effects of defense upon growth. Investigating direct links across phenotypic hierarchies is fraught with difficulty; we identify issues complicating this analysis. PMID:23749847

The Divergence of Chimpanzee Species and Subspecies as Revealed in Multipopulation Isolation-with-Migration Analyses

PubMed Central

Hey, Jody

2010-01-01

The divergence of bonobos and three subspecies of the common chimpanzee was examined under a multipopulation isolation-with-migration (IM) model with data from 73 loci drawn from the literature. A benefit of having a full multipopulation model, relative to conducting multiple pairwise analyses between sampled populations, is that a full model can reveal historical gene flow involving ancestral populations. An example of this was found in which gene flow is indicated between the western common chimpanzee subspecies and the ancestor of the central and the eastern common chimpanzee subspecies. The results of a full analysis on all four populations are strongly consistent with analyses on pairs of populations and generally similar to results from previous studies. The basal split between bonobos and common chimpanzees was estimated at 0.93 Ma (0.68–1.54 Ma, 95% highest posterior density interval), with the split among the ancestor of three common chimpanzee populations at 0.46 Ma (0.35–0.65), and the most recent split between central and eastern common chimpanzee populations at 0.093 Ma (0.041–0.157). Population size estimates mostly fell in the range from 5,000 to 10,000 individuals. The exceptions are the size of the ancestor of the common chimpanzee and the bonobo, at 17,000 (8,000–28,000) individuals, and the central common chimpanzee and its immediate ancestor with the eastern common chimpanzee, which have effective size estimates at 27,000 (16,000–44,000) and 32,000 (19,000–54,000) individuals, respectively. PMID:19955478

The divergence of chimpanzee species and subspecies as revealed in multipopulation isolation-with-migration analyses.

PubMed

Hey, Jody

2010-04-01

The divergence of bonobos and three subspecies of the common chimpanzee was examined under a multipopulation isolation-with-migration (IM) model with data from 73 loci drawn from the literature. A benefit of having a full multipopulation model, relative to conducting multiple pairwise analyses between sampled populations, is that a full model can reveal historical gene flow involving ancestral populations. An example of this was found in which gene flow is indicated between the western common chimpanzee subspecies and the ancestor of the central and the eastern common chimpanzee subspecies. The results of a full analysis on all four populations are strongly consistent with analyses on pairs of populations and generally similar to results from previous studies. The basal split between bonobos and common chimpanzees was estimated at 0.93 Ma (0.68-1.54 Ma, 95% highest posterior density interval), with the split among the ancestor of three common chimpanzee populations at 0.46 Ma (0.35-0.65), and the most recent split between central and eastern common chimpanzee populations at 0.093 Ma (0.041-0.157). Population size estimates mostly fell in the range from 5,000 to 10,000 individuals. The exceptions are the size of the ancestor of the common chimpanzee and the bonobo, at 17,000 (8,000-28,000) individuals, and the central common chimpanzee and its immediate ancestor with the eastern common chimpanzee, which have effective size estimates at 27,000 (16,000-44,000) and 32,000 (19,000-54,000) individuals, respectively.

Demographic history of a recent invasion of house mice on the isolated Island of Gough.

PubMed

Gray, Melissa M; Wegmann, Daniel; Haasl, Ryan J; White, Michael A; Gabriel, Sofia I; Searle, Jeremy B; Cuthbert, Richard J; Ryan, Peter G; Payseur, Bret A

2014-04-01

Island populations provide natural laboratories for studying key contributors to evolutionary change, including natural selection, population size and the colonization of new environments. The demographic histories of island populations can be reconstructed from patterns of genetic diversity. House mice (Mus musculus) inhabit islands throughout the globe, making them an attractive system for studying island colonization from a genetic perspective. Gough Island, in the central South Atlantic Ocean, is one of the remotest islands in the world. House mice were introduced to Gough Island by sealers during the 19th century and display unusual phenotypes, including exceptionally large body size and carnivorous feeding behaviour. We describe genetic variation in Gough Island mice using mitochondrial sequences, nuclear sequences and microsatellites. Phylogenetic analysis of mitochondrial sequences suggested that Gough Island mice belong to Mus musculus domesticus, with the maternal lineage possibly originating in England or France. Cluster analyses of microsatellites revealed genetic membership for Gough Island mice in multiple coastal populations in Western Europe, suggesting admixed ancestry. Gough Island mice showed substantial reductions in mitochondrial and nuclear sequence variation and weak reductions in microsatellite diversity compared with Western European populations, consistent with a population bottleneck. Approximate Bayesian computation (ABC) estimated that mice recently colonized Gough Island (~100 years ago) and experienced a 98% reduction in population size followed by a rapid expansion. Our results indicate that the unusual phenotypes of Gough Island mice evolved rapidly, positioning these mice as useful models for understanding rapid phenotypic evolution. © 2014 John Wiley & Sons Ltd.

A linear model of population dynamics

NASA Astrophysics Data System (ADS)

Lushnikov, A. A.; Kagan, A. I.

2016-08-01

The Malthus process of population growth is reformulated in terms of the probability w(n,t) to find exactly n individuals at time t assuming that both the birth and the death rates are linear functions of the population size. The master equation for w(n,t) is solved exactly. It is shown that w(n,t) strongly deviates from the Poisson distribution and is expressed in terms either of Laguerre’s polynomials or a modified Bessel function. The latter expression allows for considerable simplifications of the asymptotic analysis of w(n,t).

Devastating Decline of Forest Elephants in Central Africa

PubMed Central

Blake, Stephen; Wittemyer, George; Hart, John; Williamson, Elizabeth A.; Aba’a, Rostand; Abitsi, Gaspard; Ambahe, Ruffin D.; Amsini, Fidèl; Bakabana, Parfait C.; Hicks, Thurston Cleveland; Bayogo, Rosine E.; Bechem, Martha; Beyers, Rene L.; Bezangoye, Anicet N.; Boundja, Patrick; Bout, Nicolas; Akou, Marc Ella; Bene, Lambert Bene; Fosso, Bernard; Greengrass, Elizabeth; Grossmann, Falk; Ikamba-Nkulu, Clement; Ilambu, Omari; Inogwabini, Bila-Isia; Iyenguet, Fortune; Kiminou, Franck; Kokangoye, Max; Kujirakwinja, Deo; Latour, Stephanie; Liengola, Innocent; Mackaya, Quevain; Madidi, Jacob; Madzoke, Bola; Makoumbou, Calixte; Malanda, Guy-Aimé; Malonga, Richard; Mbani, Olivier; Mbendzo, Valentin A.; Ambassa, Edgar; Ekinde, Albert; Mihindou, Yves; Morgan, Bethan J.; Motsaba, Prosper; Moukala, Gabin; Mounguengui, Anselme; Mowawa, Brice S.; Ndzai, Christian; Nixon, Stuart; Nkumu, Pele; Nzolani, Fabian; Pintea, Lilian; Plumptre, Andrew; Rainey, Hugo; de Semboli, Bruno Bokoto; Serckx, Adeline; Stokes, Emma; Turkalo, Andrea; Vanleeuwe, Hilde; Vosper, Ashley; Warren, Ymke

2013-01-01

African forest elephants– taxonomically and functionally unique–are being poached at accelerating rates, but we lack range-wide information on the repercussions. Analysis of the largest survey dataset ever assembled for forest elephants (80 foot-surveys; covering 13,000 km; 91,600 person-days of fieldwork) revealed that population size declined by ca. 62% between 2002–2011, and the taxon lost 30% of its geographical range. The population is now less than 10% of its potential size, occupying less than 25% of its potential range. High human population density, hunting intensity, absence of law enforcement, poor governance, and proximity to expanding infrastructure are the strongest predictors of decline. To save the remaining African forest elephants, illegal poaching for ivory and encroachment into core elephant habitat must be stopped. In addition, the international demand for ivory, which fuels illegal trade, must be dramatically reduced. PMID:23469289

What population studies can do for business.

PubMed

Hugo, G

1991-05-01

This paper examines how specific skills essential to demography, the scientific study of human populations, can be useful in private and public sector planning. Over the past 2 decades, Australia's population has undergone profound transformations -- a shift to below replacement level fertility and a change in ethnic composition, to name a few. And these changes have reshaped the markets for goods, services, and labor. Because demography seeks to analyze and explain changes in the size, composition, and spatial distribution of people, this discipline requires certain skills that can be particularly valuable to both private and public sector planning. These skills include: 1) a sound knowledge of why and how populations change over time; 2) a wide range of concepts (the "cohort," for example) which allow demographers to analyze the dynamics of change in a population; 3) statistical techniques; and 4) life tables techniques. Having named the specific skills of demographers, the author identifies the areas of business and public administration where these skills can be most useful, areas that include the following: strategic long-term planning, marketing, market segmentation, small area analysis, household and family level analysis, projections and estimates, human resources analysis, and international population trends. Finally, the author discusses the implications of applied population analysis on the training of demographers in Australia, emphasizing the role of the Australian Population Association in improving the status of demography as an important planning tool.

mtDNA variation predicts population size in humans and reveals a major Southern Asian chapter in human prehistory.

PubMed

Atkinson, Quentin D; Gray, Russell D; Drummond, Alexei J

2008-02-01

The relative timing and size of regional human population growth following our expansion from Africa remain unknown. Human mitochondrial DNA (mtDNA) diversity carries a legacy of our population history. Given a set of sequences, we can use coalescent theory to estimate past population size through time and draw inferences about human population history. However, recent work has challenged the validity of using mtDNA diversity to infer species population sizes. Here we use Bayesian coalescent inference methods, together with a global data set of 357 human mtDNA coding-region sequences, to infer human population sizes through time across 8 major geographic regions. Our estimates of relative population sizes show remarkable concordance with the contemporary regional distribution of humans across Africa, Eurasia, and the Americas, indicating that mtDNA diversity is a good predictor of population size in humans. Plots of population size through time show slow growth in sub-Saharan Africa beginning 143-193 kya, followed by a rapid expansion into Eurasia after the emergence of the first non-African mtDNA lineages 50-70 kya. Outside Africa, the earliest and fastest growth is inferred in Southern Asia approximately 52 kya, followed by a succession of growth phases in Northern and Central Asia (approximately 49 kya), Australia (approximately 48 kya), Europe (approximately 42 kya), the Middle East and North Africa (approximately 40 kya), New Guinea (approximately 39 kya), the Americas (approximately 18 kya), and a second expansion in Europe (approximately 10-15 kya). Comparisons of relative regional population sizes through time suggest that between approximately 45 and 20 kya most of humanity lived in Southern Asia. These findings not only support the use of mtDNA data for estimating human population size but also provide a unique picture of human prehistory and demonstrate the importance of Southern Asia to our recent evolutionary past.

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.

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…

The Game of Contacts: Estimating the Social Visibility of Groups☆

PubMed Central

Salganik, Matthew J.; Mello, Maeve B.; Abdo, Alexandre H.; Bertoni, Neilane; Fazito, Dimitri; Bastos, Francisco I.

2010-01-01

Estimating the sizes of hard-to-count populations is a challenging and important problem that occurs frequently in social science, public health, and public policy. This problem is particularly pressing in HIV/AIDS research because estimates of the sizes of the most at-risk populations—illicit drug users, men who have sex with men, and sex workers—are needed for designing, evaluating, and funding programs to curb the spread of the disease. A promising new approach in this area is the network scale-up method, which uses information about the personal networks of respondents to make population size estimates. However, if the target population has low social visibility, as is likely to be the case in HIV/AIDS research, scale-up estimates will be too low. In this paper we develop a game-like activity that we call the game of contacts in order to estimate the social visibility of groups, and report results from a study of heavy drug users in Curitiba, Brazil (n = 294). The game produced estimates of social visibility that were consistent with qualitative expectations but of surprising magnitude. Further, a number of checks suggest that the data are high-quality. While motivated by the specific problem of population size estimation, our method could be used by researchers more broadly and adds to long-standing efforts to combine the richness of social network analysis with the power and scale of sample surveys. PMID:21318126

Observed oil and gas field size distributions: A consequence of the discovery process and prices of oil and gas

USGS Publications Warehouse

Drew, L.J.; Attanasi, E.D.; Schuenemeyer, J.H.

1988-01-01

If observed oil and gas field size distributions are obtained by random samplings, the fitted distributions should approximate that of the parent population of oil and gas fields. However, empirical evidence strongly suggests that larger fields tend to be discovered earlier in the discovery process than they would be by random sampling. Economic factors also can limit the number of small fields that are developed and reported. This paper examines observed size distributions in state and federal waters of offshore Texas. Results of the analysis demonstrate how the shape of the observable size distributions change with significant hydrocarbon price changes. Comparison of state and federal observed size distributions in the offshore area shows how production cost differences also affect the shape of the observed size distribution. Methods for modifying the discovery rate estimation procedures when economic factors significantly affect the discovery sequence are presented. A primary conclusion of the analysis is that, because hydrocarbon price changes can significantly affect the observed discovery size distribution, one should not be confident about inferring the form and specific parameters of the parent field size distribution from the observed distributions. ?? 1988 International Association for Mathematical Geology.

High genetic diversity in a small population: the case of Chilean blue whales

PubMed Central

Torres-Florez, Juan P; Hucke-Gaete, Rodrigo; Rosenbaum, Howard; Figueroa, Christian C

2014-01-01

It is generally assumed that species with low population sizes have lower genetic diversities than larger populations and vice versa. However, this would not be the case for long-lived species with long generation times, and which populations have declined due to anthropogenic effects, such as the blue whale (Balaenoptera musculus). This species was intensively decimated globally to near extinction during the 20th century. Along the Chilean coast, it is estimated that at least 4288 blue whales were hunted from an apparently pre-exploitation population size (k) of a maximum of 6200 individuals (Southeastern Pacific). Thus, here, we describe the mtDNA (control region) and nDNA (microsatellites) diversities of the Chilean blue whale aggregation site in order to verify the expectation of low genetic diversity in small populations. We then compare our findings with other blue whale aggregations in the Southern Hemisphere. Interestingly, although the estimated population size is small compared with the pre-whaling era, there is still considerable genetic diversity, even after the population crash, both in mitochondrial (N = 46) and nuclear (N = 52) markers (Hd = 0.890 and Ho = 0.692, respectively). Our results suggest that this diversity could be a consequence of the long generation times and the relatively short period of time elapsed since the end of whaling, which has been observed in other heavily-exploited whale populations. The genetic variability of blue whales on their southern Chile feeding grounds was similar to that found in other Southern Hemisphere blue whale feeding grounds. Our phylogenetic analysis of mtDNA haplotypes does not show extensive differentiation of populations among Southern Hemisphere blue whale feeding grounds. The present study suggests that although levels of genetic diversity are frequently used as estimators of population health, these parameters depend on the biology of the species and should be taken into account in a monitoring framework study to obtain a more complete picture of the conservation status of a population. PMID:24834336

Landsat image and sample design for water reservoirs (Rapel dam Central Chile).

PubMed

Lavanderos, L; Pozo, M E; Pattillo, C; Miranda, H

1990-01-01

Spatial heterogeneity of the Rapel reservoir surface waters is analyzed through Landsat images. The image digital counts are used with the aim or developing an aprioristic quantitative sample design.Natural horizontal stratification of the Rapel Reservoir (Central Chile) is produced mainly by suspended solids. The spatial heterogeneity conditions of the reservoir for the Spring 86-Summer 87 period were determined by qualitative analysis and image processing of the MSS Landsat, bands 1 and 3. The space-time variations of the different observed strata obtained with multitemporal image analysis.A random stratified sample design (r.s.s.d) was developed, based on the digital counts statistical analysis. Strata population size as well as the average, variance and sampling size of the digital counts were obtained by the r.s.s.d method.Stratification determined by analysis of satellite images were later correlated with ground data. Though the stratification of the reservoir is constant over time, the shape and size of the strata varys.

The Association Between Parental Mean Length of Utterance and Language Outcomes in Children With Disabilities: A Correlational Meta-Analysis.

PubMed

Sandbank, Micheal; Yoder, Paul

2016-05-01

The purpose of this correlational meta-analysis was to examine the association between parental utterance length and language outcomes in children with disabilities and whether this association varies according to other child characteristics, such as age and disability type. This association can serve as a starting point for language intervention practices for children with disabilities. We conducted a systematic search of 42 electronic databases to identify relevant studies. Twelve studies reporting on a total of 13 populations (including 257 participants) were identified. A random-effects model was used to estimate a combined effect size across all studies as well as separate effect sizes across studies in each disability category. The combined effect size across all studies suggests a weak positive association between parental input length and child language outcomes. However, subgroup analyses within disability categories suggest that this association may differ for children with autism. Results of 4 studies including 47 children with autism show that parental input length is strongly associated with positive language outcomes in this population. Present evidence suggests that clinicians should reconsider intervention practices that prescribe shorter, grammatically incomplete utterances, particularly when working with children with autism.

On the importance of controlling for effort in analysis of count survey data: Modeling population change from Christmas Bird Count data

USGS Publications Warehouse

Link, W.A.; Sauer, J.R.; Helbig, Andreas J.; Flade, Martin

1999-01-01

Count survey data are commonly used for estimating temporal and spatial patterns of population change. Since count surveys are not censuses, counts can be influenced by 'nuisance factors' related to the probability of detecting animals but unrelated to the actual population size. The effects of systematic changes in these factors can be confounded with patterns of population change. Thus, valid analysis of count survey data requires the identification of nuisance factors and flexible models for their effects. We illustrate using data from the Christmas Bird Count (CBC), a midwinter survey of bird populations in North America. CBC survey effort has substantially increased in recent years, suggesting that unadjusted counts may overstate population growth (or understate declines). We describe a flexible family of models for the effect of effort, that includes models in which increasing effort leads to diminishing returns in terms of the number of birds counted.

A Place-Oriented, Mixed-Level Regionalization Method for Constructing Geographic Areas in Health Data Dissemination and Analysis

PubMed Central

Mu, Lan; Wang, Fahui; Chen, Vivien W.; Wu, Xiao-Cheng

2015-01-01

Similar geographic areas often have great variations in population size. In health data management and analysis, it is desirable to obtain regions of comparable population by decomposing areas of large population (to gain more spatial variability) and merging areas of small population (to mask privacy of data). Based on the Peano curve algorithm and modified scale-space clustering, this research proposes a mixed-level regionalization (MLR) method to construct geographic areas with comparable population. The method accounts for spatial connectivity and compactness, attributive homogeneity, and exogenous criteria such as minimum (and approximately equal) population or disease counts. A case study using Louisiana cancer data illustrates the MLR method and its strengths and limitations. A major benefit of the method is that most upper level geographic boundaries can be preserved to increase familiarity of constructed areas. Therefore, the MLR method is more human-oriented and place-based than computer-oriented and space-based. PMID:26251551

Lake whitefish and lake herring population structure and niche in ten south-central Ontario lakes

USGS Publications Warehouse

Carl, Leon M.; McGuiness, Fiona

2006-01-01

This study compares simple fish communities of ten oligotrophic lakes in south-central Ontario. Species densities and population size structure vary significantly among these lake communities depending on fish species present beyond the littoral zone. Lake whitefish are fewer and larger in the presence of lake herring than in their absence. Diet analysis indicates that lake whitefish shift from feeding on both plankton and benthic prey when lake herring are absent to a primarily benthic feeding niche in the presence of lake herring. When benthic round whitefish are present, lake whitefish size and density decline and they move lower in the lake compared to round whitefish. Burbot are also fewer and larger in lakes with lake herring than in lakes without herring. Burbot, in turn, appear to influence the population structure of benthic coregonine species. Lower densities of benthic lake whitefish and round whitefish are found in lakes containing large benthic burbot than in lakes with either small burbot or where burbot are absent. Predation on the pelagic larvae of burbot and lake whitefish by planktivorous lake herring alters the size and age structure of these populations. As life history theory predicts, those species with poor larval survival appear to adopt a bet-hedging life history strategy of long-lived individuals as a reproductive reserve.

Dynamics of initial colonization of nonconserved perennial ryegrass by anaerobic fungi in the bovine rumen.

PubMed

Edwards, Joan E; Kingston-Smith, Alison H; Jimenez, Hugo R; Huws, Sharon A; Skøt, Kirsten P; Griffith, Gareth W; McEwan, Neil R; Theodorou, Michael K

2008-12-01

Anaerobic fungi (Neocallimastigales) are active degraders of fibrous plant material in the rumen. However, only limited information is available relating to how quickly they colonize ingested feed particles. The aim of this study was to determine the dynamics of initial colonization of forage by anaerobic fungi in the rumen and the impact of different postsampling wash procedures used to remove loosely associated microorganisms. Neocallimastigales-specific molecular techniques were optimized to ensure maximal coverage before application to assess the population size (quantitative PCR) and composition (automated ribosomal intergenic spacer analysis) of the colonizing anaerobic fungi. Colonization of perennial ryegrass (PRG) was evident within 5 min, with no consistent effect of time or wash procedure on fungal population composition. Wash procedure had no effect on population size unlike time, which had a significant effect. Colonizing fungal population size continued to increase over the incubation period after an initial lag of c. 4 min. This dynamic differs from that reported previously for rumen bacteria, where substantial colonization of PRG occurred within 5 min. The observed delay in colonization of plant material by anaerobic fungi is suggested to be primarily mediated by the time taken for fungal zoospores to locate, attach and encyst on plant material.

Influence of long-distance seed dispersal on the genetic diversity of seed rain in fragmented Pinus densiflora populations relative to pollen-mediated gene flow.

PubMed

Ozawa, Hajime; Watanabe, Atsushi; Uchiyama, Kentaro; Saito, Yoko; Ide, Yuji

2013-01-01

Long-distance dispersal (LDD) of seeds has a critical impact on species survival in patchy landscapes. However, relative to pollen dispersal, empirical data on how seed LDD affects genetic diversity in fragmented populations have been poorly reported. Thus, we attempted to indirectly evaluate the influence of seed LDD by estimating maternal and paternal inbreeding in the seed rain of fragmented 8 Pinus densiflora populations. In total, the sample size was 458 seeds and 306 adult trees. Inbreeding was estimated by common parentage analysis to evaluate gene flow within populations and by sibship reconstruction analysis to estimate gene flow within and among populations. In the parentage analysis, the observed probability that sampled seeds had the same parents within populations was significantly larger than the expected probability in many populations. This result suggested that gene dispersal was limited to within populations. In the sibship reconstruction, many donors both within and among populations appeared to contribute to sampled seeds. Significant differences in sibling ratios were not detected between paternity and maternity. These results suggested that seed-mediated gene flow and pollen-mediated gene flow from outside population contributed some extent to high genetic diversity of the seed rain (H E > 0.854). We emphasize that pine seeds may have excellent potential for gene exchange within and among populations.

Analysis of Demand for Decoders of Television Captioning for Deaf and Hearing-Impaired Children and Adults.

ERIC Educational Resources Information Center

Sherman, Renee Z.; Sherman, Joel D.

This market research report analyzed the published literature, the size of the deaf/severely hard-of-hearing population, factors that affect demand for closed-captioned television decoders, and the supply of decoders. The analysis found that the number of hearing-impaired people in the United States is between 16 and 21 million; hearing impairment…

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

Birth spacing and fertility limitation: a behavioral analysis of a nineteenth century frontier population.

PubMed

Anderton, D L; Bean, L L

1985-05-01

Our analysis of changing birth interval distributions over the course of a fertility transition from natural to controlled fertility has examined three closely related propositions. First, within both natural fertility populations (identified at the aggregate level) and cohorts following the onset of fertility limitation, we hypothesized that substantial groups of women with long birth intervals across the individually specified childbearing careers could be identified. That is, even during periods when fertility behavior at the aggregate level is consistent with a natural fertility regime, birth intervals at all parities are inversely related to completed family size. Our tabular analysis enables us to conclude that birth spacing patterns are parity dependent; there is stability in CEB-parity specific mean and birth interval variance over the entire transition. Our evidence does not suggest that the early group of women limiting and spacing births was marked by infecundity. Secondly, the transition appears to be associated with an increasingly larger proportion of women shifting to the same spacing schedules associated with smaller families in earlier cohorts. Thirdly, variations in birth spacing by age of marriage indicate that changes in birth intervals over time are at least indirectly associated with age of marriage, indicating an additional compositional effect. The evidence we have presented on spacing behavior does not negate the argument that parity-dependent stopping behavior was a powerful factor in the fertility transition. Our data also provide evidence of attempts to truncate childbearing. Specifically, the smaller the completed family size, the longer the ultimate birth interval; and ultimate birth intervals increase across cohorts controlling CEB and parity. But spacing appears to represent an additional strategy of fertility limitation. Thus, it may be necessary to distinguish spacing and stopping behavior if one wishes to clarify behavioral patterns within a population (Edlefsen, 1981; Friedlander et al., 1980; Rodriguez and Hobcraft, 1980). Because fertility transition theories imply increased attempts to limit family sizes, it is important to examine differential behavior within subgroups achieving different family sizes. It is this level of analysis which we have attempted to achieve in utilizing parity-specific birth intervals controlled by children ever born.(ABSTRACT TRUNCATED AT 400 WORDS)

Spatial variation in egg size of a top predator: Interplay of body size and environmental factors?

NASA Astrophysics Data System (ADS)

Louzao, Maite; Igual, José M.; Genovart, Meritxell; Forero, Manuela G.; Hobson, Keith A.; Oro, Daniel

2008-09-01

It is expected that nearby populations are constrained by the same ecological features shaping in turn similarity in their ecological traits. Here, we studied the spatio-temporal variability in egg size among local populations of the critically endangered Balearic shearwater Puffinus mauretanicus, a top marine predator endemic to the western Mediterranean region. Specifically we assessed whether this trait was influenced by maternal body size, as an indicator of a genetic component, and feeding ecology (through stable-carbon and nitrogen-isotope measurements), as an indicator of environmental factors. We found that egg size varied among local populations, an unexpected result at such a small spatial scale. Body size differences at the local population level only partially explained such differences. Blood isotope measurements also differed among local populations. Values of δ 15N suggested inter-population differences in trophic level, showing a similar general pattern with egg size, and suggesting a nutritional link between them whereby egg size was affected by differences in feeding resources and/or behaviour. Values of δ 13C suggested that local populations did not differ in foraging habits with respect to benthic- vs. pelagic-based food-webs. Egg size did not vary among years as did breeding performance, suggesting that a differential temporal window could affect both breeding parameters in relation to food availability. The absence of a relationship between breeding performance and egg size suggested that larger eggs might only confer an advantage during harsh conditions. Alternatively parental quality could greatly affect breeding performance. We showed that inter-population differences in egg size could be influenced by both body size and environmental factors.

The effect of loving-kindness meditation on positive emotions: a meta-analytic review.

PubMed

Zeng, Xianglong; Chiu, Cleo P K; Wang, Rong; Oei, Tian P S; Leung, Freedom Y K

2015-01-01

While it has been suggested that loving-kindness meditation (LKM) is an effective practice for promoting positive emotions, the empirical evidence in the literature remains unclear. Here, we provide a systematic review of 24 empirical studies (N = 1759) on LKM with self-reported positive emotions. The effect of LKM on positive emotions was estimated with meta-analysis, and the influence of variations across LKM interventions was further explored with subgroup analysis and meta-regression. The meta-analysis showed that (1) medium effect sizes for LKM interventions on daily positive emotions in both wait-list controlled RCTs and non-RCT studies; and (2) small to large effect sizes for the on-going practice of LKM on immediate positive emotions across different comparisons. Further analysis showed that (1) interventions focused on loving-kindness had medium effect size, but interventions focused on compassion showed small effect sizes; (2) the length of interventions and the time spent on meditation did not influence the effect sizes, but the studies without didactic components in interventions had small effect sizes. A few individual studies reported that the nature of positive emotions and individual differences also influenced the results. In sum, LKM practice and interventions are effective in enhancing positive emotions, but more studies are needed to identify the active components of the interventions, to compare different psychological operations, and to explore the applicability in clinical populations.

The effect of loving-kindness meditation on positive emotions: a meta-analytic review

PubMed Central

Zeng, Xianglong; Chiu, Cleo P. K.; Wang, Rong; Oei, Tian P. S.; Leung, Freedom Y. K.

2015-01-01

While it has been suggested that loving-kindness meditation (LKM) is an effective practice for promoting positive emotions, the empirical evidence in the literature remains unclear. Here, we provide a systematic review of 24 empirical studies (N = 1759) on LKM with self-reported positive emotions. The effect of LKM on positive emotions was estimated with meta-analysis, and the influence of variations across LKM interventions was further explored with subgroup analysis and meta-regression. The meta-analysis showed that (1) medium effect sizes for LKM interventions on daily positive emotions in both wait-list controlled RCTs and non-RCT studies; and (2) small to large effect sizes for the on-going practice of LKM on immediate positive emotions across different comparisons. Further analysis showed that (1) interventions focused on loving-kindness had medium effect size, but interventions focused on compassion showed small effect sizes; (2) the length of interventions and the time spent on meditation did not influence the effect sizes, but the studies without didactic components in interventions had small effect sizes. A few individual studies reported that the nature of positive emotions and individual differences also influenced the results. In sum, LKM practice and interventions are effective in enhancing positive emotions, but more studies are needed to identify the active components of the interventions, to compare different psychological operations, and to explore the applicability in clinical populations. PMID:26579061

Social network analysis of the genetic structure of Pacific islanders.

PubMed

Terrell, John Edward

2010-05-01

Social network analysis (SNA) is a body of theory and a set of relatively new computer-aided techniques used in the analysis and study of relational data. Recent studies of autosomal markers from over 40 human populations in the south-western Pacific have further documented the remarkable degree of genetic diversity in this part of the world. I report additional analysis using SNA methods contributing new controlled observations on the structuring of genetic diversity among these islanders. These SNA mappings are then compared with model-based network expectations derived from the geographic distances among the same populations. Previous studies found that genetic divergence among island Melanesian populations is organised by island, island size/topography, and position (coastal vs. inland), and that similarities observed correlate only weakly with an isolation-by-distance model. Using SNA methods, however, improves the resolution of among population comparison, and suggests that isolation by distance constrained by social networks together with position (coastal/inland) accounts for much of the population structuring observed. The multilocus data now available is also in accord with current thinking on the impact of major biogeographical transformations on prehistoric colonisation and post-settlement human interaction in Oceania.

Clinical evaluation of nonsyndromic dental anomalies in Dravidian population: A cluster sample analysis.

PubMed

Yamunadevi, Andamuthu; Selvamani, M; Vinitha, V; Srivandhana, R; Balakrithiga, M; Prabhu, S; Ganapathy, N

2015-08-01

To record the prevalence rate of dental anomalies in Dravidian population and analyze the percentage of individual anomalies in the population. A cluster sample analysis was done, where 244 subjects studying in a dental institution were all included and analyzed for occurrence of dental anomalies by clinical examination, excluding third molars from analysis. 31.55% of the study subjects had dental anomalies and shape anomalies were more prevalent (22.1%), followed by size (8.6%), number (3.2%) and position anomalies (0.4%). Retained deciduous was seen in 1.63%. Among the individual anomalies, Talon's cusp (TC) was seen predominantly (14.34%), followed by microdontia (6.6%) and supernumerary cusps (5.73%). Prevalence rate of dental anomalies in the Dravidian population is 31.55% in the present study, exclusive of third molars. Shape anomalies are more common, and TC is the most commonly noted anomaly. Varying prevalence rate is reported in different geographical regions of the world.

Biased distribution of IS629 among strains in different lineages of enterohemorrhagic Escherichia coli serovar O157.

PubMed

Yokoyama, Eiji; Hashimoto, Ruiko; Etoh, Yoshiki; Ichihara, Sachiko; Horikawa, Kazumi; Uchimura, Masako

2011-01-01

The distribution of insertion sequence (IS) 629 among strains of enterohemorrhagic Escherichia coli serovar O157 (O157) was investigated and compared with the strain lineages defined by lineage specific polymorphism assay-6 (LSPA-6) to demonstrate the effectiveness of IS629 analysis for population genetics analysis. Using pulsed-field gel electrophoresis and variable-number tandem repeat typing, 140 strains producing both VT1 and VT2 and 98 strains producing only VT2 were selected from a total of 592 strains isolated from patients and asymptomatic carriers in Chiba Prefecture, Japan, during 2003-2008. By LSPA-6 analysis, six strains had atypical amplicon sizes in their Z5935 loci and five strains had atypical amplicon sizes in their arp-iclR intergenic regions. Sequence analyses of PCR amplified DNAs showed that five of the six loci used for LSPA-6 analysis had tandem repeats and the allele changes were due to changes in the number of tandem repeats. Subculturing and long-term incubation was found to have no detectable effect on the lineages defined by LSPA-6 analysis, demonstrating the robustness of LSPA-6 analysis. Minimum spanning tree analysis reconstruction revealed that strains in lineage I, I/II, and II clustered on separate branches, indicating that the distribution of IS629 was biased among O157 strains in different lineages. Strains with LSPA-6 codes 231111, 211113, and 211114 had atypical amplicon sizes and were clustered in lineage I/II branch, and strains with LSPA-6 codes 212114, 221123, 221223, 222123, 222224, 242123, 252123, and 242222 had atypical amplicon sizes and clustered in lineage II branches. Linkage disequilibrium was observed in strains in every lineage when the standardized index of association was calculated using IS629 distribution data. Therefore, the distribution analysis of IS629 may be effective for population genetics analysis of O157 due to the biased IS629 distribution among strains in the three O157 lineages. Copyright © 2010 Elsevier B.V. All rights reserved.

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. © The American Genetic Association. 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Pollen flow in the wildservice tree, Sorbus torminalis (L.) Crantz. I. Evaluating the paternity analysis procedure in continuous populations.

PubMed

Oddou-Muratorio, S; Houot, M-L; Demesure-Musch, B; Austerlitz, F

2003-12-01

The joint development of polymorphic molecular markers and paternity analysis methods provides new approaches to investigate ongoing patterns of pollen flow in natural plant populations. However, paternity studies are hindered by false paternity assignment and the nondetection of true fathers. To gauge the risk of these two types of errors, we performed a simulation study to investigate the impact on paternity analysis of: (i) the assumed values for the size of the breeding male population (NBMP), and (ii) the rate of scoring error in genotype assessment. Our simulations were based on microsatellite data obtained from a natural population of the entomophilous wild service tree, Sorbus torminalis (L.) Crantz. We show that an accurate estimate of NBMP is required to minimize both types of errors, and we assess the reliability of a technique used to estimate NBMP based on parent-offspring genetic data. We then show that scoring errors in genotype assessment only slightly affect the assessment of paternity relationships, and conclude that it is generally better to neglect the scoring error rate in paternity analyses within a nonisolated population.

Population size dependency of measles epidemic that was scalable from Japanese prefectures to European countries.

PubMed

Yoshikura, Hiroshi

2018-04-27

Relation between number of measles patients (y) and population size (x) was expressed by an equation y = ax s , where a is a constant and s the slope of the plot; s was 2.04-2.17 for prefectures in Japan, i.e., the number of patients was proportional to square of the prefecture population size. For European countries that joined European Union no later than 2009, the slope was 1.43-1.87. The measles' population dependency found among prefectures in Japan was thus scalable up to European countries. It was surprising because, unlike Japan, population density in EU countries was not uniform and not proportional to the population size. The population size dependency was not observed among Western Pacific and South-East Asian countries probably on account of confounding interacting socioeconomic factors. Correlation between measles incidence and birth rate, infant mortality or GDP per capita was almost insignificant.Size distribution of local infection clusters (LICs) of measles and rubella in Japan followed power law. For measles, though the population dependency remained unchanged after "elimination", there was change in the Zipf-type plot of LIC sizes. After the "elimination", LICs linked to importation-related outbreaks in less populated prefectures emerged as the top-ranked LICs.

Demographic threats to the sustainability of Brazil nut exploitation.

PubMed

Peres, Carlos A; Baider, Claudia; Zuidema, Pieter A; Wadt, Lúcia H O; Kainer, Karen A; Gomes-Silva, Daisy A P; Salomão, Rafael P; Simões, Luciana L; Franciosi, Eduardo R N; Cornejo Valverde, Fernando; Gribel, Rogério; Shepard, Glenn H; Kanashiro, Milton; Coventry, Peter; Yu, Douglas W; Watkinson, Andrew R; Freckleton, Robert P

2003-12-19

A comparative analysis of 23 populations of the Brazil nut tree (Bertholletia excelsa) across the Brazilian, Peruvian, and Bolivian Amazon shows that the history and intensity of Brazil nut exploitation are major determinants of population size structure. Populations subjected to persistent levels of harvest lack juvenile trees less than 60 centimeters in diameter at breast height; only populations with a history of either light or recent exploitation contain large numbers of juvenile trees. A harvesting model confirms that intensive exploitation levels over the past century are such that juvenile recruitment is insufficient to maintain populations over the long term. Without management, intensively harvested populations will succumb to a process of senescence and demographic collapse, threatening this cornerstone of the Amazonian extractive economy.

Testing the 'island rule' for a tenebrionid beetle (Coleoptera, Tenebrionidae)

NASA Astrophysics Data System (ADS)

Palmer, Miquel

2002-05-01

Insular populations and their closest mainland counterparts commonly display body size differences that are considered to fit the island rule, a theoretical framework to explain both dwarfism and gigantism in isolated animal populations. The island rule is used to explain the pattern of change of body size at the inter-specific level. But the model implicitly makes also a prediction for the body size of isolated populations of a single species. It suggests that, for a hypothetical species covering a wide range of island sizes, there exists a specific island size where this species reaches the largest body size. Body size would be small (in relative terms) in the smallest islets of the species range. It would increase with island size, and reach a maximum at some specific island size. However, additional increases from such a specific island size would instead promote body size reduction, and small (in relative terms) body sizes would be found again on the largest islands. The biogeographical patterns predicted by the island rule have been described and analysed for vertebrates only (mainly mammals), but remain largely untested for insects or other invertebrates. I analyse here the pattern of body size variation between seven isolated insular populations of a flightless beetle, Asida planipennis (Coleoptera, Tenebrionidae). This is an endemic species of Mallorca, Menorca and a number of islands and islets in the Balearic archipelago (western Mediterranean). The study covers seven of the 15 known populations (i.e., there are only 15 islands or islets inhabited by the species). The populations studied fit the pattern advanced above and we could, therefore, extrapolate the island rule to a very different kind of organism. However, the small sample size of some of the populations invites some caution at this early stage.

Self-fertilization is the main sexual reproduction mechanism in native wine yeast populations.

PubMed

Cubillos, Francisco A; Vásquez, Claudia; Faugeron, Sylvain; Ganga, Angélica; Martínez, Claudio

2009-01-01

Saccharomyces cerevisiae is a model eukaryotic organism for classical genetics and genomics, and yet its ecology is still largely unknown. In this work, a population genetic analysis was performed on five yeast populations isolated from wine-making areas with different enological practices using simple sequence repeats and restriction fragment length polymorphism of mitochondrial DNA as molecular markers on 292 strains. In accordance with other studies, genome size estimation suggests that native S. cerevisiae strains are mainly homothallic and diploids. Analysis of mtDNA data showed that yeast populations from nonindustrial areas have 40% higher genetic diversity than populations isolated from industrial areas, demonstrating that industrial enological practices are likely to affect native yeast populations negatively by reducing its biodiversity. On the other hand, genetic differentiation analysis based on their microsatellite showed no correlation between genetic and geographic distance and a nonsignificant value when a Mantel test was applied. Finally, in the five populations studied, positive inbreeding (F(is)) values from 0.4 to 0.75, a low but significant level of linkage disequilibrium and a high number of multilocus genotypes were detected. These results strongly advocate that sexual reproduction is frequent enough to erase clonal signature in natural populations and that self-fertilization is the main mating system.

Factors leading to different viability predictions for a grizzly bear data set

USGS Publications Warehouse

Mills, L.S.; Hayes, S.G.; Wisdom, M.J.; Citta, J.; Mattson, D.J.; Murphy, K.

1996-01-01

Population viability analysis programs are being used increasingly in research and management applications, but there has not been a systematic study of the congruence of different program predictions based on a single data set. We performed such an analysis using four population viability analysis computer programs: GAPPS, INMAT, RAMAS/AGE, and VORTEX. The standardized demographic rates used in all programs were generalized from hypothetical increasing and decreasing grizzly bear (Ursus arctos horribilis) populations. Idiosyncracies of input format for each program led to minor differences in intrinsic growth rates that translated into striking differences in estimates of extinction rates and expected population size. In contrast, the addition of demographic stochasticity, environmental stochasticity, and inbreeding costs caused only a small divergence in viability predictions. But, the addition of density dependence caused large deviations between the programs despite our best attempts to use the same density-dependent functions. Population viability programs differ in how density dependence is incorporated, and the necessary functions are difficult to parameterize accurately. Thus, we recommend that unless data clearly suggest a particular density-dependent model, predictions based on population viability analysis should include at least one scenario without density dependence. Further, we describe output metrics that may differ between programs; development of future software could benefit from standardized input and output formats across different programs.

Estuarine sediment toxicity tests on diatoms: Sensitivity comparison for three species

NASA Astrophysics Data System (ADS)

Moreno-Garrido, Ignacio; Lubián, Luis M.; Jiménez, Begoña; Soares, Amadeu M. V. M.; Blasco, Julián

2007-01-01

Experimental populations of three marine and estuarine diatoms were exposed to sediments with different levels of pollutants, collected from the Aveiro Lagoon (NW of Portugal). The species selected were Cylindrotheca closterium, Phaeodactylum tricornutum and Navicula sp. Previous experiments were designed to determine the influence of the sediment particle size distribution on growth of the species assayed. Percentage of silt-sized sediment affect to growth of the selected species in the experimental conditions: the higher percentage of silt-sized sediment, the lower growth. In any case, percentages of silt-sized sediment less than 10% did not affect growth. In general, C. closterium seems to be slightly more sensitive to the selected sediments than the other two species. Two groups of sediment samples were determined as a function of the general response of the exposed microalgal populations: three of the six samples used were more toxic than the other three. Chemical analysis of the samples was carried out in order to determine the specific cause of differences in toxicity. After a statistical analysis, concentrations of Sn, Zn, Hg, Cu and Cr (among all physico-chemical analyzed parameters), in order of importance, were the most important factors that divided the two groups of samples (more and less toxic samples). Benthic diatoms seem to be sensitive organisms in sediment toxicity tests. Toxicity data from bioassays involving microphytobentos should be taken into account when environmental risks are calculated.

Morphometric Differentiation in Cornops aquaticum (Orthoptera: Acrididae): Associations With Sex, Chromosome, and Geographic Conditions

PubMed Central

Romero, María Luciana; Colombo, Pablo César; Remis, María Isabel

2014-01-01

Abstract The water-hyacinth grasshopper Cornops aquaticum (Bruner) (Orthoptera: Acrididae) is native to South America and inhabits lowlands from southern Mexico to central Argentina and Uruguay. This grasshopper feeds and lays eggs on species from the genera Eichhornia and Pontederia. Particularly, Eichhornia crassipes is considered “the world’s worst water weed,” and the release of C. aquaticum was proposed as a form of biological control. Morphometric variation on the chromosomally differentiated populations from the middle and lower Paraná River and its possible association with geographic, sex, and chromosomal conditions was analyzed. Significant phenotype variation in C. aquaticum population was detected. C. aquaticum presents body-size sexual dimorphism, females being bigger than males. Female-biased sexual size dimorphism for all five analyzed traits was detected. The assessment of variation in sexual size dimorphism for tegmen length showed that this trait scaled allometrically, indicating that males and females did not vary in a similar fashion. The detected allometry was consistent with Rensch’s rule demonstrating greater evolutionary divergence in male size than in female size and suggests that males are more sensitive to environmental condition. The analysis of morphometric variation in the context of chromosome constitution showed that the presence of fusion 1/6 was related to body-size variation. Fusion carriers displayed bigger body size than standard homozygotes. Besides, a positive relationship between tegmen length and the number of fused chromosomes was detected, showing a chromosome dose effect. Because the highest frequency of fusions has been found in the lower Paraná River, a marginal environment for this species, the results found would support the hypothesis that some supergenes located in the fusions may be favored in the southern populations, thus contributing to the establishment and maintenance of the polymorphism. PMID:25399431

Rapid Increase in Genome Size as a Consequence of Transposable Element Hyperactivity in Wood-White (Leptidea) Butterflies.

PubMed

Talla, Venkat; Suh, Alexander; Kalsoom, Faheema; Dinca, Vlad; Vila, Roger; Friberg, Magne; Wiklund, Christer; Backström, Niclas

2017-10-01

Characterizing and quantifying genome size variation among organisms and understanding if genome size evolves as a consequence of adaptive or stochastic processes have been long-standing goals in evolutionary biology. Here, we investigate genome size variation and association with transposable elements (TEs) across lepidopteran lineages using a novel genome assembly of the common wood-white (Leptidea sinapis) and population re-sequencing data from both L. sinapis and the closely related L. reali and L. juvernica together with 12 previously available lepidopteran genome assemblies. A phylogenetic analysis confirms established relationships among species, but identifies previously unknown intraspecific structure within Leptidea lineages. The genome assembly of L. sinapis is one of the largest of any lepidopteran taxon so far (643 Mb) and genome size is correlated with abundance of TEs, both in Lepidoptera in general and within Leptidea where L. juvernica from Kazakhstan has considerably larger genome size than any other Leptidea population. Specific TE subclasses have been active in different Lepidoptera lineages with a pronounced expansion of predominantly LINEs, DNA elements, and unclassified TEs in the Leptidea lineage after the split from other Pieridae. The rate of genome expansion in Leptidea in general has been in the range of four Mb/Million year (My), with an increase in a particular L. juvernica population to 72 Mb/My. The considerable differences in accumulation rates of specific TE classes in different lineages indicate that TE activity plays a major role in genome size evolution in butterflies and moths. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Population estimates of Nearctic shorebirds

USGS Publications Warehouse

Morrison, R.I.G.; Gill, Robert E.; Harrington, B.A.; Skagen, S.K.; Page, G.W.; Gratto-Trevor, C. L.; Haig, S.M.

2000-01-01

Estimates are presented for the population sizes of 53 species of Nearctic shorebirds occurring regularly in North America, plus four species that breed occasionally. Shorebird population sizes were derived from data obtained by a variety of methods from breeding, migration and wintering areas, and formal assessments of accuracy of counts or estimates are rarely available. Accurate estimates exist only for a few species that have been the subject of detailed investigation, and the likely accuracy of most estimates is considered poor or low. Population estimates range from a few tens to several millions. Overall, population estimates most commonly fell in the range of hundreds of thousands, particularly the low hundreds of thousands; estimated population sizes for large shorebird species currently all fall below 500,000. Population size was inversely related to size (mass) of the species, with a statistically significant negative regression between log (population size) and log (mass). Two outlying groups were evident on the regression graph: one, with populations lower than predicted, included species considered either to be "at risk" or particularly hard to count, and a second, with populations higher than predicted, included two species that are hunted. Population estimates are an integral part of conservation plans being developed for shorebirds in the United States and Canada, and may be used to identify areas of key international and regional importance.

Estimates of shorebird populations in North America

USGS Publications Warehouse

Morrison, R.I.G.; Gill, Robert E.; Harrington, B.A.; Skagen, S.K.; Page, G.W.; Gratto-Trevor, C. L.; Haig, S.M.

2001-01-01

Estimates are presented for the population sizes of 53 species of Nearctic shorebirds occurring regularly in North America, plus four species that breed occasionally. Population estimates range from a few tens to several millions. Overall, population estimates most commonly fall in the range of hundreds of thousands, particularly the low hundreds of thousands; estimated population sizes for large shorebird species currently all fall below 500 000. Population size is inversely related to size (mass) of the species, with a statistically significant negative regression between log(population size) and log(mass). Two outlying groups are evident on the regression graph: one, with populations lower than predicted, includes species considered to be either “at risk” or particularly hard to count, and a second, with populations higher than predicted, includes two species that are hunted. Shorebird population sizes were derived from data obtained by a variety of methods from breeding, migration, and wintering areas, and formal assessments of accuracy of counts or estimates are rarely available. Accurate estimates exist only for a few species that have been the subject of detailed investigation, and the likely accuracy of most estimates is considered poor or low. Population estimates are an integral part of conservation plans being developed for shorebirds in the United States and Canada and may be used to identify areas of key international and regional importance.

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 population size. Results suggest that understanding the population dynamics of a species over its range may be facilitated by taking the spatial structure of population size into account as well as by considering changes in population processes as a function of position within the range of the species. © 2014 The Authors. Journal of Animal Ecology © 2014 British Ecological Society.

Population size estimation of men who have sex with men through the network scale-up method in Japan.

PubMed

Ezoe, Satoshi; Morooka, Takeo; Noda, Tatsuya; Sabin, Miriam Lewis; Koike, Soichi

2012-01-01

Men who have sex with men (MSM) are one of the groups most at risk for HIV infection in Japan. However, size estimates of MSM populations have not been conducted with sufficient frequency and rigor because of the difficulty, high cost and stigma associated with reaching such populations. This study examined an innovative and simple method for estimating the size of the MSM population in Japan. We combined an internet survey with the network scale-up method, a social network method for estimating the size of hard-to-reach populations, for the first time in Japan. An internet survey was conducted among 1,500 internet users who registered with a nationwide internet-research agency. The survey participants were asked how many members of particular groups with known population sizes (firepersons, police officers, and military personnel) they knew as acquaintances. The participants were also asked to identify the number of their acquaintances whom they understood to be MSM. Using these survey results with the network scale-up method, the personal network size and MSM population size were estimated. The personal network size was estimated to be 363.5 regardless of the sex of the acquaintances and 174.0 for only male acquaintances. The estimated MSM prevalence among the total male population in Japan was 0.0402% without adjustment, and 2.87% after adjusting for the transmission error of MSM. The estimated personal network size and MSM prevalence seen in this study were comparable to those from previous survey results based on the direct-estimation method. Estimating population sizes through combining an internet survey with the network scale-up method appeared to be an effective method from the perspectives of rapidity, simplicity, and low cost as compared with more-conventional methods.

Joint Analysis of Binomial and Continuous Traits with a Recursive Model: A Case Study Using Mortality and Litter Size of Pigs

PubMed Central

Varona, Luis; Sorensen, Daniel

2014-01-01

This work presents a model for the joint analysis of a binomial and a Gaussian trait using a recursive parametrization that leads to a computationally efficient implementation. The model is illustrated in an analysis of mortality and litter size in two breeds of Danish pigs, Landrace and Yorkshire. Available evidence suggests that mortality of piglets increased partly as a result of successful selection for total number of piglets born. In recent years there has been a need to decrease the incidence of mortality in pig-breeding programs. We report estimates of genetic variation at the level of the logit of the probability of mortality and quantify how it is affected by the size of the litter. Several models for mortality are considered and the best fits are obtained by postulating linear and cubic relationships between the logit of the probability of mortality and litter size, for Landrace and Yorkshire, respectively. An interpretation of how the presence of genetic variation affects the probability of mortality in the population is provided and we discuss and quantify the prospects of selecting for reduced mortality, without affecting litter size. PMID:24414548

A possible divot in the Kuiper belt's scattered-object size distribution

NASA Astrophysics Data System (ADS)

Shankman, C.; Kavelaars, J.; Gladman, B.; Petit, J.

2014-07-01

The formation and evolution history of the Solar System, while not directly accessible, has measurable signatures in the present-day size distributions of the Trans-Neptunian Object (TNO) populations. The form of the size distribution is modelled as a power law with number going as size to some characteristic slope. Recent works have shown that a single power law does not match the observations across all sizes; the power law breaks to a different form [1, 2, 3]. The large- size objects record the accretion history, while the small-size objects record the collision history. The changes of size-distribution shape and slope as one moves from 'large' to 'medium' to 'small' KBOs are the signature needed to constrain the formation and collision history of the Solar System. The scattering TNOs are those TNOs undergoing strong (scattering) interactions Neptune. The scattering objects can come to pericentre in the giant planet region. This close-in pericentre passage allows for the observation of smaller objects, and thus for the constraint of the small-size end of the size distribution. Our recent analysis of the Canada France Ecliptic Plane Survey's (CFEPS) scattering objects revealed an exciting potential form for the scattering object size distribution - a divot (see Figure). Our divot (a sharp drop in the number of objects per unit size which then returns at a potentially different slope) matches our observations well and can simultaneously explain observed features in other inclined (so-called "hot") Kuiper Belt populations. In this scenario all of the hot populations would share the same source and have been implanted in the outer solar system through scattering processes. If confirmed, our divot would represent a new exciting paradigm for the formation history of the Kuiper Belt. Here we present the results of an extension of our previous work to include a new, deeper, Kuiper Belt survey. By the addition of two new faint scattering objects from this survey which, in tandem with the full characterizations of the survey's biases (acting like non- detections limits), we better constrain the form of the scattering object size distribution.

75 FR 48815 - Medicaid Program and Children's Health Insurance Program (CHIP); Revisions to the Medicaid...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-08-11

... size may be reduced by the finite population correction factor. The finite population correction is a statistical formula utilized to determine sample size where the population is considered finite rather than... program may notify us and the annual sample size will be reduced by the finite population correction...

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

Treesearch

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

2010-01-01

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

Is the Cortical Deficit in Amblyopia Due to Reduced Cortical Magnification, Loss of Neural Resolution, or Neural Disorganization?

PubMed

Clavagnier, Simon; Dumoulin, Serge O; Hess, Robert F

2015-11-04

The neural basis of amblyopia is a matter of debate. The following possibilities have been suggested: loss of foveal cells, reduced cortical magnification, loss of spatial resolution of foveal cells, and topographical disarray in the cellular map. To resolve this we undertook a population receptive field (pRF) functional magnetic resonance imaging analysis in the central field in humans with moderate-to-severe amblyopia. We measured the relationship between averaged pRF size and retinal eccentricity in retinotopic visual areas. Results showed that cortical magnification is normal in the foveal field of strabismic amblyopes. However, the pRF sizes are enlarged for the amblyopic eye. We speculate that the pRF enlargement reflects loss of cellular resolution or an increased cellular positional disarray within the representation of the amblyopic eye. The neural basis of amblyopia, a visual deficit affecting 3% of the human population, remains a matter of debate. We undertook the first population receptive field functional magnetic resonance imaging analysis in participants with amblyopia and compared the projections from the amblyopic and fellow normal eye in the visual cortex. The projection from the amblyopic eye was found to have a normal cortical magnification factor, enlarged population receptive field sizes, and topographic disorganization in all early visual areas. This is consistent with an explanation of amblyopia as an immature system with a normal complement of cells whose spatial resolution is reduced and whose topographical map is disordered. This bears upon a number of competing theories for the psychophysical defect and affects future treatment therapies. Copyright © 2015 the authors 0270-6474/15/3514740-16$15.00/0.

Do persistently fast-growing juveniles contribute disproportionately to population growth? A new analysis tool for matrix models and its application to rainforest trees.

PubMed

Zuidema, Pieter A; Brienen, Roel J W; During, Heinjo J; Güneralp, Burak

2009-11-01

Plants and animals often exhibit strong and persistent growth variation among individuals within a species. Persistently fast-growing individuals have a higher chance of reaching reproductive size, do so at a younger age, and therefore contribute disproportionately to population growth (lambda). Here we introduce a new approach to quantify this "fast-growth effect." We propose using age-size-structured matrix models in which persistently fast and slow growers are distinguished as they occur in relatively young and old age classes for a given size category. Life-cycle pathways involving fast growth can then be identified, and their contribution to lambda is quantified through loop analysis. We applied this approach to an example species, the tropical rainforest tree Cedrela odorata, that shows persistent growth variation among individuals. Loop analysis showed that juvenile trees reaching the 10-cm diameter class at below-median age contributed twice as much to lambda as slow juvenile growers. Fast growth to larger-diameter categories also contributed disproportionately to lambda. The results were robust to changes in parameter values and life-history trade-offs. These results show that the fast-growth effect can be strong in long-lived species. Persistent growth differences among individuals should therefore be accommodated for in demographic models and life-history studies.

Using Satellite Imagery to Assess Large-Scale Habitat Characteristics of Adirondack Park, New York, USA

NASA Astrophysics Data System (ADS)

McClain, Bobbi J.; Porter, William F.

2000-11-01

Satellite imagery is a useful tool for large-scale habitat analysis; however, its limitations need to be tested. We tested these limitations by varying the methods of a habitat evaluation for white-tailed deer ( Odocoileus virginianus) in the Adirondack Park, New York, USA, utilizing harvest data to create and validate the assessment models. We used two classified images, one with a large minimum mapping unit but high accuracy and one with no minimum mapping unit but slightly lower accuracy, to test the sensitivity of the evaluation to these differences. We tested the utility of two methods of assessment, habitat suitability index modeling, and pattern recognition modeling. We varied the scale at which the models were applied by using five separate sizes of analysis windows. Results showed that the presence of a large minimum mapping unit eliminates important details of the habitat. Window size is relatively unimportant if the data are averaged to a large resolution (i.e., township), but if the data are used at the smaller resolution, then the window size is an important consideration. In the Adirondacks, the proportion of hardwood and softwood in an area is most important to the spatial dynamics of deer populations. The low occurrence of open area in all parts of the park either limits the effect of this cover type on the population or limits our ability to detect the effect. The arrangement and interspersion of cover types were not significant to deer populations.

NEWLY QUENCHED GALAXIES AS THE CAUSE FOR THE APPARENT EVOLUTION IN AVERAGE SIZE OF THE POPULATION

DOE Office of Scientific and Technical Information (OSTI.GOV)

Carollo, C. M.; Bschorr, T. J.; Lilly, S. J.

2013-08-20

We use the large COSMOS sample of galaxies to study in an internally self-consistent way the change in the number densities of quenched early-type galaxies (Q-ETGs) of a given size over the redshift interval 0.2 < z < 1 in order to study the claimed size evolution of these galaxies. In a stellar mass bin at 10{sup 10.5} < M{sub galaxy} < 10{sup 11} M{sub Sun }, we see no change in the number density of compact Q-ETGs over this redshift range, while in a higher mass bin at >10{sup 11} M{sub Sun }, where we would expect merging tomore » be more significant, we find a small decrease, by {approx}30%. In both mass bins, the increase of the median sizes of Q-ETGs with time is primarily caused by the addition to the size function of larger and more diffuse Q-ETGs. At all masses, compact Q-ETGs become systematically redder toward later epochs, with a (U - V) color difference which is consistent with a passive evolution of their stellar populations, indicating that they are a stable population that does not appreciably evolve in size. We find furthermore, at all epochs, that the larger Q-ETGs (at least in the lower mass bin) have average rest-frame colors that are systematically bluer than those of the more compact Q-ETGs, suggesting that the former are indeed younger than the latter. The idea that new, large, Q-ETGs are responsible for the observed growth in the median size of the population at a given mass is also supported by analysis of the sizes and number of the star-forming galaxies that are expected to be the progenitors of the new Q-ETGs over the same period. In the low mass bin, the new Q-ETGs appear to have {approx}30% smaller half-light radii than their star-forming progenitors. This is likely due to the fading of their disks after they cease star formation. Comparison with higher redshifts shows that the median size of newly quenched galaxies roughly scales, at constant mass, as (1 + z){sup -1}. We conclude that the dominant cause of the size evolution seen in the Q-ETG population is that the average sizes and thus stellar densities of individual Q-ETGs roughly scale with the average density of the universe at the time when they were quenched, and that subsequent size changes in individual objects, through merging or other processes, are of secondary importance, especially at masses below 10{sup 11} M{sub Sun}.« less

Genetic analysis of Mexican Criollo cattle populations.

PubMed

Ulloa-Arvizu, R; Gayosso-Vázquez, A; Ramos-Kuri, M; Estrada, F J; Montaño, M; Alonso, R A

2008-10-01

The objective of this study was to evaluate the genetic structure of Mexican Criollo cattle populations using microsatellite genetic markers. DNA samples were collected from 168 animals from four Mexican Criollo cattle populations, geographically isolated in remote areas of Sierra Madre Occidental (West Highlands). Also were included samples from two breeds with Iberian origin: the fighting bull (n = 24) and the milking central American Criollo (n = 24) and one Asiatic breed: Guzerat (n = 32). Genetic analysis consisted of the estimation of the genetic diversity in each population by the allele number and the average expected heterozygosity found in nine microsatellite loci. Furthermore, genetic relationships among the populations were defined by their genetic distances. Our data shows that Mexican cattle populations have a relatively high level of genetic diversity based either on the mean number of alleles (10.2-13.6) and on the expected heterozygosity (0.71-0.85). The degree of observed homozygosity within the Criollo populations was remarkable and probably caused by inbreeding (reduced effective population size) possibly due to reproductive structure within populations. Our data shows that considerable genetic differentiation has been occurred among the Criollo cattle populations in different regions of Mexico.

Genetic diversity and structure in the Endangered Allen Cays Rock Iguana, Cyclura cychlura inornata

PubMed Central

Aplasca, Andrea C.; Iverson, John B.; Welch, Mark E.; Colosimo, Giuliano

2016-01-01

The Endangered Allen Cays Rock Iguana (Cyclura cychlura inornata) is endemic to the Allen Cays, a tiny cluster of islands in the Bahamas. Naturally occurring populations exist on only two cays (<4 ha each). However, populations of unknown origin were recently discovered on four additional cays. To investigate patterns of genetic variation among these populations, we analyzed nuclear and mitochondrial markers for 268 individuals. Analysis of three mitochondrial gene regions (2,328 bp) and data for eight nuclear microsatellite loci indicated low genetic diversity overall. Estimates of effective population sizes based on multilocus genotypes were also extremely low. Despite low diversity, significant population structuring and variation in genetic diversity measures were detected among cays. Genetic data confirm the source population for an experimentally translocated population while raising concerns regarding other, unauthorized, translocations. Reduced heterozygosity is consistent with a documented historical population decline due to overharvest. This study provides the first range-wide genetic analysis of this subspecies. We suggest strategies to maximize genetic diversity during ongoing recovery including additional translocations to establish assurance populations and additional protective measures for the two remaining natural populations. PMID:26989628

Genome-wide scan reveals LEMD3 and WIF1 on SSC5 as the candidates for porcine ear size.

PubMed

Zhang, Longchao; Liang, Jing; Luo, Weizhen; Liu, Xin; Yan, Hua; Zhao, Kebin; Shi, Huibi; Zhang, Yuebo; Wang, Ligang; Wang, Lixian

2014-01-01

The quantitative trait loci (QTL) for porcine ear size was previously reported to mainly focus on SSC5 and SSC7. Recently, a missense mutation, G32E, in PPARD in the QTL interval on SSC7 was identified as the causative mutation for ear size. However, on account of the large interval of QTL, the responsible gene on SSC5 has not been identified. In this study, an intercross population was constructed from the large-eared Minzhu, an indigenous Chinese pig breed, and the Western commercial Large White pig to examine the genetic basis of ear size diversity. A GWAS was performed to detect SNPs significantly associated with ear size. Thirty-five significant SNPs defined a 10.78-Mb (30.14-40.92 Mb) region on SSC5. Further, combining linkage disequilibrium and haplotype sharing analysis, a reduced region of 3.07-Mb was obtained. Finally, by using a selective sweep analysis, a critical region of about 450-kb interval containing two annotated genes LEMD3 and WIF1 was refined in this work. Functional analysis indicated that both represent biological candidates for porcine ear size, with potential application in breeding programs. The two genes could also be used as novel references for further study of the mechanism underlying human microtia.

The Invisible Cliff: Abrupt Imposition of Malthusian Equilibrium in a Natural-Fertility, Agrarian Society

PubMed Central

Puleston, Cedric; Tuljapurkar, Shripad; Winterhalder, Bruce

2014-01-01

Analysis of a natural fertility agrarian society with a multi-variate model of population ecology isolates three distinct phases of population growth following settlement of a new habitat: (1) a sometimes lengthy copial phase of surplus food production and constant vital rates; (2) a brief transition phase in which food shortages rapidly cause increased mortality and lessened fertility; and (3) a Malthusian phase of indefinite length in which vital rates and quality of life are depressed, sometimes strikingly so. Copial phase duration declines with increases in the size of the founding group, maximum life expectancy and fertility; it increases with habitat area and yield per hectare; and, it is unaffected by the sensitivity of vital rates to hunger. Transition phase duration is unaffected by size of founding population and area of settlement; it declines with yield, life expectancy, fertility and the sensitivity of vital rates to hunger. We characterize the transition phase as the Malthusian transition interval (MTI), in order to highlight how little time populations generally have to adjust. Under food-limited density dependence, the copial phase passes quickly to an equilibrium of grim Malthusian constraints, in the manner of a runner dashing over an invisible cliff. The three-phase pattern diverges from widely held intuitions based on standard Lotka-Verhulst approaches to population regulation, with implications for the analysis of socio-cultural evolution, agricultural intensification, bioarchaeological interpretation of food stress in prehistoric societies, and state-level collapse. PMID:24498131

Body Size Changes Among National Collegiate Athletic Association New England Division III Football Players, 1956-2014: Comparison With Age-Matched Population Controls.

PubMed

Elliott, Kayla R; Harmatz, Jerold S; Zhao, Yanli; Greenblatt, David J

2016-05-01

Collegiate football programs encourage athletes to pursue high body weights. To examine position-dependent trends over time in body size characteristics among football players in the National Collegiate Athletic Association Division III New England Small College Athletic Conference (NESCAC) from 1956 to 2014 and to compare the observed absolute and relative changes with those in age-matched male population controls. Descriptive laboratory study. Medical school affiliated with a NESCAC institution. Football team rosters from the 10-member NESCAC schools, available as public documents, were analyzed along with body size data from general population males aged 20 to 29 years from the National Health and Nutrition Examination Survey (NHANES). Body weight, height, and calculated body mass index were evaluated using analysis of variance, linear regression, and nonlinear regression to determine the distribution features of size variables and changes associated with time (year), school, and position. Among NESCAC linemen, absolute and relative changes over time in body weight and body mass index exceeded corresponding changes in the NHANES population controls. New England Small College Athletic Conference offensive linemen body weights increased by 37.5% from 1956 to 2014 (192 to 264 lb [86.4 to 118.8 kg]), compared with a 12% increase (164 to 184 lb [73.8 to 82.8 kg]) since 1961 in the NHANES population controls. Body mass index changed in parallel with body weight and exceeded 35 kg/m(2) in more than 30% of contemporary NESCAC offensive linemen. Among skill players in the NESCAC group, time-related changes in body size characteristics generally paralleled those in the NHANES controls. High body weight and body mass indices were evident in offensive linemen, even among those in Division III football programs with no athletic scholarships. These characteristics may be associated with adverse cardiovascular and metabolic outcomes. We need approaches to encourage risk modification in the postfootball lifestyles of these individuals.

Ecological and evolutionary influences on body size and shape in the Galápagos marine iguana (Amblyrhynchus cristatus).

PubMed

Chiari, Ylenia; Glaberman, Scott; Tarroso, Pedro; Caccone, Adalgisa; Claude, Julien

2016-07-01

Oceanic islands are often inhabited by endemic species that have undergone substantial morphological evolutionary change due to processes of multiple colonizations from various source populations, dispersal, and local adaptation. Galápagos marine iguanas are an example of an island endemic exhibiting high morphological diversity, including substantial body size variation among populations and sexes, but the causes and magnitude of this variation are not well understood. We obtained morphological measurements from marine iguanas throughout their distribution range. These data were combined with genetic and local environmental data from each population to investigate the effects of evolutionary history and environmental conditions on body size and shape variation and sexual dimorphism. Our results indicate that body size and shape are highly variable among populations. Sea surface temperature and island perimeter, but not evolutionary history as depicted by phylogeographic patterns in this species, explain variation in body size among populations. Conversely, evolutionary history, but not environmental parameters or island size, was found to influence variation in body shape among populations. Finally, in all populations except one, we found strong sexual dimorphism in body size and shape in which males are larger, with higher heads than females, while females have longer heads than males. Differences among populations suggest that plasticity and/or genetic adaptation may shape body size and shape variation in marine iguanas. This study will help target future investigations to address the contribution of plasticity versus genetic adaptation on size and shape variation in marine iguanas.

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.

Survival of radio-implanted drymarchon couperi (Eastern Indigo Snake) in relation to body size and sex

USGS Publications Warehouse

Hyslop, N.L.; Meyers, J.M.; Cooper, R.J.; Norton, Terry M.

2009-01-01

Drymarchon couperi (eastern indigo snake) has experienced population declines across its range primarily as a result of extensive habitat loss, fragmentation, and degradation. Conservation efforts for D. couperi have been hindered, in part, because of informational gaps regarding the species, including a lack of data on population ecology and estimates of demographic parameters such as survival. We conducted a 2- year radiotelemetry study of D. couperi on Fort Stewart Military Reservation and adjacent private lands located in southeastern Georgia to assess individual characteristics associated with probability of survival. We used known-fate modeling to estimate survival, and an information-theoretic approach, based on a priori hypotheses, to examine intraspecific differences in survival probabilities relative to individual covariates (sex, size, size standardized by sex, and overwintering location). Annual survival in 2003 and 2004 was 0.89 (95% CI = 0.73-0.97, n = 25) and 0.72 (95% CI = 0.52-0.86; n = 27), respectively. Results indicated that body size, standardized by sex, was the most important covariate determining survival of adult D. couperi, suggesting lower survival for larger individuals within each sex. We are uncertain of the mechanisms underlying this result, but possibilities may include greater resource needs for larger individuals within each sex, necessitating larger or more frequent movements, or a population with older individuals. Our results may also have been influenced by analysis limitations because of sample size, other sources of individual variation, or environmental conditions. ?? 2009 by The Herpetologists' League, Inc.

Geohistorical records indicate no impact of the Deepwater Horizon oil spill on oyster body size

PubMed Central

Durham, Stephen R.

2016-01-01

Documentation of the near- and long-term effects of the Deepwater Horizon (DWH) oil spill, one of the largest environmental disasters in US history, is still ongoing. We used a novel before-after-control-impact analysis to test the hypothesis that average body size of intertidal populations of the eastern oyster (Crassostrea virginica) inhabiting impacted areas in Louisiana decreased due to increased stress/mortality related to the oil spill. Time-averaged death assemblages of oysters were used to establish a pre-spill baseline of body-size structure for four impacted and four control locations along a 350 km stretch of Louisiana's coastline. Post-spill body sizes were then measured from live oysters at each site in order to evaluate the differences in body size between oiled (i.e. impact) and unoiled (i.e. control) locations before and after the spill. Our results indicate that average body size of oysters remained relatively unchanged after the oil spill. There were also no temporal patterns in temperature, salinity or disease prevalence that could have explained our results. Together, these findings suggest that oysters either recovered rapidly following the immediate impact of the DWH oil spill, or that its impact was not severe enough to influence short-term population dynamics of the oyster beds. PMID:28018663

Influence of harvesting pressure on demographic tactics: Implications for wildlife management

USGS Publications Warehouse

Servanty, S.; Gaillard, J.-M.; Ronchi, F.; Focardi, S.; Baubet, E.; Gimenez, O.

2011-01-01

Demographic tactics within animal populations are shaped by selective pressures. Exploitation exerts additional pressures so that differing demographic tactics might be expected among populations with differences in levels of exploitation. Yet little has been done so far to assess the possible consequences of exploitation on the demographic tactics of mammals, even though such information could influence the choice of effective management strategies. Compared with similar-sized ungulate species, wild boar Sus scrofa has high reproductive capabilities, which complicates population management. Using a perturbation analysis, we investigated how population growth rates (??) and critical life-history stages differed between two wild boar populations monitored for several years, one of which was heavily harvested and the other lightly harvested. Asymptotic ?? was 1??242 in the lightly hunted population and 1??115 in the heavily hunted population, while the ratio between the elasticity of adult survival and juvenile survival was 2??63 and 1??27, respectively. A comparative analysis including 21 other ungulate species showed that the elasticity ratio in the heavily hunted population was the lowest ever observed. Compared with expected generation times of similar-sized ungulates (more than 6years), wild boar has a fast life-history speed, especially when facing high hunting pressure. This is well illustrated by our results, where generation times were 3??6years in the lightly hunted population and only 2??3years in the heavily hunted population. High human-induced mortality combined with non-limiting food resources accounted for the accelerated life history of the hunted population because of earlier reproduction. Synthesis and applications. For wild boar, we show that when a population is facing a high hunting pressure, increasing the mortality in only one age-class (e.g. adults or juveniles) may not allow managers to limit population growth. We suggest that simulations of management strategies based on context-specific demographic models are useful for selecting interventions for population control. This type of approach allows the assessment of population response to exploitation by considering a range of plausible scenarios, improving the chance of selecting appropriate management actions. ?? 2011 The Authors. Journal of Applied Ecology ?? 2011 British Ecological Society.

Integrated investigation of the mixed origin of lunar sample 72161,11

NASA Technical Reports Server (NTRS)

Basu, A.; Des Marais, D. J.; Hayes, J. M.; Meinschein, W. G.

1975-01-01

The comminution-agglutination model and the solar-wind implantation-retention model are used to postulate the origins of the particulate components of lunar sample (72161,11), a submillimeter fraction of a surface sample for the dark mantle regolith at LRV-3. Grain-size analysis was performed by wet sieving with liquid argon, and analyses for CO2, CO, CH4, and H2 were carried out by stepwise pyrolysis in a helium atmosphere. The results indicate that the present sample is from a mature regolith, but the agglutinate content is only 30% in the particle-size range between 90 and 177 microns, indicating an apparent departure from steady state. Analyses of the carbon, methane, and hydrogen concentrations in size fractions larger than 149 microns show that the volume-correlated component of these species increases with increased grain size. It is suggested that the observed increase can be explained in terms of mixing of a dominant local population of coarser agglutinates having high carbon and hydrogen concentrations with an imported population of finer agglutinates relatively poor in carbon and hydrogen.

In vitro ovine articular chondrocyte proliferation: experiments and modelling.

PubMed

Mancuso, L; Liuzzo, M I; Fadda, S; Pisu, M; Cincotti, A; Arras, M; La Nasa, G; Concas, A; Cao, G

2010-06-01

This study focuses on analysis of in vitro cultures of chondrocytes from ovine articular cartilage. Isolated cells were seeded in Petri dishes, then expanded to confluence and phenotypically characterized by flow cytometry. The sigmoidal temporal profile of total counts was obtained by classic haemocytometry and corresponding cell size distributions were measured electronically using a Coulter Counter. A mathematical model recently proposed (1) was adopted for quantitative interpretation of these experimental data. The model is based on a 1-D (that is, mass-structured), single-staged population balance approach capable of taking into account contact inhibition at confluence. The model's parameters were determined by fitting measured total cell counts and size distributions. Model reliability was verified by predicting cell proliferation counts and corresponding size distributions at culture times longer than those used when tuning the model's parameters. It was found that adoption of cell mass as the intrinsic characteristic of a growing chondrocyte population enables sigmoidal temporal profiles of total counts in the Petri dish, as well as cell size distributions at 'balanced growth', to be adequately predicted.

Tidal saltmarsh fragmentation and persistence of San Pablo Song Sparrows (Melospiza melodia samuelis): Assessing benefits of wetland restoration in San Francisco Bay

USGS Publications Warehouse

Takekawa, John Y.; Sacks, B.N.; Woo, I.; Johnson, M.L.; Wylie, G.D.; ,

2006-01-01

The San Pablo Song Sparrow (Melospiza melodia samuelis) is one of three morphologically distinct Song Sparrow subspecies in tidal marshes of the San Francisco Bay estuary. These subspecies are rare, because as the human population has grown, diking and development have resulted in loss of 79% of the historic tidal marshes. Hundreds of projects have been proposed in the past decade to restore tidal marshes and benefit endemic populations. To evaluate the value of these restoration projects for Song Sparrows, we developed a population viability analysis (PVA) model to examine persistence of samuelis subspecies in relation to parcel size, connectivity, and catastrophe in San Pablo Bay. A total of 101 wetland parcels were identified from coverages of modern and historic tidal marshes. Parcels were grouped into eight fragments in the historical landscape and 10 in the present landscape. Fragments were defined as a group of parcels separated by >1 km, a distance that precluded regular interchange. Simulations indicated that the historic (circa 1850) samuelis population was three times larger than the modern population. However, only very high levels (>70% mortality) of catastrophe would threaten their persistence. Persistence of populations was sensitive to parcel size at a carrying capacity of <10 pairs, but connectivity of parcels was found to have little importance because habitats were dominated by a few large parcels. Our analysis indicates little risk of extinction of the samuelis subspecies with the current extent of tidal marshes, but the vulnerability of the small-est parcels suggests that restoration should create larger continuous tracts. Thus, PVA models may be useful tools for balancing the costs and benefits of restoring habitats for threatened tidal-marsh populations in wetland restoration planning.

Size and age structure of anadromous and landlocked populations of Rainbow Smelt

USGS Publications Warehouse

O'Malley, Andrew; Enterline, Claire; Zydlewski, Joseph D.

2017-01-01

Rainbow Smelt Osmerus mordax are widely distributed in both anadromous and landlocked populations throughout northeastern North America; abundance, size at age, and maximum size vary widely among populations and life histories. In the present study, size at age, von Bertalanffy growth parameters, population age distributions, and precision and bias in age assessment based on scales and sectioned otoliths were compared between ecotypes and among populations of Rainbow Smelt. To compare the ecotypes, we collected spawning adults from four anadromous and three landlocked populations in Maine during spring 2014. A significant bias was identified in only one of four scale comparisons but in four of seven otolith comparisons; however, a comparable level of precision was indicated. Anadromous populations had larger and more variable size at age and von Bertalanffy growth parameters than landlocked fish. Populations were composed of ages 1–4; six populations were dominated by age-2 or age-3 individuals, and one population was dominated by age-1 fish. These data suggest the presence of considerable plasticity among populations. A latitudinal gradient was observed in the anadromous Rainbow Smelt, which may show signs of population stress at the southern extent of their distribution.

On the number of New World founders: a population genetic portrait of the peopling of the Americas.

PubMed

Hey, Jody

2005-06-01

The founding of New World populations by Asian peoples is the focus of considerable archaeological and genetic research, and there persist important questions on when and how these events occurred. Genetic data offer great potential for the study of human population history, but there are significant challenges in discerning distinct demographic processes. A new method for the study of diverging populations was applied to questions on the founding and history of Amerind-speaking Native American populations. The model permits estimation of founding population sizes, changes in population size, time of population formation, and gene flow. Analyses of data from nine loci are consistent with the general portrait that has emerged from archaeological and other kinds of evidence. The estimated effective size of the founding population for the New World is fewer than 80 individuals, approximately 1% of the effective size of the estimated ancestral Asian population. By adding a splitting parameter to population divergence models it becomes possible to develop detailed portraits of human demographic history. Analyses of Asian and New World data support a model of a recent founding of the New World by a population of quite small effective size.

Evolutionary dynamics with fluctuating population sizes and strong mutualism.

PubMed

Chotibut, Thiparat; Nelson, David R

2015-08-01

Game theory ideas provide a useful framework for studying evolutionary dynamics in a well-mixed environment. This approach, however, typically enforces a strictly fixed overall population size, deemphasizing natural growth processes. We study a competitive Lotka-Volterra model, with number fluctuations, that accounts for natural population growth and encompasses interaction scenarios typical of evolutionary games. We show that, in an appropriate limit, the model describes standard evolutionary games with both genetic drift and overall population size fluctuations. However, there are also regimes where a varying population size can strongly influence the evolutionary dynamics. We focus on the strong mutualism scenario and demonstrate that standard evolutionary game theory fails to describe our simulation results. We then analytically and numerically determine fixation probabilities as well as mean fixation times using matched asymptotic expansions, taking into account the population size degree of freedom. These results elucidate the interplay between population dynamics and evolutionary dynamics in well-mixed systems.

Evolutionary dynamics with fluctuating population sizes and strong mutualism

NASA Astrophysics Data System (ADS)

Chotibut, Thiparat; Nelson, David R.

2015-08-01

Game theory ideas provide a useful framework for studying evolutionary dynamics in a well-mixed environment. This approach, however, typically enforces a strictly fixed overall population size, deemphasizing natural growth processes. We study a competitive Lotka-Volterra model, with number fluctuations, that accounts for natural population growth and encompasses interaction scenarios typical of evolutionary games. We show that, in an appropriate limit, the model describes standard evolutionary games with both genetic drift and overall population size fluctuations. However, there are also regimes where a varying population size can strongly influence the evolutionary dynamics. We focus on the strong mutualism scenario and demonstrate that standard evolutionary game theory fails to describe our simulation results. We then analytically and numerically determine fixation probabilities as well as mean fixation times using matched asymptotic expansions, taking into account the population size degree of freedom. These results elucidate the interplay between population dynamics and evolutionary dynamics in well-mixed systems.

Risk Analysis in Support of the Chemical Stockpile Disposal Program. Volume 1. Analysis

DTIC Science & Technology

1987-12-17

Analysis of Event Probability A-14 A.4.2 Analysis of Event Consequence A-14 A.4.2.1 Agent Release to Atmosphere A-14 A.4.2.2 Toxic P-lume Size A-16 A...Disposal Program (CSDP), which comprises several alternatives for carrying out the disposal effort (U.S. Army Toxic and Hazardous Materials Agency, 1986...or unavoidable accident or event could occur that would expose a nearby civilian population to these toxic chemicals. Such events could occur even

Assessing the roles of population density and predation risk in the evolution of offspring size in populations of a placental fish

PubMed Central

Schrader, Matthew; Travis, Joseph

2012-01-01

Population density is an ecological variable that is hypothesized to be a major agent of selection on offspring size. In high-density populations, high levels of intraspecific competition are expected to favor the production of larger offspring. In contrast, lower levels of intraspecific competition and selection for large offspring should be weaker and more easily overridden by direct selection for increased fecundity in low-density populations. Some studies have found associations between population density and offspring size consistent with this hypothesis. However, their interpretations are often clouded by a number of issues. Here, we use data from a 10-year study of nine populations of the least killifish, Heterandria formosa, to describe the associations of offspring size with habitat type, population density, and predation risk. We found that females from spring populations generally produced larger offspring than females from ponds; however, the magnitude of this difference varied among years. Across all populations, larger offspring were associated with higher densities and lower risks of predation. Interestingly, the associations between the two ecological variables (density and predation risk) and offspring size were largely independent of one another. Our results suggest that previously described genetic differences in offspring size are due to density-dependent natural selection. PMID:22957156

Directionality theory and the evolution of body size.

PubMed

Demetrius, L

2000-12-07

Directionality theory, a dynamic theory of evolution that integrates population genetics with demography, is based on the concept of evolutionary entropy, a measure of the variability in the age of reproducing individuals in a population. The main tenets of the theory are three principles relating the response to the ecological constraints a population experiences, with trends in entropy as the population evolves under mutation and natural selection. (i) Stationary size or fluctuations around a stationary size (bounded growth): a unidirectional increase in entropy; (ii) prolonged episodes of exponential growth (unbounded growth), large population size: a unidirectional decrease in entropy; and (iii) prolonged episodes of exponential growth (unbounded growth), small population size: random, non-directional change in entropy. We invoke these principles, together with an allometric relationship between entropy, and the morphometric variable body size, to provide evolutionary explanations of three empirical patterns pertaining to trends in body size, namely (i) Cope's rule, the tendency towards size increase within phyletic lineages; (ii) the island rule, which pertains to changes in body size that occur as species migrate from mainland populations to colonize island habitats; and (iii) Bergmann's rule, the tendency towards size increase with increasing latitude. The observation that these ecotypic patterns can be explained in terms of the directionality principles for entropy underscores the significance of evolutionary entropy as a unifying concept in forging a link between micro-evolution, the dynamics of gene frequency change, and macro-evolution, dynamic changes in morphometric variables.

Weeds, as ancillary hosts, pose disproportionate risk for virulent pathogen transfer to crops.

PubMed

Linde, Celeste C; Smith, Leon M; Peakall, Rod

2016-05-12

The outcome of the arms race between hosts and pathogens depends heavily on the interactions between their genetic diversity, population size and transmission ability. Theory predicts that genetically diverse hosts will select for higher virulence and more diverse pathogens than hosts with low genetic diversity. Cultivated hosts typically have lower genetic diversity and thus small effective population sizes, but can potentially harbour large pathogen population sizes. On the other hand, hosts, such as weeds, which are genetically more diverse and thus have larger effective population sizes, usually harbour smaller pathogen population sizes. Large pathogen population sizes may lead to more opportunities for mutation and hence more diverse pathogens. Here we test the predictions that pathogen neutral genetic diversity will increase with large pathogen population sizes and host diversity, whereas diversity under selection will increase with host diversity. We assessed and compared the diversity of a fungal pathogen, Rhynchosporium commune, on weedy barley grass (which have a large effective population size) and cultivated barley (low genetic diversity) using microsatellites, effector locus nip1 diversity and pathogen aggressiveness in order to assess the importance of weeds in the evolution of the neutral and selected diversity of pathogens. The findings indicated that the large barley acreage and low host diversity maintains higher pathogen neutral genetic diversity and lower linkage disequilibrium, while the weed maintains more pathotypes and higher virulence diversity at nip1. Strong evidence for more pathogen migration from barley grass to barley suggests transmission of virulence from barley grass to barley is common. Pathogen census population size is a better predictor for neutral genetic diversity than host diversity. Despite maintaining a smaller pathogen census population size, barley grass acts as an important ancillary host to R. commune, harbouring highly virulent pathogen types capable of transmission to barley. Management of disease on crops must therefore include management of weedy ancillary hosts, which may harbour disproportionate supplies of virulent pathogen strains.

Match or mismatch: the influence of phenology on size-dependent life history and divergence in population structure

USGS Publications Warehouse

Borcherding, Jost; Beeck, Peter; DeAngelis, Donald L.; Scharf, Werner R.

2010-01-01

Summary 1. In gape-limited predators, body size asymmetries determine the outcome of predator-prey interactions. Due to ontogenetic changes in body size, the intensity of intra- and interspecific interactions may change rapidly between the match situation of a predator-prey system and the mismatch situation in which competition, including competition with the prey, dominates. 2. Based on a physiologically structured population model using the European perch (Perca fluviatilis), analysis was performed on how prey density (bream, Abramis brama), initial size differences in the young-of-the-year (YOY) age cohort of the predator, and phenology (time-gap in hatching of predator and prey) influence the size structure of the predator cohort. 3. In relation to the seasonality of reproduction, the match situation of the predator-prey system occurred when perch hatched earlier than bream and when no gape-size limitations existed, leading to decreased size divergence in the predator age cohort. Decreased size divergence was also found when bream hatched much earlier than perch, preventing perch predation on bream occurring, which, in turn, increased the competitive interaction of the perch with bream for the common prey, zooplankton; i.e. the mismatch situation in which also the mean size of the age cohort of the predator decreased. 4. In between the total match and the mismatch, however, only the largest individuals of the perch age cohort were able to prey on the bream, while smaller conspecifics got trapped in competition with each other and with bream for zooplankton, leading to enlarged differences in growth that increased size divergence. 5. The modelling results were combined with 7 years of field data in a lake, where large differences in the length-frequency distribution of YOY perch were observed after their first summer. These field data corroborate that phenology and prey density per predator are important mechanisms in determining size differences within the YOY age cohort of the predator. 6. The results demonstrate that the switch between competitive interactions and a predator-prey relationship depended on phenology. This resulted in pronounced size differences in the YOY age cohort, which had far-reaching consequences for the entire predator population.

Problems with sampling desert tortoises: A simulation analysis based on field data

USGS Publications Warehouse

Freilich, J.E.; Camp, R.J.; Duda, J.J.; Karl, A.E.

2005-01-01

The desert tortoise (Gopherus agassizii) was listed as a U.S. threatened species in 1990 based largely on population declines inferred from mark-recapture surveys of 2.59-km2 (1-mi2) plots. Since then, several census methods have been proposed and tested, but all methods still pose logistical or statistical difficulties. We conducted computer simulations using actual tortoise location data from 2 1-mi2 plot surveys in southern California, USA, to identify strengths and weaknesses of current sampling strategies. We considered tortoise population estimates based on these plots as "truth" and then tested various sampling methods based on sampling smaller plots or transect lines passing through the mile squares. Data were analyzed using Schnabel's mark-recapture estimate and program CAPTURE. Experimental subsampling with replacement of the 1-mi2 data using 1-km2 and 0.25-km2 plot boundaries produced data sets of smaller plot sizes, which we compared to estimates from the 1-mi 2 plots. We also tested distance sampling by saturating a 1-mi 2 site with computer simulated transect lines, once again evaluating bias in density estimates. Subsampling estimates from 1-km2 plots did not differ significantly from the estimates derived at 1-mi2. The 0.25-km2 subsamples significantly overestimated population sizes, chiefly because too few recaptures were made. Distance sampling simulations were biased 80% of the time and had high coefficient of variation to density ratios. Furthermore, a prospective power analysis suggested limited ability to detect population declines as high as 50%. We concluded that poor performance and bias of both sampling procedures was driven by insufficient sample size, suggesting that all efforts must be directed to increasing numbers found in order to produce reliable results. Our results suggest that present methods may not be capable of accurately estimating desert tortoise populations.

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

USGS Publications Warehouse

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.

Whitebark Pine, Population Density, and Home-Range Size of Grizzly Bears in the Greater Yellowstone Ecosystem

PubMed Central

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. PMID:24520354

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.

[Comparison of application of Cochran-Armitage trend test and linear regression analysis for rate trend analysis in epidemiology study].

PubMed

Wang, D Z; Wang, C; Shen, C F; Zhang, Y; Zhang, H; Song, G D; Xue, X D; Xu, Z L; Zhang, S; Jiang, G H

2017-05-10

We described the time trend of acute myocardial infarction (AMI) from 1999 to 2013 in Tianjin incidence rate with Cochran-Armitage trend (CAT) test and linear regression analysis, and the results were compared. Based on actual population, CAT test had much stronger statistical power than linear regression analysis for both overall incidence trend and age specific incidence trend (Cochran-Armitage trend P value

Complete Streets and Adult Bicyclist Fatalities: Applying G-Computation to Evaluate an Intervention That Affects the Size of a Population at Risk.

PubMed

Mooney, Stephen J; Magee, Caroline; Dang, Kolena; Leonard, Julie C; Yang, Jingzhen; Rivara, Frederick P; Ebel, Beth E; Rowhani-Rahbar, Ali; Quistberg, D Alex

2018-05-14

"Complete Streets" policies require transportation engineers to make provisions for pedestrians, cyclists and transit users. These policies may make bicycling safer for individual cyclists while increasing overall bicycle fatalities if more individuals cycle due to improved infrastructure. We merged county-level records of Complete Streets policies with Fatality Analysis Reporting System counts of cyclist fatalities occurring between January 2000 and December 2015. Because comprehensive county cycling estimates were not available, we used bicycle commute estimates from the American Community Survey and US Census as a proxy for the cycling population, and limited analysis to 183 counties (accounting for over half the US population) for which cycle commute estimates were consistently non-zero. We used G-computation to estimate the effect of policies on overall cyclist fatalities while also accounting for potential policy effects on the size of the cycling population. Over 16 years, 5,254 cyclists died in these counties, representing 34 fatalities per 100,000 cyclist-years. We estimated that Complete Streets policies made cycling safer, averting 0.6 fatalities per 100,000 cyclist-years (95% CI: 0.3, 1.0) by encouraging a 2.4% increase in cycling and a 0.7% increase in cyclist fatalities. G-computation is a useful tool for understanding policy impact on risk and exposure.

Evaluation of tools for highly variable gene discovery from single-cell RNA-seq data.

PubMed

Yip, Shun H; Sham, Pak Chung; Wang, Junwen

2018-02-21

Traditional RNA sequencing (RNA-seq) allows the detection of gene expression variations between two or more cell populations through differentially expressed gene (DEG) analysis. However, genes that contribute to cell-to-cell differences are not discoverable with RNA-seq because RNA-seq samples are obtained from a mixture of cells. Single-cell RNA-seq (scRNA-seq) allows the detection of gene expression in each cell. With scRNA-seq, highly variable gene (HVG) discovery allows the detection of genes that contribute strongly to cell-to-cell variation within a homogeneous cell population, such as a population of embryonic stem cells. This analysis is implemented in many software packages. In this study, we compare seven HVG methods from six software packages, including BASiCS, Brennecke, scLVM, scran, scVEGs and Seurat. Our results demonstrate that reproducibility in HVG analysis requires a larger sample size than DEG analysis. Discrepancies between methods and potential issues in these tools are discussed and recommendations are made.

Is there sufficient evidence regarding signage-based stair use interventions? A sequential meta-analysis

PubMed Central

Bauman, Adrian; Milton, Karen; Kariuki, Maina; Fedel, Karla; Lewicka, Mary

2017-01-01

Objective The proliferation of studies using motivational signs to promote stair use continues unabated, with their oft-cited potential for increasing population-level physical activity participation. This study examined all stair use promotional signage studies since 1980, calculating pre-estimates and post-estimates of stair use. The aim of this project was to conduct a sequential meta-analysis to pool intervention effects, in order to determine when the evidence base was sufficient for population-wide dissemination. Design Using comparable data from 50 stair-promoting studies (57 unique estimates) we pooled data to assess the effect sizes of such interventions. Results At baseline, median stair usage across interventions was 8.1%, with an absolute median increase of 2.2% in stair use following signage-based interventions. The overall pooled OR indicated that participants were 52% more likely to use stairs after exposure to promotional signs (adjusted OR 1.52, 95% CI 1.37 to 1.70). Incremental (sequential) meta-analyses using z-score methods identified that sufficient evidence for stair use interventions has existed since 2006, with recent studies providing no further evidence on the effect sizes of such interventions. Conclusions This analysis has important policy and practice implications. Researchers continue to publish stair use interventions without connection to policymakers' needs, and few stair use interventions are implemented at a population level. Researchers should move away from repeating short-term, small-scale, stair sign interventions, to investigating their scalability, adoption and fidelity. Only such research translation efforts will provide sufficient evidence of external validity to inform their scaling up to influence population physical activity. PMID:29183924

Essential oil variation among natural populations of Lavandula multifida L. (Lamiaceae).

PubMed

Chograni, Hnia; Zaouali, Yosr; Rajeb, Chayma; Boussaid, Mohamed

2010-04-01

Volatiles from twelve wild Tunisian populations of Lavandula multifida L. growing in different bioclimatic zones were assessed by GC (RI) and GC/MS. Thirty-six constituents, representing 83.48% of the total oil were identified. The major components at the species level were carvacrol (31.81%), beta-bisabolene (14.89%), and acrylic acid dodecyl ester (11.43%). These volatiles, together with alpha-pinene, were also the main compounds discriminating the populations. According to these dominant compounds, one chemotype was revealed, a carvacrol/beta-bisabolene/acrylic acid dodecyl ester chemotype. However, a significant variation among the populations was observed for the majority of the constituents. A high chemical-population structure, estimated both by principal component analysis (PCA) and unweighted pair group method with averaging (UPGMA) cluster analysis based on Euclidean distances, was observed. Both methods allowed separation of the populations in three groups defined rather by minor than by major compounds. The population groups were not strictly concordant with their bioclimatic or geographic location. Conservation strategies should concern all populations, because of their low size and their high level of destruction. Populations exhibiting particular compounds other than the major ones should be protected first.

Construction and analysis of a giant gartersnake (Thamnophis gigas) population projection model

USGS Publications Warehouse

Rose, Jonathan P.; Ersan, Julia S. M.; Wylie, Glenn D.; Casazza, Michael L.; Halstead, Brian J.

2018-03-19

The giant gartersnake (Thamnophis gigas) is a state and federally threatened species precinctive to California. The range of the giant gartersnake has contracted in the last century because its wetland habitat has been drained for agriculture and development. As a result of this habitat alteration, giant gartersnakes now largely persist in and near rice agriculture in the Sacramento Valley, because the system of canals that conveys water for rice growing approximates historical wetland habitat. Many aspects of the demography of giant gartersnakes are unknown, including how individuals grow throughout their life, how size influences reproduction, and how survival varies over time and among populations. We studied giant gartersnakes throughout the Sacramento Valley of California from 1995 to 2016 using capture-mark-recapture to study the growth, reproduction, and survival of this threatened species. We then use these data to construct an Integral Projection Model, and analyze this demographic model to understand which vital rates contribute most to the growth rate of giant gartersnake populations. We find that giant gartersnakes exhibit indeterminate growth; growth slows as individuals’ age. Fecundity, probability of reproduction, and survival all increase with size, although survival may decline for the largest female giant gartersnakes. The population growth rate of giant gartersnakes is most influenced by the survival and growth of large adult females, and the size at which 1 year old recruits enter the population. Our results indicate that management actions benefitting these influential demographic parameters will have the greatest positive effect on giant gartersnake population growth rates, and therefore population persistence. This study informs the conservation and management of giant gartersnakes and their habitat, and illustrates the effectiveness of hierarchical Bayesian models for the study of rare and elusive species.

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.

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

PubMed Central

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

2015-01-01

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

Study design and statistical analysis of data in human population studies with the micronucleus assay.

PubMed

Ceppi, Marcello; Gallo, Fabio; Bonassi, Stefano

2011-01-01

The most common study design performed in population studies based on the micronucleus (MN) assay, is the cross-sectional study, which is largely performed to evaluate the DNA damaging effects of exposure to genotoxic agents in the workplace, in the environment, as well as from diet or lifestyle factors. Sample size is still a critical issue in the design of MN studies since most recent studies considering gene-environment interaction, often require a sample size of several hundred subjects, which is in many cases difficult to achieve. The control of confounding is another major threat to the validity of causal inference. The most popular confounders considered in population studies using MN are age, gender and smoking habit. Extensive attention is given to the assessment of effect modification, given the increasing inclusion of biomarkers of genetic susceptibility in the study design. Selected issues concerning the statistical treatment of data have been addressed in this mini-review, starting from data description, which is a critical step of statistical analysis, since it allows to detect possible errors in the dataset to be analysed and to check the validity of assumptions required for more complex analyses. Basic issues dealing with statistical analysis of biomarkers are extensively evaluated, including methods to explore the dose-response relationship among two continuous variables and inferential analysis. A critical approach to the use of parametric and non-parametric methods is presented, before addressing the issue of most suitable multivariate models to fit MN data. In the last decade, the quality of statistical analysis of MN data has certainly evolved, although even nowadays only a small number of studies apply the Poisson model, which is the most suitable method for the analysis of MN data.

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

PubMed

Mendez, Fernando L

2017-04-01

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

A multi-scale assessment of animal aggregation patterns to understand increasing pathogen seroprevalence

USGS Publications Warehouse

Brennan, Angela K.; Cross, Paul C.; Higgs, Megan D.; Edwards, W. Henry; Scurlock, Brandon M.; Creel, Scott

2014-01-01

Understanding how animal density is related to pathogen transmission is important to develop effective disease control strategies, but requires measuring density at a scale relevant to transmission. However, this is not straightforward or well-studied among large mammals with group sizes that range several orders of magnitude or aggregation patterns that vary across space and time. To address this issue, we examined spatial variation in elk (Cervus canadensis) aggregation patterns and brucellosis across 10 regions in the Greater Yellowstone Area where previous studies suggest the disease may be increasing. We hypothesized that rates of increasing brucellosis would be better related to the frequency of large groups than mean group size or population density, but we examined whether other measures of density would also explain rising seroprevalence. To do this, we measured wintering elk density and group size across multiple spatial and temporal scales from monthly aerial surveys. We used Bayesian hierarchical models and 20 years of serologic data to estimate rates of increase in brucellosis within the 10 regions, and to examine the linear relationships between these estimated rates of increase and multiple measures of aggregation. Brucellosis seroprevalence increased over time in eight regions (one region showed an estimated increase from 0.015 in 1991 to 0.26 in 2011), and these rates of increase were positively related to all measures of aggregation. The relationships were weaker when the analysis was restricted to areas where brucellosis was present for at least two years, potentially because aggregation was related to disease-establishment within a population. Our findings suggest that (1) group size did not explain brucellosis increases any better than population density and (2) some elk populations may have high densities with small groups or lower densities with large groups, but brucellosis is likely to increase in either scenario. In this case, any one control method such as reducing population density or group size may not be sufficient to reduce transmission. This study highlights the importance of examining the density-transmission relationship at multiple scales and across populations before broadly applying disease control strategies.

Post-Chelyabinsk Risk Assessment for Near Earth Objects (NEOs)

NASA Astrophysics Data System (ADS)

Boslough, M.; Harris, A. W.

2014-12-01

The widely-accepted NEO risk assessments published in the 1990s concluded that the largest asteroids (> 1 km) dominated the hazard. Even though large NEOs represent only a tiny fraction of the population because of a power-law size distribution, the potential for global catastrophe means that the contribution from these low-probability, high-consequence events is large. This conclusion led to the Spaceguard survey, which has now catalogued about 90% of these objects, none of which is on a collision course. The survey has reduced the assessed risk from this size range by more than an order of magnitude because completion is highest for the largest and most dangerous. The relative risk from objects tens of meters in diameter is therefore increasing.The absolute assessed risk from airbursts caused by objects of this size is also higher for two reasons. First, they may be more frequent than previously thought because of an underestimated population. Second, they are significantly more damaging than assumed in the original assessment because (in most cases) they more efficiently couple energy to the surface than nuclear explosions. Last year's half-megaton airburst over Chelyabinsk, Russia, appears to challenge the notion that such events are extremely rare—especially when also considering the 1908 Tunguska event along with decades of infrasound bolide data showing higher-than-expected numbers of large airbursts.We will present a new analysis of the risk based on updated estimates for the population of undiscovered NEOs, taking into account the enhanced damage potential of collisional airbursts. Merging the survey population estimates with the bolide frequency estimates suggests a population of tens-of-meters sized bodies that may be a factor of three or so greater than estimated from surveys alone. Uncertainty in the population of airburst-class NEOs remains quite large, and can only be unambiguously reduced by expanded surveys focused on objects in the tens-of-meters size range. Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy under Contract DE-AC04-94AL85000.

Estimates of population genetic diversity in brown bullhead catfish by DNA fingerprinting

DOE Office of Scientific and Technical Information (OSTI.GOV)

Roth, A.C.; Wessendarp, T.K.; Gordon, D.A.

Estimates of population genetic diversity may be a sensitive indicator of environmental impact, since limiting the effective breeding population by any means will result in loss of some variant genotypes, as has been demonstrated by allozyme analysis. DNA fingerprinting techniques are also coming into use for population analyses, and the authors chose to apply fingerprinting analysis three populations of brown bullhead catfish collected in Northern Ohio. DNA was isolated from the red blood cells of individual fish. Purified DNAs were digested with EcoR1 restriction enzyme; the digests were then sized on a 1% agarose gel, transferred to nylon membranes andmore » probed with a radiolabeled M13 probe using the Westneat hybridization protocol (Southern blotting). This method effects fragments containing VNTR (variable number of tandem repeat) sequences complementary to the M13, which are highly variable among individual catfish. Hybridized bands were visualized by a Molecular Dynamics phosphorimager and recorded and analyzed with its proprietary Imagequant image analysis program, Excel and SAS. A total of 10 variable bands were identified and their presence or absence scored in each individual. These data were analyzed to determine between and within-population similarity indices as well as population heterozygosity and genetic diversity measures.« less

FORMATOMATIC: a program for converting diploid allelic data between common formats for population genetic analysis.

PubMed

Manoukis, Nicholas C

2007-07-01

There has been a great increase in both the number of population genetic analysis programs and the size of data sets being studied with them. Since the file formats required by the most popular and useful programs are variable, automated reformatting or conversion between them is desirable. formatomatic is an easy to use program that can read allelic data files in genepop, raw (csv) or convert formats and create data files in nine formats: raw (csv), arlequin, genepop, immanc/bayesass +, migrate, newhybrids, msvar, baps and structure. Use of formatomatic should greatly reduce time spent reformatting data sets and avoid unnecessary errors.

Integrating data from multiple sources for insights into demographic processes: Simulation studies and proof of concept for hierarchical change-in-ratio models.

PubMed

Nilsen, Erlend B; Strand, Olav

2018-01-01

We developed a model for estimating demographic rates and population abundance based on multiple data sets revealing information about population age- and sex structure. Such models have previously been described in the literature as change-in-ratio models, but we extend the applicability of the models by i) using time series data allowing the full temporal dynamics to be modelled, by ii) casting the model in an explicit hierarchical modelling framework, and by iii) estimating parameters based on Bayesian inference. Based on sensitivity analyses we conclude that the approach developed here is able to obtain estimates of demographic rate with high precision whenever unbiased data of population structure are available. Our simulations revealed that this was true also when data on population abundance are not available or not included in the modelling framework. Nevertheless, when data on population structure are biased due to different observability of different age- and sex categories this will affect estimates of all demographic rates. Estimates of population size is particularly sensitive to such biases, whereas demographic rates can be relatively precisely estimated even with biased observation data as long as the bias is not severe. We then use the models to estimate demographic rates and population abundance for two Norwegian reindeer (Rangifer tarandus) populations where age-sex data were available for all harvested animals, and where population structure surveys were carried out in early summer (after calving) and late fall (after hunting season), and population size is counted in winter. We found that demographic rates were similar regardless whether we include population count data in the modelling, but that the estimated population size is affected by this decision. This suggest that monitoring programs that focus on population age- and sex structure will benefit from collecting additional data that allow estimation of observability for different age- and sex classes. In addition, our sensitivity analysis suggests that focusing monitoring towards changes in demographic rates might be more feasible than monitoring abundance in many situations where data on population age- and sex structure can be collected.

cgCorrect: a method to correct for confounding cell-cell variation due to cell growth in single-cell transcriptomics

NASA Astrophysics Data System (ADS)

Blasi, Thomas; Buettner, Florian; Strasser, Michael K.; Marr, Carsten; Theis, Fabian J.

2017-06-01

Accessing gene expression at a single-cell level has unraveled often large heterogeneity among seemingly homogeneous cells, which remains obscured when using traditional population-based approaches. The computational analysis of single-cell transcriptomics data, however, still imposes unresolved challenges with respect to normalization, visualization and modeling the data. One such issue is differences in cell size, which introduce additional variability into the data and for which appropriate normalization techniques are needed. Otherwise, these differences in cell size may obscure genuine heterogeneities among cell populations and lead to overdispersed steady-state distributions of mRNA transcript numbers. We present cgCorrect, a statistical framework to correct for differences in cell size that are due to cell growth in single-cell transcriptomics data. We derive the probability for the cell-growth-corrected mRNA transcript number given the measured, cell size-dependent mRNA transcript number, based on the assumption that the average number of transcripts in a cell increases proportionally to the cell’s volume during the cell cycle. cgCorrect can be used for both data normalization and to analyze the steady-state distributions used to infer the gene expression mechanism. We demonstrate its applicability on both simulated data and single-cell quantitative real-time polymerase chain reaction (PCR) data from mouse blood stem and progenitor cells (and to quantitative single-cell RNA-sequencing data obtained from mouse embryonic stem cells). We show that correcting for differences in cell size affects the interpretation of the data obtained by typically performed computational analysis.

Global human capital: integrating education and population.

PubMed

Lutz, Wolfgang; KC, Samir

2011-07-29

Almost universally, women with higher levels of education have fewer children. Better education is associated with lower mortality, better health, and different migration patterns. Hence, the global population outlook depends greatly on further progress in education, particularly of young women. By 2050, the highest and lowest education scenarios--assuming identical education-specific fertility rates--result in world population sizes of 8.9 and 10.0 billion, respectively. Better education also matters for human development, including health, economic growth, and democracy. Existing methods of multi-state demography can quantitatively integrate education into standard demographic analysis, thus adding the "quality" dimension.

Genetic analysis of the Venezuelan Criollo horse.

PubMed

Cothran, E G; Canelon, J L; Luis, C; Conant, E; Juras, R

2011-10-07

Various horse populations in the Americas have an origin in Spain; they are remnants of the first livestock introduced to the continent early in the colonial period (16th and 17th centuries). We evaluated genetic variability within the Venezuelan Criollo horse and its relationship with other horse breeds. We observed high levels of genetic diversity within the Criollo breed. Significant population differentiation was observed between all South American breeds. The Venezuelan Criollo horse showed high levels of genetic diversity, and from a conservation standpoint, there is no immediate danger of losing variation unless there is a large drop in population size.

Demographic collapse and low genetic diversity of the Irrawaddy dolphin population inhabiting the Mekong River

PubMed Central

Beasley, Isabel; Ackermann, Corinne Y.; Lieckfeldt, Dietmar; Ludwig, Arne; Ryan, Gerard E.; Bejder, Lars; Parra, Guido J.; Wolfensberger, Rebekka; Spencer, Peter B. S.

2018-01-01

In threatened wildlife populations, it is important to determine whether observed low genetic diversity may be due to recent anthropogenic pressure or the consequence of historic events. Historical size of the Irrawaddy dolphin (Orcaella brevirostris) population inhabiting the Mekong River is unknown and there is significant concern for long-term survival of the remaining population as a result of low abundance, slow reproduction rate, high neonatal mortality, and continuing anthropogenic threats. We investigated population structure and reconstructed the demographic history based on 60 Irrawaddy dolphins samples collected between 2001 and 2009. The phylogenetic analysis indicated reciprocal monophyly of Mekong River Orcaella haplotypes with respect to haplotypes from other populations, suggesting long-standing isolation of the Mekong dolphin population from other Orcaella populations. We found that at least 85% of all individuals in the two main study areas: Kratie and Stung Treng, bore the same mitochondrial haplotype. Out of the 21 microsatellite loci tested, only ten were polymorphic and exhibited very low levels of genetic diversity. Both individual and frequency-based approaches suggest very low and non-significant genetic differentiation of the Mekong dolphin population. Evidence for recent bottlenecks was equivocal. Some results suggested a recent exponential decline in the Mekong dolphin population, with the current size being only 5.2% of the ancestral population. In order for the Mekong dolphin population to have any potential for long-term survival, it is imperative that management priorities focus on preventing any further population fragmentation or genetic loss, reducing or eliminating anthropogenic threats, and promoting connectivity between all subpopulations. PMID:29298312

Latino Adolescent Educational Affiliation Profiles

ERIC Educational Resources Information Center

Gonzalez, Laura M.; Cavanaugh, Alyson M.; Taylor, Laura K.; Stein, Gabriela L.; Mayton, Heather N.

2017-01-01

Supporting postsecondary access for Latino adolescents is important due to the size of the population and mixed evidence of progress. In order to better understand the college-going and school belonging attitudes of Latinos, we used an exploratory latent profile analysis to identify the "educational affiliation" profiles present in a…

Conservation Status of the Indo-Pacific Humpback Dolphin (Sousa chinensis) in the Northern Beibu Gulf, China.

PubMed

Chen, Bingyao; Xu, Xinrong; Jefferson, Thomas A; Olson, Paula A; Qin, Qiurong; Zhang, Hongke; He, Liwen; Yang, Guang

2016-01-01

There has been very little previous research on Indo-Pacific humpback dolphins (Sousa chinensis) in the Beibu Gulf of southern China. Here, we report on the population size, habitat and ecology, threats, and overall conservation status of this putative population. 'Population size' was estimated based on photo-identification mark/recapture analysis. It was estimated to number a total of 398-444 individuals (95% CI: 393-506), with two apparently distinct groups in the Dafengjiang-Nanliujiang Estuary and at Shatian-Caotan. Movements of dolphins in the Beibu Gulf appear to be limited, with high site fidelity. These dolphins were found to occur mainly in shallow coastal waters near estuaries. The main threats are fisheries interactions (including by-catch), vessel traffic, mariculture operations, dolphin-watching tourism, and habitat degradation (including marine construction activities and large-scale land reclamation). Although the conservation status of this putative population has been considered to be better than that of other populations of the species in more northern areas of China, there is still reason for strong concern about its future, and several management recommendations are made. © 2016 Elsevier Ltd. All rights reserved.

Effective population size and genetic conservation criteria for bull trout

Treesearch

Bruce E. Rieman; F. W. Allendorf

2001-01-01

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

Assessment of diversity among populations of Rauvolfia serpentina Benth. Ex. Kurtz. from Southern Western Ghats of India, based on chemical profiling, horticultural traits and RAPD analysis.

PubMed

Nair, Vadakkemuriyil Divya; Raj, Rajan Pillai Dinesh; Panneerselvam, Rajaram; Gopi, Ragupathi

2014-01-01

Genetic, morphological and chemical variations of ten natural populations of Rauvolfia serpentina Benth. Ex. Kurtz. from Southern Western Ghats of India were assessed using RAPD markers reserpine content and morphological traits. An estimate of genetic diversity and differentiation between genotypes of breeding germplasm is of key importance for its improvement. Populations were collected from different geographical regions. Data obtained through three different methods were compared and the correlation among them was estimated. Statistical analysis showed significant differences for all horticultural characteristics among the accessions suggesting that selection for relevant characteristics could be possible. Variation in the content of Reserpine ranges from 0.192 g/100 g (population from Tusharagiri) to 1.312 g/100 g (population from Aryankavu). A high diversity within population and high genetic differentiation among them based on RAPDs were revealed caused both by habitat fragmentation of the low size of most populations and the low level of gene flow among them. The UPGMA dendrogram and PCA analysis based on reserpine content yielded higher separation among populations indicated specific adaptation of populations into clusters each of them including populations closed to their geographical origin. Genetic, chemical and morphological data were correlated based on Mantel test. Given the high differentiation among populations conservation strategies should take into account genetic diversity and chemical variation levels in relation to bioclimatic and geographic location of populations. Our results also indicate that RAPD approach along with horticultural analysis seemed to be best suited for assessing with high accuracy the genetic relationships among distinct R. serpentina accessions. © 2013.

Worldwide orthopaedic research activity 2010-2014: Publication rates in the top 15 orthopaedic journals related to population size and gross domestic product.

PubMed

Hohmann, Erik; Glatt, Vaida; Tetsworth, Kevin

2017-06-18

To perform a bibliometric analysis of publications rates in orthopedics in the top 15 orthopaedic journals. Based on their 2015 impact factor, the fifteen highest ranked orthopaedic journals between January 2010 and December 2014 were used to establish the total number of publications; cumulative impact factor points (IF) per country were determined, and normalized to population size, GDP, and GDP/capita, comparison to the median country output and the global leader. Twenty-three thousand and twenty-one orthopaedic articles were published, with 66 countries publishing. The United States had 8149 publications, followed by the United Kingdom (1644) and Japan (1467). The highest IF was achieved by the United States (24744), United Kingdom (4776), and Japan (4053). Normalized by population size Switzerland lead. Normalized by GDP, Croatia was the top achiever. Adjusting GDP/capita, for publications and IF, China, India, and the United States were the leaders. Adjusting for population size and GDP, 28 countries achieved numbers of publications to be considered at least equivalent with the median academic output. Adjusting GDP/capita only China and India reached the number of publications to be considered equivalent to the current global leader, the United States. Five countries were responsible for 60% of the orthopaedic research output over this 5-year period. After correcting for GDP/capita, only 28 of 66 countries achieved a publication rate equivalent to the median country. The United States, United Kingdom, South Korea, Japan, and Germany were the top five countries for both publication totals and cumulative impact factor points.

Abundance and size changes in the calcareous nannofossil Schizosphaerella - relation to sea-level and palaeoenvironmental change across the Sinemurian to earliest Toarcian of the Paris Basin

NASA Astrophysics Data System (ADS)

Peti, Leonie; Thibault, Nicolas

2017-04-01

The nannolith Schizosphaerella spp. was predominant in Early Jurassic calcareous nannofossil assemblages. Previous studies have shown a significant drop in abundance and mean size of Schizosphaerella during the early Toarcian Oceanic Anoxic Event which has been interpreted by some authors either as a calcification crisis due to increased pCO2, or as a response to increased nutrient availability, and/or greenhouse warming. Abundance and size changes in Schizosphaerella have here been thoroughly investigated throughout the upper Sinemurian to lowermost Toarcian (Early Jurassic) of the Sancerre-Couy core (Paris Basin) based on 116 samples. Our results show a stepwise rise in abundance of Schizosphaerella in the lower part of the investigated section and a rise in abundance of coccoliths during the major transgression of the Sinemurian, confirming that Schizosphaerella was better adapted to proximal areas than coccoliths. Mixture analysis of the biometric measurements show the existence of three populations of Schizosphaerella, interpreted as different morphotypes with different ecological affinities. Proximal, cool environmental conditions of the upper Sinemurian are associated with a dominance of the large population of Schizosphaerella. A dominance of the medium population, corresponds to cool surface waters and more distal conditions. Warm episodes are systematically linked to a dominance of the small population. Therefore we propose that the size response of Schizosphaerella throughout the Early Jurassic was rather a change in abundance of different ecophenotypes or (sub-) species of Schizosphaerella, with distinct affinities to temperature and proximal/distal environmental conditions.

Characterisation of a garnet population from the Sikkim Himalaya: implications for the mechanisms and rates of porphyroblast crystallisation

NASA Astrophysics Data System (ADS)

George, Freya; Gaidies, Fred

2016-04-01

Analysis of porphyroblast distribution in metamorphic rocks yields insight into the processes controlling metamorphic reaction rates. By coupling this textural record with microprobe analysis and phase-equilibria and diffusion modelling, a detailed view of the nucleation and growth history of metamorphic minerals can be obtained. In this study, we comprehensively characterise the 3D distribution and compositional variation of a garnet population in a garnet-grade pelitic schist of the Lesser Himalayan Sequence (Sikkim), in order to investigate both the rates and kinetic controls of porphyroblastic crystallisation. Quantification of the size, shape and spatial distribution of garnet using high-resolution μ-computed X-ray tomography and statistical analysis reveals a log-normal crystal size distribution, systematic variation of aspect ratio with crystal size, and a significantly clustered garnet texture in the study sample. The latter is indicative of interface-controlled nucleation and growth, with nucleation sites controlled principally by a heterogeneous precursor assemblage. At length-scales less than 0.7 mm, there is evidence for adjacent grains that are on average smaller than the mean size of the population; this minor ordering is attributed to secondary redistribution of porphyroblast centers and reduction of crystal sizes due to syn-kinematic growth and resorption, respectively. Geochemical traverses through centrally sectioned garnet crystals of variable size highlight several features: (1) core compositions of even the smallest crystals preserve primary prograde growth zonation, with little evidence for diffusional modification in any crystal size; (2) rim compositions are within error between grains, suggestive of sample-scale equilibration of the growth medium at the time of cessation of crystallisation; (3) different grains of equal radii display equivalent compositional zoning; and (4) gradients of compositional profiles display a steepening trend in progressively smaller grain sizes, converse to anticipated trends based on classic kinetic crystallisation theory. The observed systematic behaviour is interpreted to reflect interface-controlled rates of crystallisation, with a decrease in the rate of crystal growth of newly nucleated grains as the crystallisation interval proceeds. Numerical simulations of garnet growth successfully reproduce observed core and rim compositions, and simulations of intracrystalline diffusion yield rapid heating/cooling rates along the P-T path, in excess of 100 °C/Ma. Radial garnet crystallisation is correspondingly rapid, with minimum growth rates of 1.5 mm/Ma in the smallest crystals. Simulations suggest progressive nucleation of new generations of garnet occurred with an exponentially decreasing frequency along the prograde path; however, measured gradients indicate that core compositions developed more slowly than predicted by the model, potentially resulting in a more evenly distributed pattern of nucleation.

Multi-parameter analysis using photovoltaic cell-based optofluidic cytometer

PubMed Central

Yan, Chien-Shun; Wang, Yao-Nan

2016-01-01

A multi-parameter optofluidic cytometer based on two low-cost commercial photovoltaic cells and an avalanche photodetector is proposed. The optofluidic cytometer is fabricated on a polydimethylsiloxane (PDMS) substrate and is capable of detecting side scattered (SSC), extinction (EXT) and fluorescence (FL) signals simultaneously using a free-space light transmission technique without the need for on-chip optical waveguides. The feasibility of the proposed device is demonstrated by detecting fluorescent-labeled polystyrene beads with sizes of 3 μm, 5 μm and 10 μm, respectively, and label-free beads with a size of 7.26 μm. The detection experiments are performed using both single-bead population samples and mixed-bead population samples. The detection results obtained using the SSC/EXT, EXT/FL and SSC/FL signals are compared with those obtained using a commercial flow cytometer. It is shown that the optofluidic cytometer achieves a high detection accuracy for both single-bead population samples and mixed-bead population samples. Consequently, the proposed device provides a versatile, straightforward and low-cost solution for a wide variety of point-of-care (PoC) cytometry applications. PMID:27699122

Crash and rebound of indigenous populations in lowland South America

NASA Astrophysics Data System (ADS)

Hamilton, Marcus J.; Walker, Robert S.; Kesler, Dylan C.

2014-04-01

Lowland South America has long been a battle-ground between European colonization and indigenous survival. Initial waves of European colonization brought disease epidemics, slavery, and violence that had catastrophic impacts on indigenous cultures. In this paper we focus on the demography of 238 surviving populations in Brazil. We use longitudinal censuses from all known indigenous Brazilian societies to quantify three demographic metrics: 1) effects of European contact on indigenous populations; 2) empirical estimates of minimum viable population sizes; and 3) estimates of post-contact population growth rates. We use this information to conduct population viability analysis (PVA). Our results show that all surviving populations suffered extensive mortality during, and shortly after, contact. However, most surviving populations exhibit positive growth rates within the first decade post-contact. Our findings paint a positive demographic outlook for these indigenous populations, though long-term survival remains subject to powerful externalities, including politics, economics, and the pervasive illegal exploitation of indigenous lands.

Rocky Mountain Center for Conservation Genetics and Systematics

USGS Publications Warehouse

Oyler-McCance, S.J.; Quinn, T.W.

2005-01-01

The use of molecular genetic tools has become increasingly important in addressing conservation issues pertaining to plants and animals. Genetic information can be used to augment studies of population dynamics and population viability, investigate systematic, refine taxonomic definitions, investigate population structure and gene flow, and document genetic diversity in a variety of plant and animal species. Further, genetic techniques are being used to investigate mating systems through paternity analysis, and analyze ancient DNA samples from museum specimens, and estimate population size and survival rates using DNA as a unique marker. Such information is essential for the sound management of small, isolated populations of concern and is currently being used by universities, zoos, the U.S. Fish and Wildlife Service, and numerous state fish and wildlife agencies.

Population Size Estimation of Men Who Have Sex with Men in Tbilisi, Georgia; Multiple Methods and Triangulation of Findings.

PubMed

Sulaberidze, Lela; Mirzazadeh, Ali; Chikovani, Ivdity; Shengelia, Natia; Tsereteli, Nino; Gotsadze, George

2016-01-01

An accurate estimation of the population size of men who have sex with men (MSM) is critical to the success of HIV program planning and to monitoring of the response to epidemic as a whole, but is quite often missing. In this study, our aim was to estimate the population size of MSM in Tbilisi, Georgia and compare it with other estimates in the region. In the absence of a gold standard for estimating the population size of MSM, this study reports a range of methods, including network scale-up, mobile/web apps multiplier, service and unique object multiplier, network-based capture-recapture, Handcock RDS-based and Wisdom of Crowds methods. To apply all these methods, two surveys were conducted: first, a household survey among 1,015 adults from the general population, and second, a respondent driven sample of 210 MSM. We also conducted a literature review of MSM size estimation in Eastern European and Central Asian countries. The median population size of MSM generated from all previously mentioned methods was estimated to be 5,100 (95% Confidence Interval (CI): 3,243~9,088). This corresponds to 1.42% (95%CI: 0.9%~2.53%) of the adult male population in Tbilisi. Our size estimates of the MSM population (1.42% (95%CI: 0.9%~2.53%) of the adult male population in Tbilisi) fall within ranges reported in other Eastern European and Central Asian countries. These estimates can provide valuable information for country level HIV prevention program planning and evaluation. Furthermore, we believe, that our results will narrow the gap in data availability on the estimates of the population size of MSM in the region.

Longevity of clonal plants: why it matters and how to measure it

PubMed Central

de Witte, Lucienne C.; Stöcklin, Jürg

2010-01-01

Background Species' life-history and population dynamics are strongly shaped by the longevity of individuals, but life span is one of the least accessible demographic traits, particularly in clonal plants. Continuous vegetative reproduction of genets enables persistence despite low or no sexual reproduction, affecting genet turnover rates and population stability. Therefore, the longevity of clonal plants is of considerable biological interest, but remains relatively poorly known. Scope Here, we critically review the present knowledge on the longevity of clonal plants and discuss its importance for population persistence. Direct life-span measurements such as growth-ring analysis in woody plants are relatively easy to take, although, for many clonal plants, these methods are not adequate due to the variable growth pattern of ramets and difficult genet identification. Recently, indirect methods have been introduced in which genet size and annual shoot increments are used to estimate genet age. These methods, often based on molecular techniques, allow the investigation of genet size and age structure of whole populations, a crucial issue for understanding their viability and persistence. However, indirect estimates of clonal longevity are impeded because the process of ageing in clonal plants is still poorly understood and because their size and age are not always well correlated. Alternative estimators for genet life span such as somatic mutations have recently been suggested. Conclusions Empirical knowledge on the longevity of clonal species has increased considerably in the last few years. Maximum age estimates are an indicator of population persistence, but are not sufficient to evaluate turnover rates and the ability of long-lived clonal plants to enhance community stability and ecosystem resilience. In order to understand the dynamics of populations it will be necessary to measure genet size and age structure, not only life spans of single individuals, and to use such data for modelling of genet dynamics. PMID:20880935

Analyzing hidden populations online: topic, emotion, and social network of HIV-related users in the largest Chinese online community.

PubMed

Liu, Chuchu; Lu, Xin

2018-01-05

Traditional survey methods are limited in the study of hidden populations due to the hard to access properties, including lack of a sampling frame, sensitivity issue, reporting error, small sample size, etc. The rapid increase of online communities, of which members interact with others via the Internet, have generated large amounts of data, offering new opportunities for understanding hidden populations with unprecedented sample sizes and richness of information. In this study, we try to understand the multidimensional characteristics of a hidden population by analyzing the massive data generated in the online community. By elaborately designing crawlers, we retrieved a complete dataset from the "HIV bar," the largest bar related to HIV on the Baidu Tieba platform, for all records from January 2005 to August 2016. Through natural language processing and social network analysis, we explored the psychology, behavior and demand of online HIV population and examined the network community structure. In HIV communities, the average topic similarity among members is positively correlated to network efficiency (r = 0.70, p < 0.001), indicating that the closer the social distance between members of the community, the more similar their topics. The proportion of negative users in each community is around 60%, weakly correlated with community size (r = 0.25, p = 0.002). It is found that users suspecting initial HIV infection or first in contact with high-risk behaviors tend to seek help and advice on the social networking platform, rather than immediately going to a hospital for blood tests. Online communities have generated copious amounts of data offering new opportunities for understanding hidden populations with unprecedented sample sizes and richness of information. It is recommended that support through online services for HIV/AIDS consultation and diagnosis be improved to avoid privacy concerns and social discrimination in China.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhu Qin, E-mail: zhuqin@fudan.edu.cn; Peng Xizhe, E-mail: xzpeng@fudan.edu.cn

This study examines the impacts of population size, population structure, and consumption level on carbon emissions in China from 1978 to 2008. To this end, we expanded the stochastic impacts by regression on population, affluence, and technology model and used the ridge regression method, which overcomes the negative influences of multicollinearity among independent variables under acceptable bias. Results reveal that changes in consumption level and population structure were the major impact factors, not changes in population size. Consumption level and carbon emissions were highly correlated. In terms of population structure, urbanization, population age, and household size had distinct effects onmore » carbon emissions. Urbanization increased carbon emissions, while the effect of age acted primarily through the expansion of the labor force and consequent overall economic growth. Shrinking household size increased residential consumption, resulting in higher carbon emissions. Households, rather than individuals, are a more reasonable explanation for the demographic impact on carbon emissions. Potential social policies for low carbon development are also discussed. - Highlights: Black-Right-Pointing-Pointer We examine the impacts of population change on carbon emissions in China. Black-Right-Pointing-Pointer We expand the STIRPAT model by containing population structure factors in the model. Black-Right-Pointing-Pointer The population structure includes age structure, urbanization level, and household size. Black-Right-Pointing-Pointer The ridge regression method is used to estimate the model with multicollinearity. Black-Right-Pointing-Pointer The population structure plays a more important role compared with the population size.« less

Does population size affect genetic diversity? A test with sympatric lizard species.

PubMed

Hague, M T J; Routman, E J

2016-01-01

Genetic diversity is a fundamental requirement for evolution and adaptation. Nonetheless, the forces that maintain patterns of genetic variation in wild populations are not completely understood. Neutral theory posits that genetic diversity will increase with a larger effective population size and the decreasing effects of drift. However, the lack of compelling evidence for a relationship between genetic diversity and population size in comparative studies has generated some skepticism over the degree that neutral sequence evolution drives overall patterns of diversity. The goal of this study was to measure genetic diversity among sympatric populations of related lizard species that differ in population size and other ecological factors. By sampling related species from a single geographic location, we aimed to reduce nuisance variance in genetic diversity owing to species differences, for example, in mutation rates or historical biogeography. We compared populations of zebra-tailed lizards and western banded geckos, which are abundant and short-lived, to chuckwallas and desert iguanas, which are less common and long-lived. We assessed population genetic diversity at three protein-coding loci for each species. Our results were consistent with the predictions of neutral theory, as the abundant species almost always had higher levels of haplotype diversity than the less common species. Higher population genetic diversity in the abundant species is likely due to a combination of demographic factors, including larger local population sizes (and presumably effective population sizes), faster generation times and high rates of gene flow with other populations.

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

PubMed Central

2013-01-01

Background Effective population sizes of 140 populations (including 60 dog breeds, 40 sheep breeds, 20 cattle breeds and 20 horse breeds) were computed using pedigree information and six different computation methods. Simple demographical information (number of breeding males and females), variance of progeny size, or evolution of identity by descent probabilities based on coancestry or inbreeding were used as well as identity by descent rate between two successive generations or individual identity by descent rate. Results Depending on breed and method, effective population sizes ranged from 15 to 133 056, computation method and interaction between computation method and species showing a significant effect on effective population size (P < 0.0001). On average, methods based on number of breeding males and females and variance of progeny size produced larger values (4425 and 356, respectively), than those based on identity by descent probabilities (average values between 93 and 203). Since breeding practices and genetic substructure within dog breeds increased inbreeding, methods taking into account the evolution of inbreeding produced lower effective population sizes than those taking into account evolution of coancestry. The correlation level between the simplest method (number of breeding males and females, requiring no genealogical information) and the most sophisticated one ranged from 0.44 to 0.60 according to species. Conclusions When choosing a method to compute effective population size, particular attention should be paid to the species and the specific genetic structure of the population studied. PMID:23281913

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

Comparative biology of the crab Goniopsis cruentata: geographic variation of body size, sexual maturity, and allometric growth

NASA Astrophysics Data System (ADS)

de Lira, José Jonathas Pereira Rodrigues; Calado, Tereza Cristina dos Santos; Rezende, Carla Ferreira; Silva, José Roberto Feitosa

2015-12-01

Geographic variation of phenotypic traits is common across species and is often associated with variation in environmental conditions. Here, we found larger bodies and larger size at maturity in a northward, lower latitude population of the crab Goniopsis cruentata, which inhabits a hotter, drier environment in comparison with a southward, higher latitude population. Furthermore, the juvenile male gonopods grow more relative to body size in the population characterized by maturation at a smaller size. In contrast, the female abdomen widens at a higher rate among the late maturing population. These results provide further evidence that local environmental conditions play a role in phenotypic variation between populations inhabiting different latitudes. Moreover, they also show that variation in size at maturity and body size can lead to divergent allometric patterns of sexual characteristics that can have a sex-specific response.

[Fenetic analysis of aboriginal and introduced sable (Martes zibellina) populations in Russia].

PubMed

Monakhov, V G

2001-09-01

Using standard and mulivariate statistic methods, an epigenetic character--foramina in fossa condyloidei inferior, FFCI--was studied in sable populations. This character was shown to be most frequent in southeastern populations of the species (Primorye and the Baikal region) while its distribution in the remaining part of the range was polyclinal. The expression of FFCI was directly associated with coat color and longitude, and inversely associated with skull size. This trend was broken by some western populations formed in the 1950s by introduction, which exhibited stable morphological differences with adjacent aboriginal sable populations. Most populations of the species exhibit differences in the manifestation of the character. Frequency of the FFCI manifestation can be used as an additional population characteristic, an associative diagnostic character that shows high discriminating capability in detecting phenogenetic relationships of intraspecific groups.

Matrix population models from 20 studies of perennial plant populations

USGS Publications Warehouse

Ellis, Martha M.; Williams, Jennifer L.; Lesica, Peter; Bell, Timothy J.; Bierzychudek, Paulette; Bowles, Marlin; Crone, Elizabeth E.; Doak, Daniel F.; Ehrlen, Johan; Ellis-Adam, Albertine; McEachern, Kathryn; Ganesan, Rengaian; Latham, Penelope; Luijten, Sheila; Kaye, Thomas N.; Knight, Tiffany M.; Menges, Eric S.; Morris, William F.; den Nijs, Hans; Oostermeijer, Gerard; Quintana-Ascencio, Pedro F.; Shelly, J. Stephen; Stanley, Amanda; Thorpe, Andrea; Tamara, Ticktin; Valverde, Teresa; Weekley, Carl W.

2012-01-01

Demographic transition matrices are one of the most commonly applied population models for both basic and applied ecological research. The relatively simple framework of these models and simple, easily interpretable summary statistics they produce have prompted the wide use of these models across an exceptionally broad range of taxa. Here, we provide annual transition matrices and observed stage structures/population sizes for 20 perennial plant species which have been the focal species for long-term demographic monitoring. These data were assembled as part of the "Testing Matrix Models" working group through the National Center for Ecological Analysis and Synthesis (NCEAS). In sum, these data represent 82 populations with >460 total population-years of data. It is our hope that making these data available will help promote and improve our ability to monitor and understand plant population dynamics.

Matrix population models from 20 studies of perennial plant populations

USGS Publications Warehouse

Ellis, Martha M.; Williams, Jennifer L.; Lesica, Peter; Bell, Timothy J.; Bierzychudek, Paulette; Bowles, Marlin; Crone, Elizabeth E.; Doak, Daniel F.; Ehrlen, Johan; Ellis-Adam, Albertine; McEachern, Kathryn; Ganesan, Rengaian; Latham, Penelope; Luijten, Sheila; Kaye, Thomas N.; Knight, Tiffany M.; Menges, Eric S.; Morris, William F.; den Nijs, Hans; Oostermeijer, Gerard; Quintana-Ascencio, Pedro F.; Shelly, J. Stephen; Stanley, Amanda; Thorpe, Andrea; Tamara, Ticktin; Valverde, Teresa; Weekley, Carl W.

2012-01-01

Demographic transition matrices are one of the most commonly applied population models for both basic and applied ecological research. The relatively simple framework of these models and simple, easily interpretable summary statistics they produce have prompted the wide use of these models across an exceptionally broad range of taxa. Here, we provide annual transition matrices and observed stage structures/population sizes for 20 perennial plant species which have been the focal species for long-term demographic monitoring. These data were assembled as part of the 'Testing Matrix Models' working group through the National Center for Ecological Analysis and Synthesis (NCEAS). In sum, these data represent 82 populations with >460 total population-years of data. It is our hope that making these data available will help promote and improve our ability to monitor and understand plant population dynamics.

The eco-evolutionary responses of a generalist consumer to resource competition.

PubMed

Abrams, Peter A

2012-10-01

This article explores the combined evolutionary and ecological responses of resource uptake abilities in a generalist consumer to exploitative competition for one resource using a simple 2-resource model. It compares the sizes of ecologically and evolutionarily caused changes in population densities in cases where the original consumer has a strong or a weak trade-off in its abilities to consume the two resources. The analysis also compares the responses of the original species to competition when the competitor's population size is or is not limited by the shared resource. Although divergence in resource use traits in the resident generalist consumer is expected under all scenarios when resources are substitutable, the changes in population densities of the resources and resident consumer frequently differ between scenarios. The population of the original consumer often decreases as a result of its own adaptive divergence, and this decrease is often much greater than the initial ecological decrease. If the evolving consumer has a strong trade-off, the overlapped resource increases in equilibrium population density in response to being consumed by a generalist competitor. Some of these predictions differ qualitatively in alternative scenarios involving sustained variation in population densities or nutritionally essential resources. © 2012 The Author(s). Evolution© 2012 The Society for the Study of Evolution.

Models to compare management options for a protogynous fish.

PubMed

Heppell, Selina S; Heppell, Scott A; Coleman, Felicia C; Koenig, Christopher C

2006-02-01

Populations of gag (Mycteroperca microlepis), a hermaphroditic grouper, have experienced a dramatic shift in sex ratio over the past 25 years due to a decline in older age classes. The highly female-skewed sex ratio can be predicted as a consequence of increased fishing mortality that truncates the age distribution, and raises some concern about the overall fitness of the population. Management efforts may need to be directed toward maintenance of sex ratio as well as stock size, with evaluations of recruitment based on sex ratio or male stock size in addition to the traditional female-based stock-recruitment relationship. We used two stochastic, age-structured models to heuristically compare the effects of reducing fishing mortality on different life history stages and the relative impact of reductions in fertilization rates that may occur with highly skewed sex ratios. Our response variables included population size, sex ratio, lost egg fertility, and female spawning stock biomass. Population growth rates were highest for scenarios that reduced mortality for female gag (nearshore closure), while improved sex ratios were obtained most quickly with spawning reserves. The effect of reduced fertility through sex ratio bias was generally low but depended on the management scenario employed. Our results demonstrate the utility of evaluation of fishery management scenarios through model analysis and simulation, the synergistic interaction of life history and response to changes in mortality rates, and the importance of defining management goals.

Analysis of field size distributions, LACIE test sites 5029, 5033, and 5039, Anhwei Province, People's Republic of China

NASA Technical Reports Server (NTRS)

Podwysocki, M. H.

1976-01-01

A study was made of the field size distributions for LACIE test sites 5029, 5033, and 5039, People's Republic of China. Field lengths and widths were measured from LANDSAT imagery, and field area was statistically modeled. Field size parameters have log-normal or Poisson frequency distributions. These were normalized to the Gaussian distribution and theoretical population curves were made. When compared to fields in other areas of the same country measured in the previous study, field lengths and widths in the three LACIE test sites were 2 to 3 times smaller and areas were smaller by an order of magnitude.

Meta-analysis of multiple outcomes: a multilevel approach.

PubMed

Van den Noortgate, Wim; López-López, José Antonio; Marín-Martínez, Fulgencio; Sánchez-Meca, Julio

2015-12-01

In meta-analysis, dependent effect sizes are very common. An example is where in one or more studies the effect of an intervention is evaluated on multiple outcome variables for the same sample of participants. In this paper, we evaluate a three-level meta-analytic model to account for this kind of dependence, extending the simulation results of Van den Noortgate, López-López, Marín-Martínez, and Sánchez-Meca Behavior Research Methods, 45, 576-594 (2013) by allowing for a variation in the number of effect sizes per study, in the between-study variance, in the correlations between pairs of outcomes, and in the sample size of the studies. At the same time, we explore the performance of the approach if the outcomes used in a study can be regarded as a random sample from a population of outcomes. We conclude that although this approach is relatively simple and does not require prior estimates of the sampling covariances between effect sizes, it gives appropriate mean effect size estimates, standard error estimates, and confidence interval coverage proportions in a variety of realistic situations.

Population Size Estimation of Men Who Have Sex with Men through the Network Scale-Up Method in Japan

PubMed Central

Ezoe, Satoshi; Morooka, Takeo; Noda, Tatsuya; Sabin, Miriam Lewis; Koike, Soichi

2012-01-01

Background Men who have sex with men (MSM) are one of the groups most at risk for HIV infection in Japan. However, size estimates of MSM populations have not been conducted with sufficient frequency and rigor because of the difficulty, high cost and stigma associated with reaching such populations. This study examined an innovative and simple method for estimating the size of the MSM population in Japan. We combined an internet survey with the network scale-up method, a social network method for estimating the size of hard-to-reach populations, for the first time in Japan. Methods and Findings An internet survey was conducted among 1,500 internet users who registered with a nationwide internet-research agency. The survey participants were asked how many members of particular groups with known population sizes (firepersons, police officers, and military personnel) they knew as acquaintances. The participants were also asked to identify the number of their acquaintances whom they understood to be MSM. Using these survey results with the network scale-up method, the personal network size and MSM population size were estimated. The personal network size was estimated to be 363.5 regardless of the sex of the acquaintances and 174.0 for only male acquaintances. The estimated MSM prevalence among the total male population in Japan was 0.0402% without adjustment, and 2.87% after adjusting for the transmission error of MSM. Conclusions The estimated personal network size and MSM prevalence seen in this study were comparable to those from previous survey results based on the direct-estimation method. Estimating population sizes through combining an internet survey with the network scale-up method appeared to be an effective method from the perspectives of rapidity, simplicity, and low cost as compared with more-conventional methods. PMID:22563366

Spatiotemporal analysis of gene flow in Chesapeake Bay Diamondback Terrapins (Malaclemys terrapin)

USGS Publications Warehouse

Converse, Paul E.; Kuchta, Shawn R; Roosenburg, Willem R; Henry, Paula F.; Haramis, G. Michael; King, Timothy L.

2015-01-01

There is widespread concern regarding the impacts of anthropogenic activities on connectivity among populations of plants and animals, and understanding how contemporary and historical processes shape metapopulation dynamics is crucial for setting appropriate conservation targets. We used genetic data to identify population clusters and quantify gene flow over historical and contemporary time frames in the Diamondback Terrapin (Malaclemys terrapin). This species has a long and complicated history with humans, including commercial over-harvesting and subsequent translocation events during the early twentieth century. Today, terrapins face threats from habitat loss and mortality in fisheries bycatch. To evaluate population structure and gene flow among Diamondback Terrapin populations in the Chesapeake Bay region, we sampled 617 individuals from 15 localities, and screened individuals at 12 polymorphic microsatellite loci. Our goals were to demarcate metapopulation structure, quantify genetic diversity, estimate effective population sizes, and document temporal changes in gene flow. We found that terrapins in the Chesapeake Bay region harbor high levels of genetic diversity and form four populations. Effective population sizes were variable. Among most population comparisons, estimates of historical and contemporary terrapin gene flow were generally low (m ≈ 0.01). However, we detected a substantial increase in contemporary gene flow into Chesapeake Bay from populations outside the bay, as well as between two populations within Chesapeake Bay, possibly as a consequence of translocations during the early twentieth century. Our study shows that inferences across multiple time scales are needed to evaluate population connectivity, especially as recent changes may identify threats to population persistence.

Drought survival is a threshold function of habitat size and population density in a fish metapopulation.

PubMed

White, Richard S A; McHugh, Peter A; McIntosh, Angus R

2016-10-01

Because smaller habitats dry more frequently and severely during droughts, habitat size is likely a key driver of survival in populations during climate change and associated increased extreme drought frequency. Here, we show that survival in populations during droughts is a threshold function of habitat size driven by an interaction with population density in metapopulations of the forest pool dwelling fish, Neochanna apoda. A mark-recapture study involving 830 N. apoda individuals during a one-in-seventy-year extreme drought revealed that survival during droughts was high for populations occupying pools deeper than 139 mm, but declined steeply in shallower pools. This threshold was caused by an interaction between increasing population density and drought magnitude associated with decreasing habitat size, which acted synergistically to increase physiological stress and mortality. This confirmed two long-held hypotheses, firstly concerning the interactive role of population density and physiological stress, herein driven by habitat size, and secondly, the occurrence of drought survival thresholds. Our results demonstrate how survival in populations during droughts will depend strongly on habitat size and highlight that minimum habitat size thresholds will likely be required to maximize survival as the frequency and intensity of droughts are projected to increase as a result of global climate change. © 2016 John Wiley & Sons Ltd.

Non-parametric estimation of population size changes from the site frequency spectrum.

PubMed

Waltoft, Berit Lindum; Hobolth, Asger

2018-06-11

Changes in population size is a useful quantity for understanding the evolutionary history of a species. Genetic variation within a species can be summarized by the site frequency spectrum (SFS). For a sample of size n, the SFS is a vector of length n - 1 where entry i is the number of sites where the mutant base appears i times and the ancestral base appears n - i times. We present a new method, CubSFS, for estimating the changes in population size of a panmictic population from an observed SFS. First, we provide a straightforward proof for the expression of the expected site frequency spectrum depending only on the population size. Our derivation is based on an eigenvalue decomposition of the instantaneous coalescent rate matrix. Second, we solve the inverse problem of determining the changes in population size from an observed SFS. Our solution is based on a cubic spline for the population size. The cubic spline is determined by minimizing the weighted average of two terms, namely (i) the goodness of fit to the observed SFS, and (ii) a penalty term based on the smoothness of the changes. The weight is determined by cross-validation. The new method is validated on simulated demographic histories and applied on unfolded and folded SFS from 26 different human populations from the 1000 Genomes Project.

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

PubMed

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

2017-01-01

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

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 effect of social organization on bias in population estimation could be removed by using POPAN with specific parameter combinations, to obtain population size estimates in a social species. PMID:28306735

Extensive long-distance pollen dispersal and highly outcrossed mating in historically small and disjunct populations of Acacia woodmaniorum (Fabaceae), a rare banded iron formation endemic.

PubMed

Millar, Melissa A; Coates, David J; Byrne, Margaret

2014-10-01

Understanding patterns of pollen dispersal and variation in mating systems provides insights into the evolutionary potential of plant species and how historically rare species with small disjunct populations persist over long time frames. This study aims to quantify the role of pollen dispersal and the mating system in maintaining contemporary levels of connectivity and facilitating persistence of small populations of the historically rare Acacia woodmaniorum. Progeny arrays of A. woodmaniorum were genotyped with nine polymorphic microsatellite markers. A low number of fathers contributed to seed within single pods; therefore, sampling to remove bias of correlated paternity was implemented for further analysis. Pollen immigration and mating system parameters were then assessed in eight populations of varying size and degree of isolation. Pollen immigration into small disjunct populations was extensive (mean minimum estimate 40 % and mean maximum estimate 57 % of progeny) and dispersal occurred over large distances (≤1870m). Pollen immigration resulted in large effective population sizes and was sufficient to ensure adaptive and inbreeding connectivity in small disjunct populations. High outcrossing (mean tm = 0·975) and a lack of apparent inbreeding suggested that a self-incompatibility mechanism is operating. Population parameters, including size and degree of geographic disjunction, were not useful predictors of pollen dispersal or components of the mating system. Extensive long-distance pollen dispersal and a highly outcrossed mating system are likely to play a key role in maintaining genetic diversity and limiting negative genetic effects of inbreeding and drift in small disjunct populations of A. woodmaniorum. It is proposed that maintenance of genetic connectivity through habitat and pollinator conservation will be a key factor in the persistence of this and other historically rare species with similar extensive long-distance pollen dispersal and highly outcrossed mating systems. © The Author 2014. Published by Oxford University Press on behalf of the Annals of Botany Company.

AFLP markers reveal high clonal diversity and extreme longevity in four key arctic-alpine species.

PubMed

de Witte, Lucienne C; Armbruster, Georg F J; Gielly, Ludovic; Taberlet, Pierre; Stöcklin, Jürg

2012-03-01

We investigated clonal diversity, genet size structure and genet longevity in populations of four arctic-alpine plants (Carex curvula, Dryas octopetala, Salix herbacea and Vaccinium uliginosum) to evaluate their persistence under past climatic oscillations and their potential resistance to future climate change. The size and number of genets were determined by an analysis of amplified fragment length polymorphisms and a standardized sampling design in several European arctic-alpine populations, where these species are dominant in the vegetation. Genet age was estimated by dividing the size by the annual horizontal size increment from in situ growth measurements. Clonal diversity was generally high but differed among species, and the frequency distribution of genet size was strongly left-skewed. The largest C. curvula genet had an estimated minimum age of c. 4100 years and a maximum age of c. 5000 years, although 84.8% of the genets in this species were <200 years old. The oldest genets of D. octopetala, S. herbacea and V. uliginosum were found to be at least 500, 450 and 1400 years old, respectively. These results indicate that individuals in the studied populations have survived pronounced climatic oscillations, including the Little Ice Age and the postindustrial warming. The presence of genets in all size classes and the dominance of presumably young individuals suggest repeated recruitment over time, a precondition for adaptation to changing environmental conditions. Together, persistence and continuous genet turnover may ensure maximum ecosystem resilience. Thus, our results indicate that long-lived clonal plants in arctic-alpine ecosystems can persist, despite considerable climatic change. © 2011 Blackwell Publishing Ltd.