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  • 1.
    Jonzen, Niclas
    et al.
    Dept Theoret Ecol, Lund Univ, Lund, Sweden.
    Pople, Tony
    Dept Primary Ind & Fisheries, Brisbane Qld , Australia.
    Knape, Jonas
    Dept Theoret Ecol, Lund Univ, Lund, Sweden.
    Sköld, Martin
    Örebro University, Swedish Business School at Örebro University.
    Stochastic demography and population dynamics in the red kangaroo Macropus rufus2010In: Journal of Animal Ecology, ISSN 0021-8790, E-ISSN 1365-2656, Vol. 79, no 1, p. 109-116Article in journal (Refereed)
    Abstract [en]

    1. Many organisms inhabit strongly fluctuating environments but their demography and population dynamics are often analysed using deterministic models and elasticity analysis, where elasticity is defined as the proportional change in population growth rate caused by a proportional change in a vital rate. Deterministic analyses may not necessarily be informative because large variation in a vital rate with a small deterministic elasticity may affect the population growth rate more than a small change in a less variable vital rate having high deterministic elasticity. 2. We analyse a stochastic environment model of the red kangaroo (Macropus rufus), a species inhabiting an environment characterized by unpredictable and highly variable rainfall, and calculate the elasticity of the stochastic growth rate with respect to the mean and variability in vital rates. 3. Juvenile survival is the most variable vital rate but a proportional change in the mean adult survival rate has a much stronger effect on the stochastic growth rate. 4. Even if changes in average rainfall have a larger impact on population growth rate, increased variability in rainfall may still be important also in long-lived species. The elasticity with respect to the standard deviation of rainfall is comparable to the mean elasticities of all vital rates but the survival in age class 3 because increased variation in rainfall affects both the mean and variability of vital rates. 5. Red kangaroos are harvested and, under the current rainfall pattern, an annual harvest fraction of c. 20% would yield a stochastic growth rate about unity. However, if average rainfall drops by more than c. 10%, any level of harvesting may be unsustainable, emphasizing the need for integrating climate change predictions in population management and increase our understanding of how environmental stochasticity translates into population growth rate.

  • 2. Knape, Jonas
    et al.
    Jonzén, Niclas
    Sköld, Martin
    Örebro University, Swedish Business School at Örebro University.
    Kikkawa, Jiro
    McCallum, Hamish
    Individual heterogeneity and senescence in Silvereyes on Heron Island2011In: Ecology, ISSN 0012-9658, E-ISSN 1939-9170, Vol. 92, no 4, p. 813-820Article in journal (Refereed)
    Abstract [en]

    Individual heterogeneity and correlations between life history traits play a fundamental role in life history evolution and population dynamics. Unobserved individual heterogeneity in survival can be a nuisance for estimation of age effects at the individual level by causing bias due to mortality selection. We jointly analyze survival and breeding output from successful breeding attempts in an island population of Silvereyes (Zosterops lateralis chlorocephalus) by fitting models that incorporate age effects and individual heterogeneity via random effects. The number of offspring produced increased with age of parents in their first years of life but then eventually declined with age. A similar pattern was found for the probability of successful breeding. Annual survival declined with age even when individual heterogeneity was not accounted for. The rate of senescence in survival, however, depends on the variance of individual heterogeneity and vice versa; hence, both cannot be simultaneously estimated with precision. Model selection supported individual heterogeneity in breeding performance, but we found no correlation between individual heterogeneity in survival and breeding performance. We argue that individual random effects, unless unambiguously identified, should be treated as statistical nuisance or taken as a starting point in a search for mechanisms rather than given direct biological interpretation.

  • 3.
    Knape, Jonas
    et al.
    Lund University.
    Jonzén, Niclas
    Lund University.
    Sköld, Martin
    Örebro University, Swedish Business School at Örebro University.
    Sokolov, Leonid
    Multivariate state space modelling of bird migration count data2009In: Environmental and Ecological Statistics, ISSN 1352-8505, E-ISSN 1573-3009, Vol. 3, no 1, p. 59-79Article in journal (Refereed)
    Abstract [en]

    We analyse 54 year long time series data on the numbers of common redstart (Phoenicurus phoenicurus), common whitethroat (Sylvia communis), garden warbler (Sylvia borin) and lesser whitethroat (Sylvia curruca) trapped in spring and autumn at Ottenby Bird Observatory, Sweden. The Ottenby time series could potentially serve as a reference on how much information on population change is available in count data on migrating birds. To investigate this, we combine spring and autumn data in a Bayesian state-space model trying to separate demographic signals and observation noise. The spring data are assumed to be a measure of the breeding population size, whereas the autumn data measure the population size after reproduction. At the demographic level we include seasonal density dependence and model winter dynamics as a function of precipitation in the Sahel region, south of the Sahara desert, where these species are known to spend the winter. Results show that the large fluctuations in the data restrict what conclusions can be drawn about the dynamics of the species. Annual catches are highly correlated between species and we show that a likely explanation for this is that trapping numbers are strongly dependent on local weather conditions. A comparative analysis of a related data set from the Courish Spit, Russia, gives rather different dynamics which may be caused by low information in the two data sets, but also by distinct populations passing Ottenby and the Courish Spit. This highlights the difficulty of validating results of the analyses when abundance indices derived by other methods or from other populations do not agree.

  • 4.
    Knape, Jonas
    et al.
    Lund University.
    Sköld, Martin
    Örebro University, Swedish Business School at Örebro University.
    Jonzén, Niclas
    Lund University.
    Åkesson, Mikael
    Lund University.
    Bensch, Staffan
    Lund University.
    Hansson, Bengt
    Lund University.
    Hasselquist, Dennis
    Lund University.
    An analysis of hatching success in the great reed warbler Acrocephalus arundinaceus2008In: Oikos, ISSN 0030-1299, E-ISSN 1600-0706, no 117, p. 430-438Article in journal (Refereed)
    Abstract [en]

    Hatching success is a potentially important fitness component for avian species. Previous studies of hatching success in natural populations have primarily focused on effects of inbreeding but a general understanding of variation in hatching success is lacking. We analyse data on hatching success in a population of great reed warblers Acrocephalus arundinaceus in Lake Kvismaren in south central Sweden. The effects of a range of covariates, including three measures of inbreeding as well as effects of classifications in the data (such as identities of individuals), on hatching success are analysed simultaneously. This is done by means of fitting Bayesian binomial mixed models using Markov chain Monte Carlo methods. Using random effects for each individual parent we check for unexplained variation in hatching success among male and female individuals and compare it to effects of covariates such as degree of inbreeding. Model selection showed that there was a significant amount of unexplained variation in hatching probability between females. This was manifested by a few females laying eggs with a substantially lower hatching success than the majority of the females. The deviations were of the same order of magnitude as the significant effect of parent relatedness on hatching success. Whereas the negative effect of parent relatedness on hatchability is an expression of inbreeding, the female individual effect is not due to inbreeding and could reflect maternal effects, that females differ in fertilisation and/or incubation ability, or an over representation of genetic components from the female acting on the early developing embryo.

  • 5.
    Papaspiliopoulos, Omiros
    et al.
    Lancaster University.
    Roberts, Gareth O.
    Lancaster University.
    Sköld, Martin
    Örebro University, Department of Business, Economics, Statistics and Informatics.
    A general framework for the parametrisation of hierarchical models2007In: Statistical Science, ISSN 0883-4237, E-ISSN 2168-8745, Vol. 22, no 1, p. 59-73Article in journal (Refereed)
    Abstract [en]

    In this paper, we describe centering and noncentering methodology as complementary techniques for use in parametrization of broad classes of hierarchical models, with a view to the construction of effective MCMC algorithms for exploring posterior distributions from these models. We give a clear qualitative understanding as to when centering and noncentering work well, and introduce theory concerning the convergence time complexity of Gibbs samplers using centered and noncentered parametrizations. We give general recipes for the construction of noncentered parametrizations, including an auxiliary variable technique called the state-space expansion technique. We also describe partially noncentered methods, and demonstrate their use in constructing robust Gibbs sampler algorithms whose convergence properties are not overly sensitive to the data.

  • 6.
    Sköld, Martin
    Örebro University, Swedish Business School at Örebro University.
    Improving density estimators of discretely observed processes by interpolation2009In: Journal of Statistical Planning and Inference, ISSN 0378-3758, E-ISSN 1873-1171, Vol. 139, no 6, p. 1847-1855Article in journal (Refereed)
    Abstract [en]

    We consider density estimation for a smooth stationary process Xt, tR, based on a discrete sample Yi=XΔi, i=0,…,n=T/Δ. By a suitable interpolation scheme of order p, we augment data to form an approximation Xp,t, t[0,T], of the continuous-time process and base our density estimate on the augmented sample path. Our results show that this can improve the rate of convergence (measured in terms of n) of the density estimate. Among other things, this implies that recording n observations using a small Δ can be more efficient than recording n independent observations.

  • 7.
    Sköld, Martin
    et al.
    Örebro University, Department of Business, Economics, Statistics and Informatics.
    Rydén, Tobias
    Lund University.
    Samuelsson, Viktoria
    Lund University.
    Bratt, Charlotte
    Lund University.
    Ekblad, Lars
    Lund University.
    Olsson, Håkan
    Lund University.
    Baldetorp, Bo
    Lund University.
    Regression analysis and modelling of data acquisition for SELDI-TOF mass spectrometry2007In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 23, no 11, p. 1401-1409Article in journal (Refereed)
    Abstract [en]

    Motivation: Pre-processing of SELDI-TOF mass spectrometry data is currently performed on a largel y ad hoc basis. This makes comparison of results from independent analyses troublesome and does not provide a framework for distinguishing different sources of variation in data.

    Results: In this article, we consider the task of pooling a large number of single-shot spectra, a task commonly performed automatically by the instrument software. By viewing the underlying statistical problem as one of heteroscedastic linear regression, we provide a framework for introducing robust methods and for dealing with missing data resulting from a limited span of recordable intensity values provided by the instrument. Our framework provides an interpretation of currently used methods as a maximum-likelihood estimator and allows theoretical derivation of its variance. We observe that this variance depends crucially on the total number of ionic species, which can vary considerably between different pooled spectra. This variation in variance can potentially invalidate the results from naive methods of discrimination/classification and we outline appropriate data transformations. Introducing methods from robust statistics did not improve the standard errors of the pooled samples. Imputing missing values however—using the EM algorithm—had a notable effect on the result; for our data, the pooled height of peaks which were frequently truncated increased by up to 30%.

  • 8.
    Stjernqvist, Susann
    et al.
    Lund University.
    Rydén, Tobias
    Lund University.
    Sköld, Martin
    Örebro University, Department of Business, Economics, Statistics and Informatics.
    Staaf, Johan
    Continuous-index hidden Markov modelling of array CGH copy number data2007In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 23, no 8, p. 1006-1014Article in journal (Refereed)
    Abstract [en]

    Motivation: In recent years, a range of techniques for analysis and segmentation of array comparative genomic hybridization (aCGH) data have been proposed. For array designs in which clones are of unequal lengths, are unevenly spaced or overlap, the discrete-index view typically adopted by such methods may be questionable or improved.

    Results: We describe a continuous-index hidden Markov model for aCGH data as well as a Monte Carlo EM algorithm to estimate its parameters. It is shown that for a dataset from the BT-474 cell line analysed on 32K BAC tiling microarrays, this model yields considerably better model fit in terms of lag-1 residual autocorrelations compared to a discrete-index HMM, and it is also shown how to use the model for e.g. estimation of change points on the base-pair scale and for estimation of conditional state probabilities across the genome. In addition, the model is applied to the Glioblastoma Multiforme data used in the comparative study by Lai et al. (Lai,W.R. et al. (2005) Comparative analysis of algorithms for identifying amplifications and deletions in array CGH data. Bioinformatics, 21, 3763–3370.) giving result similar to theirs but with certain features highlighted in the continuous-index setting

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