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Estimating sampling error of evolutionary statistics based on genetic covariance matrices using maximum likelihood 下载免费PDF全文
We explore the estimation of uncertainty in evolutionary parameters using a recently devised approach for resampling entire additive genetic variance–covariance matrices ( G ). Large‐sample theory shows that maximum‐likelihood estimates (including restricted maximum likelihood, REML) asymptotically have a multivariate normal distribution, with covariance matrix derived from the inverse of the information matrix, and mean equal to the estimated G . This suggests that sampling estimates of G from this distribution can be used to assess the variability of estimates of G , and of functions of G . We refer to this as the REML‐MVN method. This has been implemented in the mixed‐model program WOMBAT. Estimates of sampling variances from REML‐MVN were compared to those from the parametric bootstrap and from a Bayesian Markov chain Monte Carlo (MCMC) approach (implemented in the R package MCMCglmm). We apply each approach to evolvability statistics previously estimated for a large, 20‐dimensional data set for Drosophila wings. REML‐MVN and MCMC sampling variances are close to those estimated with the parametric bootstrap. Both slightly underestimate the error in the best‐estimated aspects of the G matrix. REML analysis supports the previous conclusion that the G matrix for this population is full rank. REML‐MVN is computationally very efficient, making it an attractive alternative to both data resampling and MCMC approaches to assessing confidence in parameters of evolutionary interest. 相似文献
3.
Matthias Brendel Anna Jaworska Eric Grie?inger Christina R?tzer Steffen Burgold Franz-Josef Gildehaus Janette Carlsen Paul Cumming Karlheinz Baumann Christian Haass Harald Steiner Peter Bartenstein Jochen Herms Axel Rominger 《PloS one》2015,10(2)
We aimed to compare [18F]-florbetaben PET imaging in four transgenic mouse strains modelling Alzheimer’s disease (AD), with the main focus on APPswe/PS2 mice and C57Bl/6 mice serving as controls (WT). A consistent PET protocol (N = 82 PET scans) was used, with cortical standardized uptake value ratio (SUVR) relative to cerebellum as the endpoint. We correlated methoxy-X04 staining of β-amyloid with PET results, and undertook ex vivo autoradiography for further validation of a partial volume effect correction (PVEC) of PET data. The SUVR in APPswe/PS2 increased from 0.95±0.04 at five months (N = 5) and 1.04±0.03 (p<0.05) at eight months (N = 7) to 1.07±0.04 (p<0.005) at ten months (N = 6), 1.28±0.06 (p<0.001) at 16 months (N = 6) and 1.39±0.09 (p<0.001) at 19 months (N = 6). SUVR was 0.95±0.03 in WT mice of all ages (N = 22). In APPswe/PS1G384A mice, the SUVR was 0.93/0.98 at five months (N = 2) and 1.11 at 16 months (N = 1). In APPswe/PS1dE9 mice, the SUVR declined from 0.96/0.96 at 12 months (N = 2) to 0.91/0.92 at 24 months (N = 2), due to β-amyloid plaques in cerebellum. PVEC reduced the discrepancy between SUVR-PET and autoradiography from −22% to +2% and increased the differences between young and aged transgenic animals. SUVR and plaque load correlated highly between strains for uncorrected (R = 0.94, p<0.001) and PVE-corrected (R = 0.95, p<0.001) data. We find that APPswe/PS2 mice may be optimal for longitudinal amyloid-PET monitoring in planned interventions studies. 相似文献
4.
Mari L. Fischer Axel Hochkirch Mike Heddergott Christoph Schulze Helena E. Anheyer-Behmenburg Johannes Lang Frank-Uwe Michler Ulf Hohmann Hermann Ansorge Lothar Hoffmann Roland Klein Alain C. Frantz 《PloS one》2015,10(5)
Biological invasions provide excellent study systems to understand evolutionary, genetic and ecological processes during range expansions. There is strong evidence for positive effects of high propagule pressure and the associated higher genetic diversity on invasion success, but some species have become invasive despite small founder numbers. The raccoon (Procyon lotor) is often considered as a typical example for such a successful invasion resulting from a small number of founders. The species’ largest non-native population in Germany is commonly assumed to stem from a small number of founders and two separate founding events in the 1930s and 1940s. In the present study we analyzed 407 raccoons at 20 microsatellite loci sampled from the invasive range in Western Europe to test if these assumptions are correct. Contrary to the expectations, different genetic clustering methods detected evidence for at least four independent introduction events that gave rise to genetically differentiated subpopulations. Further smaller clusters were either artifacts or resulted from founder events at the range margin and recent release of captive individuals. We also found genetic evidence for on-going introductions of individuals. Furthermore a novel randomization process was used to determine the potential range of founder population size that would suffice to capture all the alleles present in a cluster. Our results falsify the assumption that this species has become widespread and abundant despite being genetically depauperate and show that historical records of species introductions may be misleading. 相似文献
5.
Waldo Galle Niels De Temmerman Karen Allacker Ronald De Meyer 《The International Journal of Life Cycle Assessment》2017,22(8):1191-1209
Purpose
To evaluate the long-term advantage of reusing building elements, including reduced material consumption and waste production, life cycle assessments are purposeful. To translate these assessments in relevant design advices, it is necessary to model accurately the service life of the considered elements and acknowledge the related uncertainties. Practical methods to do this are nevertheless lacking. In reaction, this paper proposes a new assessment method: geometric service life modelling and discounting.Methods
The developed method is extensively parametric. Its formulas express an element’s service life in terms of a limited number of variables. This facilitates the evaluation of large series of elements as well as the automation of uncertainty analyses. Further, the method tackles different modelling complexities such as the interaction between replacements and refurbishments. Taking into account these complexities aligns the assessments with realistic service lives. For the presentation of the developed method, a focus on life cycle costing is chosen.Results and discussion
In this paper, the outcomes of the newly developed method are compared to those of an existing calculation method and benchmarked with the manual modelling and assessment of 390 simplified building elements. This comparison is based on three indicators characterising the methods’ accuracy: the number of interventions, their individual impact and their resulting net present value. For each indicator, geometric discounting led to a considerable increase of accuracy compared to the existing method.Conclusions
From this comparison, it is concluded that geometric service life modelling and discounting offers not only a well-defined procedure for parametrised life cycle assessment studies, this method is also more accurate than the existing one. Moreover, the uncertainty analyses it facilitates illustrate how detailed assessment outcomes and relevant design advices about the effectiveness of element reuse can be obtained. Nevertheless, further research about the method’s practical implementation is required.6.
J W Zolg R S Lanciotti M Wendlinger W A Meyer 《Applied and environmental microbiology》1990,56(9):2755-2760
Blood samples to be tested for the presence of parasite DNA by using specific DNA probes are routinely stored in our laboratory as high-salt lysates (HSL). To safeguard against the risk of accidental infection with etiological agents such as the human immunodeficiency virus type 1 (HIV-1) while manipulating large numbers of blood samples in preparation for DNA probing, we determined the residual infectivity of HIV-1 after exposure to HSL components. Both high-titer virus stocks or provirus-carrying cells, suspended either in tissue culture medium or freshly drawn blood, were completely inactivated upon contact with the HSL components. This was verified by the absence of any detectable HIV-1-specific antigen in the supernatants of long-term cultures and the absence of virus-specific DNA fragments after amplification by polymerase chain reaction with DNA from such cultures as target DNA. These results support the conclusion that the virus is in fact completely inactivated by contact with the HSL components, rendering blood specimens stored as HSL noninfectious in regard to HIV-1. 相似文献
7.
N J Gonchoroff J J Ryan T K Kimlinger T E Witzig P R Greipp J S Meyer J A Katzmann 《Cytometry》1990,11(5):642-646
Since the publication of paraffin block extraction procedures, flow cytometric analysis of DNA ploidy and S-phase of tumor specimens has been widely applied. DNA aneuploidy, DNA tetraploid (elevated G2/M), and elevated S-phase are clinically significant in some tumor systems. True DNA tetraploid cell lines will contain a large 4c population and perhaps an 8c population; samples with cell aggregates will also contain a 6c population. Microscopic examination of samples having a 6c peak revealed nuclei with adhering debris and doublets, triplets, and larger nuclear aggregates. After sonication, a uniform suspension of single nuclei without adherent debris was seen. In addition to reducing the percent of G2/M cells, sonication also reduced S-phase percent such that it was closer to the bromodeoxyuridine labeling index. The DNA ploidy classification of specimens was also compared pre- and post-sonication. Four of 96 breast cancer samples changed classification; all were specimens in which the histogram became cleaner and a small DNA aneuploid peak became apparent after sonication. 相似文献
8.
An analogue of the periodogram method for unequally spaced data is presented with a view to resolving the frequency structure of the observations. The algorithm is explicitly based on the sequential least squares procedure. In particular, the key concept is that the with-in-plot spectral analysis can be augmented by the between-plot information to make inferences about common characteristics. It is also shown how the between-plot random variations can be incorporated into the multiple harmonic regression model. A detailed spectral analysis investigates the periodic fluctuations in four cardio-circulatory variables, measured by autorhythmometric observation by eight men at rest and extending over a time span of 2 years. The spectral curves show the existence of circadian and circaseptan rhythmicities. The amplitude modulation of the dian rhythm by circaseptan variation is assimilated with the rhythmicity of work during the week. The blood-pressure variables situate their maximum annual peak in the winter period. These quasi-periodic fluctuations appear to be related to the amount of physical activity performed in time by the subjects. 相似文献
9.
Y Jouanneau C Meyer J Gaillard P M Vignais 《Biochemical and biophysical research communications》1990,171(1):273-279
A ferredoxin was purified anaerobically from Rhodobacter capsulatus grown photoheterotrophically with excess ammonia. This ferredoxin, called ferredoxin II (FdII), had a molecular weight of approximatively 15,000 by gel filtration and 14,000 by SDS polyacrylamide gel electrophoresis indicating that it is monomeric. Its absorption spectrum (oxidized form) exhibited maxima at 280 nm and 400 nm; the A400/A280 ratio had a calculated value of 0.55. Chemical determination of its iron and sulfur atom content, the value of the extinction coefficient at 400 nm (epsilon 400 = 26.8 mM-1 cm-1) and EPR spectra indicated that ferredoxin II contained one [3Fe-4S] and one [4Fe-4S] cluster. Upon reduction with excess dithionite only the [3Fe-4S] cluster became reduced. The reduction of both clusters was achieved by using 5-deazaflavin as photocatalyst. Ferredoxin II was also purified from bacteria grown under nitrogen limiting (nif derepressing) conditions. In in vitro assays, ferredoxin II catalyzed electron transport between illuminated chloroplasts and nitrogenase. 相似文献
10.
Jason M. Meyer Ailing Ji Lei Cai Deneys R. van der Westhuyzen 《Journal of lipid research》2014,55(8):1648-1656
Scavenger receptor-mediated uptake of oxidized LDL (oxLDL) is thought to be the major mechanism of foam cell generation in atherosclerotic lesions. Recent data has indicated that native LDL is also capable of contributing to foam cell formation via low-affinity receptor-independent LDL particle pinocytosis and selective cholesteryl ester (CE) uptake. In the current investigation, Cu2+-induced LDL oxidation was found to inhibit macrophage selective CE uptake. Impairment of selective CE uptake was significant with LDL oxidized for as little as 30 min and correlated with oxidative fragmentation of apoB. In contrast, LDL aggregation, LDL CE oxidation, and the enhancement of scavenger receptor-mediated LDL particle uptake required at least 3 h of oxidation. Selective CE uptake did not require expression of the LDL receptor (LDL-R) and was inhibited similarly by LDL oxidation in LDL-R−/− versus WT macrophages. Inhibition of selective uptake was also observed when cells were pretreated or cotreated with minimally oxidized LDL, indicating a direct inhibitory effect of this oxLDL on macrophages. Consistent with the effect on LDL CE uptake, minimal LDL oxidation almost completely prevented LDL-induced foam cell formation. These data demonstrate a novel inhibitory effect of mildly oxidized LDL that may reduce foam cell formation in atherosclerosis. 相似文献