Intraspecific genetic variation of a Fagus sylvatica population in a temperate forest derived from airborne imaging spectroscopy time series

1. The growing pace of environmental change has increased the need for large‐scale monitoring of biodiversity. Declining intraspecific genetic variation is likely a critical factor in biodiversity loss, but is especially difficult to monitor: assessments of genetic variation are commonly based on measuring allele pools, which requires sampling of individuals and extensive sample processing, limiting spatial coverage. Alternatively, imaging spectroscopy data from remote platforms may hold the potential to reveal genetic structure of populations. In this study, we investigated how differences detected in an airborne imaging spectroscopy time series correspond to genetic variation within a population of Fagus sylvatica under natural conditions.
2. We used multi‐annual APEX (Airborne Prism Experiment) imaging spectrometer data from a temperate forest located in the Swiss midlands (Laegern, 47°28'N, 8°21'E), along with microsatellite data from F. sylvatica individuals collected at the site. We identified variation in foliar reflectance independent of annual and seasonal changes which we hypothesize is more likely to correspond to stable genetic differences. We established a direct connection between the spectroscopy and genetics data by using partial least squares (PLS) regression to predict the probability of belonging to a genetic cluster from spectral data.
3. We achieved the best genetic structure prediction by using derivatives of reflectance and a subset of wavebands rather than full‐analyzed spectra. Our model indicates that spectral regions related to leaf water content, phenols, pigments, and wax composition contribute most to the ability of this approach to predict genetic structure of F. sylvatica population in natural conditions.
4. This study advances the use of airborne imaging spectroscopy to assess tree genetic diversity at canopy level under natural conditions, which could overcome current spatiotemporal limitations on monitoring, understanding, and preventing genetic biodiversity loss imposed by requirements for extensive in situ sampling.

     

Semiparametric Regression in Size-Biased Sampling

Summary .  Size-biased sampling arises when a positive-valued outcome variable is sampled with selection probability proportional to its size. In this article, we propose a semiparametric linear regression model to analyze size-biased outcomes. In our proposed model, the regression parameters of covariates are of major interest, while the distribution of random errors is unspecified. Under the proposed model, we discover that regression parameters are invariant regardless of size-biased sampling. Following this invariance property, we develop a simple estimation procedure for inferences. Our proposed methods are evaluated in simulation studies and applied to two real data analyses.     

Analysis of Multiply Matched Retrospective Studies When Risk Factor Under Study is Discrete,With Two or More Levels

The odds ratio is known to closely approximate the relative risk when the disease is rare. Logistic regression models are often used to estimate such odds ratios, but here a different model is used which avoids the assumptions implicit in logistic modelling; it also has the advantage of providing a test of homogeneity for odds rat os in situations where the logistic model cannot.     

Joint multiple quantitative trait loci mapping for allometries of body compositions and metabolic traits to body weights in broiler

In order to map quantitative trait loci (QTLs) for allometries of body compositions and metabolic traits in chicken, we phenotypically characterize the allometric growths of multiple body components and metabolic traits relative to BWs using joint allometric scaling models and then establish random regression models (RRMs) to fit genetic effects of markers and minor polygenes derived from the pedigree on the allometric scalings. Prior to statistically inferring the QTLs for the allometric scalings by solving the RRMs, the LASSO technique is adopted to rapidly shrink most of marker genetic effects to zero. Computer simulation analysis confirms the reliability and adaptability of the so-called LASSO-RRM mapping method. In the F₂ population constructed by multiple families, we formulate two joint allometric scaling models of body compositions and metabolic traits, in which six of nine body compositions are tested as significant, while six of eight metabolic traits are as significant. For body compositions, a total of 14 QTLs, of which 9 dominant, were detected to be associated with the allometric scalings of drumstick, fat, heart, shank, liver and spleen to BWs; while for metabolic traits, a total of 19 QTLs also including 9 dominant be responsible for the allometries of T4, IGFI, IGFII, GLC, INS, IGR to BWs. The detectable QTLs or highly linked markers can be used to regulate relative growths of the body components and metabolic traits to BWs in marker-assisted breeding of chickens.     

Body size and area‐incidence relationships: is there a general pattern?

Aim This paper tests firstly for the existence of a general relationship between body size of terrestrial animals and their incidence across habitat patches of increasing size, and secondly for differences in this relationship between insects and vertebrates. Location The analysis was based on the occupancy pattern of 50 species from 15 different landscapes in a variety of ecosystems ranging from Central European grassland to Asian tropical forest. Methods The area‐occupancy relationship was described by incidence functions that were calculated using logistic regression. A correlation analysis between body size of the species and the patch area referring to the two given points of the incidence function was performed. In order to test for an effect of taxon (insects vs. vertebrates), an analysis of covariance was conducted. Results In all species, the incidence was found to increase with increasing patch area. The macroecological analysis showed a significant relationship between the incidence in habitat patches and the body size of terrestrial animals. The area requirement was found to increase linearly with increasing body size on a log‐log scale. This relationship did not differ significantly between insects and vertebrates. Conclusions The approach highlighted in this paper is to associate incidence functions with body size. The results suggest that body size is a general but rather rough predictor for the area requirements of animals. The relationship seems valid for a wide range of body sizes of terrestrial animals. However, further studies including isolation of habitats as well as additional species traits into the macroecological analysis of incidence functions are needed.     

The role of duplication in the expression of a variable surface glycoprotein gene of Trypanosoma brucei

The variable surface glycoprotein (VSG) genes of Trypanosoma brucei have been classified into two groups depending upon whether or not duplication of the genes is observed when they are expressed. We report here the observation of duplication apparently linked to expression of the ILTaT 1.3 gene in the ETaR 1 trypanosome stock. In the ILTaR 1 stock, expression of the ILTaT 1.3 VSG did not involve a new duplication, but instead activation of a preexisting gene copy that had been apparently generated earlier by a duplication event analogous to that directly observed in the ETaR 1 trypanosomes. The results suggest that the well-characterised gene duplications found with other VSG genes are common to all VSG genes but are not directly responsible for controlling expression. All currently available data can be accommodated by a model that assumes that gene duplication and replacement occurs independently of antigenic switching.     

Comparing Stochastically Restricted Linear Estimators in a Regression Model

Conditions for superiority of the minimum dispersion estimator over another with respect to the covariance matrix are derived when the vector parameter of a regression model is subject to competing stochastic restrictions. The restrictions may also consist both of a deterministic part and a stochastic part.     

Effect of pea bacterial blight (Pseudomonas syringae pv. pisi) on the yield of spring sown combining peas (Pisum sativum)

Field trials to examine the effect of pea bacterial blight (Pseudomonas syringae pv. pisi) (Psp) on the yield of combining peas were carried out at five sites (HRI Wellesbourne, ADAS Rosemaund, ADAS Terrington, PGRO, SASA East Craigs) in the UK in 1990, 1991 and 1992. Healthy seed, cv. Solara, and seed naturally infected with Psp Race 2 was sown in large plots (c. 200 m²) in the open or under nets to prevent bird damage by pigeons. Despite relatively low disease severity levels (< 15% leaf area) and separation by at least 12 m of cv. Consort (resistant to Race 2) between plots there was considerable spread of disease into plots sown with healthy seed. Regression analysis demonstrated a significant relationship between yield and disease. Of the disease measurements examined, disease severity on the leaves (stipules) at growth stage 208 was found to be the best predictor of yield. A model containing environmental and bird damage terms, in addition to disease, suggested that a yield loss of 0.98 t/ha would be expected for a disease severity score of 1, equivalent to 5% leaf area affected, at growth stage 208.     

Seemingly Unrelated Generalized Linear Models

By using deviance standardized residuals, the seemingly unrelated regression estimation procedure is extended to generalized linear models, and fitted by an iterative procedure. The matrix of cross products of standardized residuals is asymptotically multivariate normal, and can be used for further multivariate analyses and for hypothesis testing.