Prediction of multivariate spatial random field with continuous, count and ordinal outcomes

absen

A regional allometry for the Congo basin forests based on the largest ever destructive sampling

International audienceThe estimation and monitoring of the huge amount of carbon contained in tropical forests, and specifically in the above-ground biomass (AGB) of trees, is needed for the successful implementation of climate change mitigation strategies. Its accuracy depends on the availability of reliable allometric equations to convert forest inventory data into AGB estimates. In this study, we tested whether central African forests are really different from other tropical forests with respect to biomass allometry, and further examined the regional variation in tropical tree allometry across the Congo basin forests. Following the same standardized protocol, trees were destructively sampled for AGB in six sites representative of terra firme forests. We fitted regional and local allometric models, including tree diameter, wood specific gravity, tree height, and crown radius in the AGB predictors. We also evaluated the AGB predictions at the tree level across the six sites of our new models and of existing allometric models, including the pantropical equations developed by Chave et al. (2014, 2005) and the local equations developed by Ngomanda et al. (2014) in Gabon. With a total of 845 tropical trees belonging to 55 African species and covering a large range of diameters (up to 200 cm), the original data presented here can be considered as the largest ever destructive sampling for a tropical region. Regional allometric models were established and including tree height and crown radius had a small but significant effect on AGB predictions. In contrast to our expectations, tree height and crown radius did not explain much between-site variation. Examining the performance of general models (pantropical or regional) versus local models (site-specific), we found little advantage of using local equations. Earlier pantropical equations developed for moist forests were found to provide reasonable predictions of tree AGB in most sites, though the wettest sites, i.e., evergreen forests in Equatorial Guinea and, to a lesser extent in Gabon, tended to show a wet forest allometry. For the Congo basin forests, except in Equatorial Guinea where local models might be preferred, we recommend using our regional models, and otherwise the most recent pantropical models, that were validated here. These results constitute a critical step for the estimation and monitoring of biomass/carbon stocks contained in the second largest contiguous block of tropical forests worldwide, and the successful implementation of climate change mitigation strategies, such as REDD+

Hierarchical Bayesian model for Gaussian, Poisson and ordinal random fields

As most georeferenced data sets are multivariate and concern variables of different kinds, spatial mapping methods must be able to deal with such data. The main difficulties are the prediction of non Gaussian variables and the modelling of the dependence between processes. The aim of this paper is to propose a new approach that permits simultaneous modelling of Gaussian, count and ordinal spatial processes. We consider a hierarchical model implemented within a Bayesian framework. The method used for Gaussian and count variables is based on the generalized linear mixed models. Ordinal variable is taken into account through a generalization of the ordinal probit model. We use a moving average approach to model the spatial dependence between the processes. The proposed model is applied to pedological data collected in French Guiana

Effect of Yb3+ concentration on optical properties of Yb:CaF2 transparent ceramics

International audienceIn Yb:CaF2, the coordination of Yb3+ in the CaF2 lattice determines the spectroscopic properties that make Yb:CaF2 a good candidate for high power laser applications. In this work, we measure the optical absorption, emission, and fluorescence lifetime of 0.1, 1, 5, and 10 at% Yb:CaF2 ceramics to determine whether Yb3+ substitutes as hexamer clusters giving rise to the tenability and long fluorescent lifetime observed in Yb:CaF2 single crystals. Absorption and emission spectra show that the concentration of Yb3+ present in hexamer clusters, as opposed to isolated ions, increases with increasing Yb3+ content. Fluorescence lifetime also increases with increasing Yb3+ content. Laser testing on a 1 at% Yb:CaF2 transparent ceramic demonstrates that these materials are viable laser gain media

CCR gene in Eucalyptus: a model of functional variability in forest trees

La variabilité nucléotidique du gène codant la Cinnamoyl CoA Reductase (CCR) et ses effets sur le taux de lignine est étudiée au sein d’une population d’Eucalyptus urophylla S.T. Blake. La presque totalité de la séquence (94%, 3220 paires de bases) est décrite pour 15 individus. Le gène est hautement polymorphe et présente 131 mutations ponctuelles (SNP) ainsi que divers autres types de mutations. Les fragments exoniques présentent 10 SNP non synonymes dont 5 dans l’exon 5. La séquence promotrice (694 pb) est décrite pour les deux allèles d’un des géniteurs. Elle regroupe 5 SNPs. La variabilité fonctionnelle de ce promoteur sera étudiée grâce à son expression dans Arabidopsis thaliana. L’analyse de la teneur en lignine de 348 arbres appartenant à 35 familles de pleins frères obtenues avec ces 15 géniteurs montre que ce caractère présente un fort contrôle génétique additif (h²=0.76). Un nouvel algorithme type MCMC a été développé pour procéder aux études d’association sur 208 descendants génotypés grâce à un marqueur microsatellite présent dans le gène CCR. Les résultats montrent qu’une part importante de la variance du taux de lignine est due au polymorphisme du gène CCR. Ces résultats laissent envisager le développement d’une sélection précoce assistée par marqueurs.Nucleotidic polymorphism of Cinnamoyl CoA Reductase (CCR) gene and its relation with lignin content is studied within a breeding population of Eucalyptus urophylla S.T. Blake (“Timor Mountain Gum”). The nearly full sequence (94%) are obtained for 15 parental trees. This gene (3220 bp) is highly polymorphic showing 131 single nucleotide polymorphism (SNP), 17 insertion-deletions (INDEL), 1 polyA sequence and a microsatellite site. Exons fragments encompass 10 non-synonymous SNPs, half of them within exon 5 (194 bp). Fifteen different haplotypes are reconstructed based on the polymorphism of exon 4 and intron 4. CCR promoting sequence (694 bp) including all the known regulatory sequences is described for the two alleles of one of the genitor trees displaying QTL and CCR gene colocalization in its genetic map. Five SNPs are present. Functional variability of the promoting sequence will be studied in planta through genetic modification of Arabidopsis thaliana. Lignin content was assessed within a sample of 35 full sib families (348 individuals) generated with the 15 parental trees, showing a high genetic additive control for this trait (h²=0.76). A new algorithm based on Reversible-jump MCMC was developed in order to implement association studies. Half of the progeny trees (208) were genotyped using the microsatellite fragment. The results show that a significant part of the observed genetic variance of lignin content is due to the nucleotide polymorphism of the studied gene. Those preliminary results look promising in order to develop early gene assisted selection for eucalyptus clones used as raw material in charcoal and paper production

Un modèle de variabilité fonctionnelle chez les arbres forestiers : le gène CCR d'eucalyptus

National audienceNucleotidic polymorphism of Cinnamoyl CoA Reductase (CCR) gene and its relation with lignin content is studied within a breeding population of Eucalyptus urophylla S.T. Blake (“Timor Mountain Gum”). The nearly full sequence (94%) are obtained for 15 parental trees. This gene (3220 bp) is highly polymorphic showing 131 single nucleotide polymorphism (SNP), 17 insertion-deletions (INDEL), 1 polyA sequence and a microsatellite site. Exons fragments encompass 10 non-synonymous SNPs, half of them within exon 5 (194 bp). Fifteen different haplotypes are reconstructed based on the polymorphism of exon 4 and intron 4. CCR promoting sequence (694 bp) including all the known regulatory sequences is described for the two alleles of one of the genitor trees displaying QTL and CCR gene colocalization in its genetic map. Five SNPs are present. Functional variability of the promoting sequence will be studied in planta through genetic modification of Arabidopsis thaliana. Lignin content was assessed within a sample of 35 full sib families (348 individuals) generated with the 15 parental trees, showing a high genetic additive control for this trait (h²=0.76). A new algorithm based on Reversible-jump MCMC was developed in order to implement association studies. Half of the progeny trees (208) were genotyped using the microsatellite fragment. The results show that a significant part of the observed genetic variance of lignin content is due to the nucleotide polymorphism of the studied gene. Those preliminary results look promising in order to develop early gene assisted selection for eucalyptus clones used as raw material in charcoal and paper production.La variabilité nucléotidique du gène codant la Cinnamoyl CoA Reductase (CCR) et ses effets sur le taux de lignine est étudiée au sein d’une population d’Eucalyptus urophylla S.T. Blake. La presque totalité de la séquence (94%, 3220 paires de bases) est décrite pour 15 individus. Le gène est hautement polymorphe et présente 131 mutations ponctuelles (SNP) ainsi que divers autres types de mutations. Les fragments exoniques présentent 10 SNP non synonymes dont 5 dans l’exon 5. La séquence promotrice (694 pb) est décrite pour les deux allèles d’un des géniteurs. Elle regroupe 5 SNPs. La variabilité fonctionnelle de ce promoteur sera étudiée grâce à son expression dans Arabidopsis thaliana. L’analyse de la teneur en lignine de 348 arbres appartenant à 35 familles de pleins frères obtenues avec ces 15 géniteurs montre que ce caractère présente un fort contrôle génétique additif (h²=0.76). Un nouvel algorithme type MCMC a été développé pour procéder aux études d’association sur 208 descendants génotypés grâce à un marqueur microsatellite présent dans le gène CCR. Les résultats montrent qu’une part importante de la variance du taux de lignine est due au polymorphisme du gène CCR. Ces résultats laissent envisager le développement d’une sélection précoce assistée par marqueurs

CCR gene in Eucalyptus: a model of functional variability in forest trees

La variabilité nucléotidique du gène codant la Cinnamoyl CoA Reductase (CCR) et ses effets sur le taux de lignine est étudiée au sein d’une population d’Eucalyptus urophylla S.T. Blake. La presque totalité de la séquence (94%, 3220 paires de bases) est décrite pour 15 individus. Le gène est hautement polymorphe et présente 131 mutations ponctuelles (SNP) ainsi que divers autres types de mutations. Les fragments exoniques présentent 10 SNP non synonymes dont 5 dans l’exon 5. La séquence promotrice (694 pb) est décrite pour les deux allèles d’un des géniteurs. Elle regroupe 5 SNPs. La variabilité fonctionnelle de ce promoteur sera étudiée grâce à son expression dans Arabidopsis thaliana. L’analyse de la teneur en lignine de 348 arbres appartenant à 35 familles de pleins frères obtenues avec ces 15 géniteurs montre que ce caractère présente un fort contrôle génétique additif (h²=0.76). Un nouvel algorithme type MCMC a été développé pour procéder aux études d’association sur 208 descendants génotypés grâce à un marqueur microsatellite présent dans le gène CCR. Les résultats montrent qu’une part importante de la variance du taux de lignine est due au polymorphisme du gène CCR. Ces résultats laissent envisager le développement d’une sélection précoce assistée par marqueurs.Nucleotidic polymorphism of Cinnamoyl CoA Reductase (CCR) gene and its relation with lignin content is studied within a breeding population of Eucalyptus urophylla S.T. Blake (“Timor Mountain Gum”). The nearly full sequence (94%) are obtained for 15 parental trees. This gene (3220 bp) is highly polymorphic showing 131 single nucleotide polymorphism (SNP), 17 insertion-deletions (INDEL), 1 polyA sequence and a microsatellite site. Exons fragments encompass 10 non-synonymous SNPs, half of them within exon 5 (194 bp). Fifteen different haplotypes are reconstructed based on the polymorphism of exon 4 and intron 4. CCR promoting sequence (694 bp) including all the known regulatory sequences is described for the two alleles of one of the genitor trees displaying QTL and CCR gene colocalization in its genetic map. Five SNPs are present. Functional variability of the promoting sequence will be studied in planta through genetic modification of Arabidopsis thaliana. Lignin content was assessed within a sample of 35 full sib families (348 individuals) generated with the 15 parental trees, showing a high genetic additive control for this trait (h²=0.76). A new algorithm based on Reversible-jump MCMC was developed in order to implement association studies. Half of the progeny trees (208) were genotyped using the microsatellite fragment. The results show that a significant part of the observed genetic variance of lignin content is due to the nucleotide polymorphism of the studied gene. Those preliminary results look promising in order to develop early gene assisted selection for eucalyptus clones used as raw material in charcoal and paper production