Browsing by Subject "15 Vida de ecosistemas terrestres"

The Gaussian copula is a powerful tool that has been widely used to model spatial and/or temporal correlated data with arbitrary marginal distributions. However, this kind of model can potentially be too restrictive since it expresses a reflection symmetric dependence. In this paper, we propose a new spatial copula model that makes it possible to obtain random fields with arbitrary marginal distributions with a type of dependence that can be reflection symmetric or not. Particularly, we propose a new random field with uniform marginal distributions that can be viewed as a spatial generalization of the classical Clayton copula model. It is obtained through a power transformation of a specific instance of a beta random field which in turn is obtained using a transformation of two independent Gamma random fields. For the proposed random field, we study the second-order properties and we provide analytic expressions for the bivariate distribution and its correlation. Finally, in the reflection symmetric case, we study the associated geometrical properties. As an application of the proposed model we focus on spatial modeling of data with bounded support. Specifically, we focus on spatial regression models with marginal distribution of the beta type. In a simulation study, we investigate the use of the weighted pairwise composite likelihood method for the estimation of this model. Finally, the effectiveness of our methodology is illustrated by analyzing point-referenced vegetation index data using the Gaussian copula as benchmark. Our developments have been implemented in an open-source package for the R statistical environment.

The Actinomycetota (formerly Actinobacteria) genus Clavibacter includes phytopathogens with devasting effects in several crops. Clavibacter michiganensis, the causal agent of tomato bacterial canker, is the most notorious species of the genus. Yet, its origin and natural reservoirs remain elusive, and its populations show pathogenicity profiles with unpredictable plant disease outcomes. Here, we generate and analyse a decade-long genomic dataset of Clavibacter from wild and commercial tomato cultivars, providing evolutionary insights that directed phenotypic characterization. Our phylogeny situates the last common ancestor of C. michiganensis next to Clavibacter isolates from grasses rather than to the sole strain we could isolate from wild tomatoes. Pathogenicity profiling of C. michiganensis isolates, together with C. phaseoli and C. californiensis as sister taxa and the wild tomato strain, was found to be congruent with the proposed phylogenetic relationships. We then identified gene enrichment after the evolutionary event, leading to the appearance of the C. michiganesis clade, including known pathogenicity factors but also hitherto unnoticed genes with the ability to encode adaptive traits for a pathogenic lifestyle. The holistic perspective provided by our evolutionary analyses hints towards a host shift event as the origin of C. michiganensis as a tomato pathogen and the existence of pathogenic genes that remain to be characterized.