Search

Additional file 1. Supplementary information regarding precise definitions of static centralities (Section S1), variance in the simulated outbreak sizes (Section S2), the relative weight of markets and assembly centres in highly ranked nodes (Section S3), the impact of using different yearly datasets to compute centralities (Section S4), the impact of varying epidemic parameters (Section S5), and the impact of varying random walk parameters to approximate TempoRank measures (Section S6).

International audience

A variety of methods based on coalescent theory have been developed to infer demographic history from gene sequences sampled from natural populations. The “skyline plot” and related approaches are commonly employed as exible prior distributions for phylogenetic trees in the Bayesian analysis of pathogen gene sequences. In this work we extend the classic and generalised skyline plot methods to phylogenies that contain one or more multifurcations (i.e.hard polytomies). We use the theory of Λ-coalescents (specifically, Beta(2α,α)-coalescents) to develop the “multifurcating skyline plot”, which estimates a piecewise constant function of effective population size through time, conditional on a time-scaled multifurcating phylogeny. We implement a smoothing procedure and extend the method to serially-sampled (heterochronous) data, but we do not address here the problem of estimating trees with multifurcations from gene sequence alignments. We validate our estimator on simulated data using maximum likelihood and find that parameters of the Beta(2α,α)-coalescent process can be estimated accurately. Lastly we apply the multifurcating skyline plot to a molecular clock phylogeny of 1,610 Ebola virus sequences from the 2014-2016 West African outbreak. We artificially collapse short branches in this empirical phylogeny in order to mimic different levels of multifurcation and show that variance in the reproductive success of the pathogen through time can be estimated by combining the skyline plot with epidemiological case count data.

International audience; We present an extension of the Gromov-Hausdorff metric on the set of compact metric spaces: the Gromov-Hausdorff-Prokhorov metric on the set of compact metric spaces endowed with a finite measure. We then extend it to the non-compact case by describing a metric on the set of rooted complete locally compact length spaces endowed with a locally finite measure. We prove that this space with the extended Gromov-Hausdorff-Prokhorov metric is a Polish space. This generalization is needed to define Lévy trees, which are (possibly unbounded) random real trees endowed with a locally finite measure.

In this thesis, we study continuum tree-valued processes. First, we define an abstract framework for these processes, by constructing a metric on the space of locally compact, complete R-trees, endowed with a locally finite Borel measure. This topology, called Gromov-Hausdorff-Prokhorov topology, allows for the definition of tree-valued Markov processes. We then give a new construction of the pruning process of Abraham-Delmas-Voisin, which is an example of a Lévy tree-valued process. Our construction reveals a new genealogical structure of Lévy trees. Furthermore, it is a path wise construction, which describes the transitions of the process explicitly. We apply this description to the study of certain stopping times, such as the first moment the process crosses a given height. We describe the process at that time through a new spinal decomposition. Finally, we focus on the Aldous-Pitman fragmentation of Aldous's Brownian tree. Following Abraham and Delmas, we study the effect of the fragmentation on discrete subtrees of the Brownian tree. The number of cuts needed to isolate the root, suitably renormalized, converges towards a Rayleigh-distributed random variable; we prove a Central Limit Theorem describing the fluctuations around this limit, Cette thèse est consacrée à l'étude de certains processus aléatoires à valeurs dans les arbres continus. Nous définissons d'abord un cadre conceptuel pour cette étude, en construisant une topologie polonaise sur l'espace des R-arbres localement compacts, complets et munis d'une mesure borélienne localement finie. Cette topologie, dite de Gromov-Hausdorff-Prokhorov, permet alors la définition de processus de Markov à valeurs arbre. Nous donnons ensuite une nouvelle construction du processus d'élagage d'Abraham-Delmas-Voisin, qui est un exemple de processus qui prend ses valeurs dans les arbres de Lévy. Notre construction, qui dévoile une nouvelle structure généalogique des arbres de Lévy, est trajectorielle, et permet d'identifier explicitement les transitions du processus d'élagage. Nous appliquons cette description à l'étude de certains temps d'arrêt, comme le premier temps auquel le processus franchit une hauteur donnée. Nous décrivons le processus à cet instant grâce à une nouvelle décomposition de type spinal. Enfin, nous nous intéressons à la fragmentation d'Aldous-Pitman de l'arbre brownien d'Aldous. En particulier, nous étudions, à la suite d'Abraham et Delmas, l'effet de cette fragmentation sur les sous-arbres discrets de l'arbre brownien. Le nombre de coupures nécessaires avant d'isoler la racine, convenablement renormalisé, converge vers une variable aléatoire de Rayleigh ; nous donnons un théorème central limite qui précise les fluctuations autour de cette limite

[This corrects the article DOI: 10.1093/ve/vez031.].