Related papers: Probabilistic Models for the (sub)Tree(s) of Life
When an advantageous mutation occurs in a population, the favorable allele may spread to the entire population in a short time, an event known as a selective sweep. As a result, when we sample $n$ individuals from a population and trace…
Phylogenetic trees describe the relationships between species in the evolutionary process, and provide information about the rates of diversification. To understand the mechanisms behind macroevolution, we consider a class of multitype…
Diversification is nested, and early models suggested this could lead to a great deal of evolutionary redundancy in the Tree of Life. This result is based on a particular set of branch lengths produced by the common coalescent, where…
Phylogenetic species trees typically represent the speciation history as a bifurcating tree. Speciation events that simultaneously create more than two descendants, thereby creating polytomies in the phylogeny, are possible. Moreover, the…
We study the Potts model on locally tree-like random graphs of arbitrary degree distribution. Using a population dynamics algorithm we numerically solve the problem exactly. We confirm our results with simulations. Comparisons with a…
$\Lambda$-coalescents model genealogies of samples of individuals from a large population by means of a family tree whose branches have lengths. The tree's leaves represent the individuals, and the lengths of the adjacent edges indicate the…
Coalescent theory combined with statistical modeling allows us to estimate effective population size fluctuations from molecular sequences of individuals sampled from a population of interest. When sequences are sampled serially through…
Early literature on genome rearrangement modelling views the problem of computing evolutionary distances as an inherently combinatorial one. In particular, attention was given to estimating distances using the minimum number of events…
We present Collaborative Trees, a novel tree model designed for regression prediction, along with its bagging version, which aims to analyze complex statistical associations between features and uncover potential patterns inherent in the…
Habitat loss is one of the biggest threats facing plant species nowadays. We formulate a simple mathematical model of seed dispersal on reduced habitats to discuss survival of the species in relation to the habitat size and seeds production…
Binary trees are fundamental objects in models of evolutionary biology and population genetics. Here, we discuss some of their combinatorial and structural properties as they depend on the tree class considered. Furthermore, the process by…
Population genetics theory has laid the foundations for genomics analyses including the recent burst in genome scans for selection and statistical inference of past demographic events in many prokaryote, animal and plant species.…
We consider a random tree and introduce a metric in the space of trees to define the ``mean tree'' as the tree minimizing the average distance to the random tree. When the resulting metric space is compact we have laws of large numbers and…
We consider the compact space of pairs of nested partitions of $\mathbb N$, where by analogy with models used in molecular evolution, we call "gene partition" the finer partition and "species partition" the coarser one. We introduce the…
In data analysis, latent variables play a central role because they help provide powerful insights into a wide variety of phenomena, ranging from biological to human sciences. The latent tree model, a particular type of probabilistic…
Random forests is a state-of-the-art supervised machine learning method which behaves well in high-dimensional settings although some limitations may happen when $p$, the number of predictors, is much larger than the number of observations…
Sweepstakes reproduction refers to a highly skewed individual recruitment success without involving natural selection and may apply to individuals in broadcast spawning populations characterised by Type III survivorship. We consider an…
Understanding the patterns and processes of diversification of life in the planet is a key challenge of science. The Tree of Life represents such diversification processes through the evolutionary relationships among the different taxa, and…
This is a survey article on trees, with a modest number of proofs to give a flavor of the way these topologies can be efficiently handled. Trees are defined in set-theorist fashion as partially ordered sets in which the elements below each…
We consider general Gaussian latent tree models in which the observed variables are not restricted to be leaves of the tree. Extending related recent work, we give a full semi-algebraic description of the set of covariance matrices of any…