相关论文: Five Statistical Questions about the Tree of Life

The goal of these lectures is to review some mathematical aspects of random tree models used in evolutionary biology to model gene trees or species trees. We start with stochastic models of tree shapes (finite trees without edge lengths),…

Evolution has fascinated quantitative and physical scientists for decades: how can the random process of mutation, recombination, and duplication of genetic information generate the diversity of life? What determines the rate of evolution?…

Theoretical ecologists have long sought to understand how the persistence of populations depends on biotic and abiotic factors. Classical work showed that demographic stochasticity causes the mean time to extinction to increase…

An early burst of speciation followed by a subsequent slowdown in the rate of diversification is commonly inferred from molecular phylogenies. This pattern is consistent with some verbal theory of ecological opportunity and adaptive…

One of the classical questions in evolutionary biology is how evolutionary processes are coupled at the gene and species level. With this motivation, we compare the topological properties (mainly the depth scaling, as a characterization of…

Phylogenetic networks are increasingly used in evolutionary biology to represent the history of species that have undergone reticulate events such as horizontal gene transfer, hybrid speciation and recombination. One of the most fundamental…

As researchers collect increasingly large molecular data sets to reconstruct the Tree of Life, the heterogeneity of signals in the genomes of diverse organisms poses challenges for traditional phylogenetic analysis. A class of phylogenetic…

The constant rate birth--death process is a popular null model for speciation and extinction. If one removes extinct and non-sampled lineages, this process induces `reconstructed trees' which describe the relationship between extant…

An evolutionary tree is a cascade of bifurcations starting from a single common root, generating a growing set of daughter species as time goes by. Species here is a general denomination for biological species, spoken languages or any other…

We propose the following simple stochastic model for phylogenetic trees. New types are born and die according to a birth and death chain. At each birth we associate a fitness to the new type sampled from a fixed distribution. At each death…

Bayesian inference is now a leading technique for reconstructing phylogenetic trees from aligned sequence data. In this short note, we formally show that the maximum posterior tree topology provides a statistically consistent estimate of a…

We present a stochastic model for the size of a taxon in paleobiology, in which we allow for the evolution of new taxon members, and both individual and catastrophic extinction events. The model uses ideas from the theory of birth and death…

We consider a neutral haploid population whose generations are not overlapping and whose size is large and constantly of $N$ individuals. Any generation is replaced by a new one and any individual has a single parent. We do not choose the…

Recent methodological advances are enabling better examination of speciation and extinction processes and patterns. A major open question is the origin of large discrepancies in species number between groups of the same age. Existing…

We propose a stochastic model for evolution. Births and deaths of species occur with constant probabilities. Each new species is associated with a fitness sampled from the uniform distribution on [0,1]. Every time there is a death event…

The selection of the most suitable evolutionary model to analyze the given molecular data is usually left to biologist's choice. In his famous book, J Felsenstein suggested that certain linear equations satisfied by the expected…

Time evolution of number of species (genera, families, and others), population of them, and size distribution of present ones and life times are studied in terms of a new model, where population of each genetic taxon increases by a (random)…

Genomic data are rapidly resolving the tree of living species calibrated to time, the timetree of life, which will provide a framework for research in diverse fields of science. Previous analyses of taxonomically restricted timetrees have…

We consider branching processes with interaction in continuous time, both with values in the integers and in the reals (in the second case we restrict ourselves to continuous processes), which model the evolution of the size of a…

The ongoing explosion of genome sequence data is transforming how we reconstruct and understand the histories of biological systems. Across biological scales, from individual cells to populations and species, trees-based models provide a…