Related papers: A model of macro-evolution as a branching process …
We introduce a population dynamics model, where individual genomes are represented by bit-strings. Selection is described by death probabilities which depend on these genomes, and new individuals continuously replace the ones that die,…
We introduce a one-parametric family of tree growth models, in which branching probabilities decrease with branch age $\tau$ as $\tau^{-\alpha}$. Depending on the exponent $\alpha$, the scaling of tree depth with tree size $n$ displays a…
The branching structure of biological evolution confers statistical dependencies on phenotypic trait values in related organisms. For this reason, comparative macroevolutionary studies usually begin with an inferred phylogeny that describes…
We propose a class of evolutionary models that involves an arbitrary exchangeable process as the breeding process and different selection schemes. In those models, a new genome is born according to the breeding process, and then a genome is…
A discrete time branching process where the offspring distribution is generation-dependent, and the number of reproductive individuals is controlled by a random mechanism is considered. This model is a Markov chain but, in general, the…
A class of models for large-scale evolution and mass extinctions is presented. These models incorporate environmental changes on all scales, from influences on a single species to global effects. This is a step towards a unified picture of…
There have been many studies to examine whether one trait is correlated with another trait across a group of present-day species (for example, do species with larger brains tend to have longer gestation times. Since the introduction of the…
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…
Tip-driven growth processes underlie the development of many plants. To date, tip-driven growth processes have been modelled as an elongating path or series of segments without taking into account lateral expansion during elongation.…
Phylogenetic diversity is a measure for describing how much of an evolutionary tree is spanned by a subset of species. If one applies this to the (unknown) subset of current species that will still be present at some future time, then this…
We study a model of growing planar tree graphs where in each time step we separate the tree into two components by splitting a vertex and then connect the two pieces by inserting a new link between the daughter vertices. This model…
Bio-inspired paradigms are proving to be useful in analyzing propagation and dissemination of information in networks. In this paper we explore the use of multi-type branching processes to analyse viral properties of content in a social…
Textual analysis of typical microbial genomes reveals that they have the statistical characteristics of a DNA sequence of a much shorter length. This peculiar property supports an evolutionary model in which a genome evolves by random…
Null models of binary phylogenetic trees are useful for testing hypotheses on real world phylogenies. In this paper we consider phylogenies as binary trees without edge lengths together with a sampling measure and encode them as algebraic…
Diffusion and flow matching approaches to generative modeling have shown promise in domains where the state space is continuous, such as image generation or protein folding & design, and discrete, exemplified by diffusion large language…
Phylogenetics uses alignments of molecular sequence data to learn about evolutionary trees relating species. Along branches, sequence evolution is modelled using a continuous-time Markov process characterised by an instantaneous rate…
Real networks often grow through the sequential addition of new nodes that connect to older ones in the graph. However, many real systems evolve through the branching of fundamental units, whether those be scientific fields, countries, or…
Bayesian phylogenetics is vital for understanding evolutionary dynamics, and requires accurate and efficient approximation of posterior distributions over trees. In this work, we develop a variational Bayesian approach for ultrametric…
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…
Forward-time models of diversification (i.e., speciation and extinction) produce phylogenetic trees that grow "vertically" as time goes by. Pruning the extinct lineages out of such trees leads to natural models for reconstructed trees…