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We propose a mathematical framework for natural selection in finite populations. Traditionally, many of the selection-based processes used to describe cultural and genetic evolution (such as imitation and birth-death models) have been…
Phylogeny is the study of the relations between biological entities. From it, the need to compare tree-like graphs has risen and several metrics were established and researched, but since there is no definitive way to compare them, its…
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…
Evolution is the process of optimal adaptation of biological populations to their living environments. This is expressed via the concept of fitness, defined as relative reproductive success. However, it has been pointed out that this…
Reconstructing the density fluctuations in the early Universe that evolved into the distribution of galaxies we see today is a challenge of modern cosmology [ref.]. An accurate reconstruction would allow us to test cosmological models by…
We describe the simulation method of modelling the population evolution using Monte Carlo based on the Penna model. Individuals in the populations are represented by their diploid genomes. Genes expressed after the minimum reproduction age…
We study the probabilities of evolution based on random mutations and natural selection. We conclude that evolution to multicellular eukaryots, or even prokaryots, is unlikely to be the result of only random mutations. Complex organisms…
Given a sample of genome sequences from an asexual population, can one predict its evolutionary future? Here we demonstrate that the branching patterns of reconstructed genealogical trees contains information about the relative fitness of…
Predicting the adaptation of populations to a changing environment is crucial to assess the impact of human activities on biodiversity. Many theoretical studies have tackled this issue by modeling the evolution of quantitative traits…
A probabilistic reconstruction of genealogies in a polyploid population (from 2x to 4x) is investigated, by considering genetic data analyzed as the probability of allele presence in a given genotype. Based on the likelihood of all possible…
Although extensive behavioral changes often exist between closely related animal species, our understanding of the genetic basis underlying the evolution of behavior has remained limited. Here, we propose a new framework to study behavioral…
We study evolving genealogies, i.e. processes that take values in the space of (marked) ultra-metric measure spaces and satisfy some sort of "consistency" condition. This condition is based on the observation that the genealogical distance…
Evolutionary dynamics are shaped by a variety of fundamental, generic drivers, including spatial structure, ecology, and selection pressure. These drivers impact the trajectory of evolution, and have been hypothesized to influence…
It is increasingly evident that there is more to biological evolution than natural selection; moreover, the concept of evolution is not limited to biology. We propose an integrative framework for characterizing how entities evolve, in which…
We consider the evolution of populations under the joint action of mutation and differential reproduction, or selection. The population is modelled as a finite-type Markov branching process in continuous time, and the associated…
Reproducibility is a confused terminology. In this paper, I take a fundamental view on reproducibility rooted in the scientific method. The scientific method is analysed and characterised in order to develop the terminology required to…
Ancestral state reconstruction is one of the most important tasks in evolutionary biology. Conditions under which we can reliably reconstruct the ancestral state have been studied for both discrete and continuous traits. However, the…
We show that the quadratic measure need not be postulated, but follows from the compatibility of two structural features of physical processes: linear reversible evolution prior to the formation of persistent records, and multiplicative…
Understanding how genotypes map onto phenotypes, fitness, and eventually organisms is arguably the next major missing piece in a fully predictive theory of evolution. We refer to this generally as the problem of the genotype-phenotype map.…
Deep generative models produce data according to a learned representation, e.g. diffusion models, through a process of approximation computing possible samples. Approximation can be understood as reconstruction and the large datasets used…