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Ecological systems are governed by complex interactions which are mainly nonlinear. In order to capture this complexity and nonlinearity, statistical models recently gained popularity. However, although these models are commonly applied in…
Genomic regions (or loci) displaying outstanding correlation with some environmental variables are likely to be under selection and this is the rationale of recent methods of identifying selected loci and retrieving functional information…
A review of the mechanisms of speciation is performed. The mechanisms of the evolution of species, taking into account the feedback of the state of the environment and mechanisms of the emergence of complexity, are considered. It is shown…
Deterministic continuum models formulated in terms of non-local partial differential equations for the evolutionary dynamics of populations structured by phenotypic traits have been used recently to address open questions concerning the…
In a complex community, species continuously adapt to each other. On rare occasions, the adaptation of a species can lead to the extinction of others, and even its own. "Adaptive dynamics" is the standard mathematical framework to describe…
The rapid development of sequencing technologies represents new opportunities for population genetics research. It is expected that genomic data will increase our ability to reconstruct the history of populations. While this increase in…
In order to accommodate the empirical fact that population structures are rarely simple, modern studies of evolutionary dynamics allow for complicated and highly-heterogeneous spatial structures. As a result, one of the most difficult…
Predicting competitive outcomes typically requires fitting dynamical models to data, from which interaction strengths and coexistence indicators such as invasion criteria can be produced. Methods that allow to propagate parameter…
In this contribution, we discuss the basic concepts of genotypes and phenotypes in tree-based GP (TGP), and then analyze their behavior using five benchmark datasets. We show that TGP exhibits the same behavior that we can observe in other…
Organismal phenotypes emerge from a complex set of genotypic interactions. While technological advances in sequencing provide a quantitative description of an organism's genotype, characterization of an organism's physical phenotype lags…
Modeling environmental ecosystems is essential for effective resource management, sustainable development, and understanding complex ecological processes. However, traditional data-driven methods face challenges in capturing inherently…
The evolution and function of imitation have always been placed within the confines of animal learning and associated with its crucial role in cultural transmission and cultural evolution. Can imitation evolve as a form of phenotypic…
Planning with generative models has emerged as an effective decision-making paradigm across a wide range of domains, including reinforcement learning and autonomous navigation. While continuous replanning at each timestep might seem…
Generative models have fundamentally reshaped the landscape of decision-making, reframing the problem from pure scalar reward maximization to high-fidelity trajectory generation and distribution matching. This paradigm shift addresses…
The expansion of a population into new habitat is a transient process that leaves its footprints in the genetic composition of the expanding population. How the structure of the environment shapes the population front and the evolutionary…
The theory of life history evolution provides a powerful framework to understand the evolutionary dynamics of pathogens in both epidemic and endemic situations. This framework, however, relies on the assumption that pathogen populations are…
This paper concerns the modeling and numerical simulation of the process of speciation. In particular, given conditions for which one or more speciation events within an ecosystem occur, our aim is to develop the necessary modeling and…
We present a coherent Bayesian framework for selection of the most likely model from the five genetic models (genotypic, additive, dominant, co-dominant, and recessive) commonly used in genetic association studies. The approach uses a…
Phylogenetic analyses of gene expression have great potential for addressing a wide range of questions. These analyses will, for example, identify genes that have evolutionary shifts in expression that are correlated with evolutionary…
The aim of this manuscript is to contain the arguments and define the theoretical objects for building a general framework to model population dynamics from the ground up, relying mainly on the probabilistic landscapes defining the dynamics…