种群与进化
The influence of climate on mosquito-borne diseases like dengue and chikungunya is well-established, but comprehensively tracking long-term spatial and temporal trends across large areas has been hindered by fragmented data and limited…
Airborne infection risk analysis is usually performed for enclosed spaces where susceptible individuals are exposed to infectious airborne respiratory droplets by inhalation. It is usually based on exponential, dose-response models of which…
Recent pandemics triggered the development of a number of mathematical models and computational tools apt at curbing the socio-economic impact of these and future pandemics. The need to acquire solid estimates from the data led to the…
In recent years, there has been an effort to extend the classical notion of phylogenetic balance, originally defined in the context of trees, to networks. One of the most natural ways to do this is with the so-called $B_2$ index. In this…
In this paper, we study the problem of cost optimisation of individual-based institutional incentives (reward, punishment, and hybrid) for guaranteeing a certain minimal level of cooperative behaviour in a well-mixed, finite population. In…
In a recent paper, the question of determining the fraction of binary trees that contain a fixed pattern known as the snowflake was posed. We show that this fraction goes to 1, providing two very different proofs: a purely combinatorial one…
In this paper we introduce some simple models, based on rolling dice, to explore mechanisms proposed to explain planetary habitability. The idea is to study these selection mechanisms in an analytically tractable setting, isolating their…
Autocatalysis is thought to have played an important role in the earliest stages of the origin of life. An autocatalytic cycle (AC) is a set of reactions that results in stoichiometric increase in its constituent chemicals. When the…
The drift-barrier hypothesis states that random genetic drift constrains the refinement of a phenotype under natural selection. The influence of effective population size and the genome-wide deleterious mutation rate were studied…
The origin of life must have been preceded by Darwin-like evolutionary dynamics that could propagate it. How did that adaptive dynamics arise? And from what prebiotic molecules? Using evolutionary invasion analysis, we develop a universal…
Interest in the inference of evolutionary networks relating species or populations has grown with the increasing recognition of the importance of hybridization, gene flow and admixture, and the availability of large-scale genomic data.…
The inverse Potts problem to infer a Boltzmann distribution for homologous protein sequences from their single-site and pairwise amino acid frequencies recently attracts a great deal of attention in the studies of protein structure and…
Models of conformity and anti-conformity have typically focused on cultural traits with nominal (unordered) variants, such as baby names, strategies (cooperate/defect), or the presence/absence of an innovation. There have been fewer studies…
An important problem in evolutionary genomics is to investigate whether a certain trait measured on each sample is associated with the sample phylogenetic tree. The phylogenetic tree represents the shared evolutionary history of the samples…
We developed a mathematical model to investigate the role of indirect transmission in the spread of infectious diseases, using the illustrative example of sarcoptic mange as a case study. This disease can be transmitted through direct…
The Wright-Fisher model describes a biological population containing a finite number of individuals. In this work we consider a Wright-Fisher model for a randomly mating population, where selection and mutation act at an unlinked locus. The…
We consider the dynamics imposed by natural selection on the populations of two competing, sexually reproducing, haploid species. In this setting, the fitness of any genome varies over time due to the changing population mix of the…
In silico evolution instantiates the processes of heredity, variation, and differential reproductive success (the three "ingredients" for evolution by natural selection) within digital populations of computational agents. Consequently,…
Phylogenetic networks can represent evolutionary events that cannot be described by phylogenetic trees, such as hybridization, introgression, and lateral gene transfer. Studying phylogenetic networks under a statistical model of DNA…
Lampreys are one of the oldest species in the world, living longer than dinosaurs, which is related to the ability to change the sex ratio during their lifespan. In this paper, to understand how sex ratio and food quantity affect the…