Related papers: A conditional likelihood is required to estimate t…
Evolution is a dynamic process. The two classical forces of evolution are mutation and selection. Assuming small mutation rates, evolution can be predicted based solely on the fitness differences between phenotypes. Predicting an…
Density ratio estimation in high dimensions can be reframed as integrating a certain quantity, the time score, over probability paths which interpolate between the two densities. In practice, the time score has to be estimated based on…
Evolutionary models for populations of constant size are frequently studied using the Moran model, the Wright-Fisher model, or their diffusion limits. When evolution is neutral, a random genealogy given through Kingman's coalescent is used…
Classical stochastic demography predicts that environmental stochasticity reduces population growth rates and, thereby, can increase extinction risk. In contrast, the SAS-CFF model demonstrates that environmental stochasticity can promote…
On rugged fitness landscapes where sign epistasis is common, adaptation can often involve either individually beneficial "uphill" mutations or more complex mutational trajectories involving fitness valleys or plateaus. The dynamics of the…
Pervasive natural selection can strongly influence observed patterns of genetic variation, but these effects remain poorly understood when multiple selected variants segregate in nearby regions of the genome. Classical population genetics…
Selection, mutation and random drift affect the dynamics of allele frequencies and consequently of quantitative traits. While the macroscopic dynamics of quantitative traits can be measured, the underlying allele frequencies are typically…
We obtain general inequalities constraining the difference between the average of an arbitrary function of a phenotypic trait, which includes the fitness landscape of the trait itself, in the presence or in the absence of natural selection.…
It is becoming routine to obtain datasets on DNA sequence variation across several thousands of chromosomes, providing unprecedented opportunity to infer the underlying biological and demographic forces. Such data make it vital to study…
The ability to calculate precise likelihood ratios is fundamental to many STEM areas, such as decision-making theory, biomedical science, and engineering. However, there is no assumption-free statistical methodology to achieve this. For…
We consider populations evolving according to natural selection, mutation, and recombination, and assume that the genomes of all or a representative selection of individuals are known. We pose the problem if it is possible to infer fitness…
We examine a model of biological evolution of Eigen's quasispecies in a holey fitness landscape, where the fitness of a site is either 0 (lethal site) or a uniform positive constant (viable site). So, the evolution dynamics is determined by…
In recent years we have been able to gather large amounts of genomic data at a fast rate, creating situations where the number of variables greatly exceeds the number of observations. In these situations, most models that can handle a…
We consider a model of a population of fixed size $N$ undergoing selection. Each individual acquires beneficial mutations at rate $\mu_N$, and each beneficial mutation increases the individual's fitness by $s_N$. Each individual dies at…
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…
Identifying drivers of complex traits from the noisy signals of genetic variation obtained from high throughput genome sequencing technologies is a central challenge faced by human geneticists today. We hypothesize that the variants…
Traditionally evolution is seen as a process where from a pool of possible variations of a population (e.g. biological species or industrial goods) a few variations get selected which survive and proliferate, whereas the others vanish.…
Functional effects of different mutations are known to combine to the total effect in highly nontrivial ways. For the trait under evolutionary selection (`fitness'), measured values over all possible combinations of a set of mutations yield…
When an advantageous mutation occurs in a population, the favorable allele may spread to the entire population in a short time, an event known as a selective sweep. As a result, when we sample $n$ individuals from a population and trace…
Causal analysis may be affected by selection bias, which is defined as the systematic exclusion of data from a certain subpopulation. Previous work in this area focused on the derivation of identifiability conditions. We propose instead a…