Related papers: Footprints of ancient balanced polymorphisms in ge…
In evolution, the effects of a single deleterious mutation can sometimes be compensated for by a second mutation which recovers the original phenotype. Such epistatic interactions have implications for the structure of genome space -…
The shape of allele-frequency clines maintained by migration-selection balance depends not only on the properties of migration and selection, but also on the dominance relations among alleles and on linkage to other loci under selection. We…
A probability model is presented for the dynamics of mutation-selection balance in a haploid infinite-population infinite-sites setting sufficiently general to cover mutation-driven changes in full age-specific demographic schedules. The…
Polyploidization is an evolutionary process by which a species acquires multiple copies of its complete set of chromosomes. The reticulate nature of the signal left behind by it means that phylogenetic networks offer themselves as a…
We consider two versions of stochastic population models with mutation and selection. The first approach relies on a multitype branching process; here, individuals reproduce and change type (i.e., mutate) independently of each other,…
For a genetic locus carrying a strongly beneficial allele which has just fixed in a large population, we study the ancestry at a linked neutral locus. During this ``selective sweep'' the linkage between the two loci is broken up by…
Comparative analyses of phylogenetic trees typically require identical taxon sets, however, in practice, trees often include distinct but overlapping taxa. Pruning non-shared leaves discards phylogenetic signal, whereas tree completion can…
During the course of evolution, an organism's genome can undergo changes that affect the large-scale structure of the genome. These changes include gene gain, loss, duplication, chromosome fusion, fission, and rearrangement. When gene gain…
We study a continuous-time dynamical system that models the evolving distribution of genotypes in an infinite population where genomes may have infinitely many or even a continuum of loci, mutations accumulate along lineages without…
Identifying undocumented or potential future interactions among species is a challenge facing modern ecologists. Recent link prediction methods rely on trait data, however large species interaction databases are typically sparse and…
The deterministic selection-recombination equation describes the evolution of the genetic type composition of a population under selection and recombination in a law of large numbers regime. So far, an explicit solution has seemed out of…
This article evaluates bias in one class of methods used to estimate archaic admixture in modern humans. These methods study the pattern of allele sharing among modern and archaic genomes. They are sensitive to "ghost" admixture, which…
The problem of intermediates in the fossil record has been frequently discussed ever since Darwin. The extent of `gaps' (missing transitional stages) has been used to argue against gradual evolution from a common ancestor. Traditionally,…
When organisms adapt to spatially heterogeneous environments, selection may drive divergence at multiple genes. If populations under divergent selection also exchange migrants, we expect genetic differentiation to be high at selected loci,…
Weak purifying selection, acting on many linked mutations, may play a major role in shaping patterns of molecular evolution in natural populations. Yet efforts to infer these effects from DNA sequence data are limited by our incomplete…
Natural selection acts on traits at different scales, often with opposing consequences. This article identifies the particular forces that act at each scale and how those forces combine to determine the overall evolutionary outcome. A…
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…
The statistical estimation of phylogenies is always associated with uncertainty, and accommodating this uncertainty is an important component of modern phylogenetic comparative analysis. The birth-death polytomy resolver is a method of…
Following genetic ancestry in eukaryote populations poses several open problems due to sexual reproduction and recombination. The history of extant genetic material is usually modeled backwards in time, but tracking chromosomes at a large…
Biochemical and regulatory interactions central to biological networks are expected to cause extensive genetic interactions or epistasis affecting the heritability of complex traits and the distribution of genotypes in populations. However,…