In this study, we investigate natural selection in a pine phylogeny. DNA sequences from 18
nuclear genes were used to construct a very well-supported species tree including 10 pine …

Background The introduction of DNA-based molecular markers made a revolution in
biological systematics. However, in cases of very recent divergence events, the neutral …

Phylogenetic analyses can also enable insight into evolutionary and ecological dynamics
such as selection pressure and frequency dependent selection in digital evolution systems …

Abstract The Ontology for Avida (OntoAvida) aims to develop an integrated vocabulary for
the description of Avida, the most widely used computational approach for performing …

The inference of population dynamics from molecular sequence data is becoming an
important new method for the surveillance of infectious diseases. Here, we examine how …

Digital evolution is a branch of artificial life in which self-replicating computer programs—
digital organisms—mutate and evolve within a user-defined computational environment. In …

Nucleotide substitution models used in molecular phylogenetics do not account for
nucleotide sequences evolving under selection, yet selection is rarely tested for. If non …

Over the past 30 years, digital evolution research has established itself as a valuable
technique in biology, bridging experimental research with computational modeling (Ray …

Results from the artificial life community show that under some conditions evolving
populations converge on broader, but less fit peaks in the fitness landscape and avoid more …

Background Avida is a computer program that performs evolution experiments with digital
organisms. Previous work has used the program to study the evolutionary origin of complex …