Infections are one of the major selective pressures acting on humans, and host-pathogen
interactions contribute to shaping the genetic diversity of both organisms. Evolutionary …

Over the past two decades, comparative sequence analysis using codon-substitution
models has been honed into a powerful and popular approach for detecting signatures of …

We present BUSTED, a new approach to identifying gene-wide evidence of episodic
positive selection, where the non-synonymous substitution rate is transiently greater than the …

Background Photolyases and cryptochromes are evolutionarily related flavoproteins, which
however perform distinct physiological functions. Photolyases (PHR) are evolutionarily …

Background Hypoxia-inducible factor (HIF) is a master regulator that mediates major
changes in gene expression under hypoxic conditions. Though HIF family has been …

A major current molecular evolution challenge is to link comparative genomic patterns to
species' biology and ecology. Breeding systems are pivotal because they affect many …

Investigating the history of natural selection among closely related species can elucidate
how genomes diverge in response to disparate environmental pressures. Molecular …

Genes underlying signal reception should evolve to maximize signal detection in a particular
environment. In animals, opsins, the protein component of visual pigments, are predicted to …

Background The primary energy-producing pathway in eukaryotic cells, the oxidative
phosphorylation (OXPHOS) system, comprises proteins encoded by both mitochondrial and …

Amino acid preferences vary across sites and time. While variation across sites is widely
accepted, the extent and frequency of temporal shifts are contentious. Our understanding of …