The CODEML program in the PAML package has been widely used to analyze protein-
coding gene sequences to estimate the synonymous and nonsynonymous rates (d S and d …

Comparative analyses of natural and mutated sequences have been used to probe
mechanisms of gene expression, but small sample sizes may produce biased outcomes. We …

Substitution models of evolution describe the process of genetic variation through fixed
mutations and constitute the basis of the evolutionary analysis at the molecular level. Almost …

Within plastid-bearing species, the mutation rate of the plastid genome is often assumed to
be greater than that of the mitochondrial genome. This assumption is based on early …

Highlights•Multifactorial study designs result in improved prediction power.•More focus
should be placed on directional targeting to cell compartments.•Previously neglected inside …

Positive selection is widely estimated from protein coding sequence alignments by the
nonsynonymous-to-synonymous ratio ω. Increasingly elaborate codon models are used in a …

The iconic mountains of the Pantepui biogeographical region host many early-diverging
endemic animal and plant lineages, concurring with Conan Doyle's novel about an ancient …

The genus Pipa is a species-poor clade of Neotropical frogs and one of the most bizarre-
looking due to many highly derived anatomical traits related to their fully aquatic lifestyle …

Background Eukaryotic genes typically form independent evolutionary lineages through
either speciation or gene duplication events. Generally, gene copies resulting from …

Why are humans susceptible to certain illnesses but not others? Diseases such as gout and
hypertension have plagued us for centuries. The prevalence of gout in the United States has …