Abstract paml, currently in version 4, is a package of programs for phylogenetic analyses of
DNA and protein sequences using maximum likelihood (ML). The programs may be used to …

The rate and mechanism of protein sequence evolution have been central questions in
evolutionary biology since the 1960s. Although the rate of protein sequence evolution …

Phylogenetic species recognition and species concepts in fungi. Fungal Genetics and
Biology 31, 000–000. The operational species concept, ie, the one used to recognize …

Approximate methods for estimating the numbers of synonymous and nonsynonymous
substitutions between two DNA sequences involve three steps: counting of synonymous and …

The unit of adaptation is usually thought to be a gene or set of interacting genes, rather than
the whole genome, and this may be true of species differentiation. Defining species on the …

Several codon-based models for the evolution of protein-coding DNA sequences are
developed that account for varying selection intensity among amino acid sites. The “neutral …

The field of molecular evolution has experienced explosive growth in recent years due to the
rapid accumulation of genetic sequence data, continuous improvements to computer …

Many genes that mediate sexual reproduction, such as those involved in gamete
recognition, diverge rapidly, often as a result of adaptive evolution. This widespread …

It is only in the past five years that studies of speciation have truly entered the molecular era.
Recent molecular analyses of a handful of genes that are involved in maintaining …

▪ Abstract Molecular clocks have profoundly influenced modern views on the timing of
important events in evolutionary history. We review recent advances in estimating …