Despite their name, synonymous mutations have significant consequences for cellular
processes in all taxa. As a result, an understanding of codon bias is central to fields as …

In a wide variety of organisms, synonymous codons are used with different frequencies, a
phenomenon known as codon bias. Population genetic studies have shown that …

Comparative analysis of multiple genomes in a phylogenetic framework dramatically
improves the precision and sensitivity of evolutionary inference, producing more robust …

The vast amount of data generated by genome projects and the recent development of
population genetics models make comparative sequence analyses a very powerful …

It has been hypothesized that individually-rare hidden structural variants (SVs) could
account for a significant fraction of variation in complex traits. Here we identified more than …

Charles Darwin proposed that evolution occurs primarily by natural selection, but this view
has been controversial from the beginning. Two of the major opposing views have been …

The three species of the Drosophila simulans clade—the cosmopolitan species, D.
simulans, and the two island endemic species, D. mauritiana and D. sechellia—are …

Codon usage bias of 1,117 Drosophila melanogaster genes, as well as fewer D.
pseudoobscura and D. virilis genes, was examined from the perspective of relative …

Short insertions and deletions (indels) are the second most abundant form of human genetic
variation, but our understanding of their origins and functional effects lags behind that of …

Natural selection and demographic forces can have similar effects on patterns of DNA
polymorphism. Therefore, to infer selection from samples of DNA sequences, one must …