Estimating the proportion of adaptive substitutions (α) is of primary importance to uncover
the determinants of adaptation in comparative genomic studies. Several methods have been …

The evolution of molecular quantitative traits, such as codon usage bias or base
frequencies, can be explained as the result of mutational biases alone, or as the result of …

The redundancy in the genetic code means that apart from methionine and tryptophan, an
amino acid is encoded by at least two codons. Different codons for the same amino acid are …

In our previous study, we described sequence assembly and organization of the complete
mitochondrial genome of a threatened labeonine fish, Cirrhinus reba (GenBank accession …

A stringent branch-site codon model was used to detect positive selection in vertebrate
evolution. We show that the test is robust to the large evolutionary distances involved …

Protein coding genes can contain specific motifs within their nucleotide sequence that
function as a signal for various biological pathways. The presence of such sequence motifs …

Aditama R, Tanjung ZA, Sudania WM, Nugroho YA, Utomo C, Liwang T. 2020. Analysis of
codon usage bias reveals optimal codons in Elaeis guineensis. Biodiversitas 21: 5331 …

Codon usage bias (CUB), where certain codons are used more frequently than expected by
chance, is a ubiquitous phenomenon and occurs across the tree of life. The dominant …

The recent increase in genomic data is revealing an unexpected perspective of gene loss as
a pervasive source of genetic variation that can cause adaptive phenotypic diversity. This …

Patterns of synonymous codon usage are determined by the forces of mutation, selection
and drift. We elaborate on previous population genetic models of codon usage to …