On the causes of evolutionary transition:transversion bias

Arlin Stoltzfus; Ryan W. Norris

In many early works, this bias is presented as a ratio of differences, which makes the expected ratio a complex function of the degree of sequence divergence. As the use of rate models became routine in comparative sequence analysis, the phenomenon of transition bias was redefined as a bias in instantaneous rates, relative to a null model of equal rates. Because every nucleotide site (e.g., a G site) may experience 1 type of transition (G A) at rate α, and 2 types of transversion (G C, G T) at rate β, the aggregate rate ratio of transitions to transversions has a null expectation of R = α/(2β) = 0.5. In some contexts, the ratio is expressed differently as κ = α/β = 1. When considering amino acid changes, it is more relevant to compare the 116 possible transitions and 276 possible transversions that change a codon so as to encode a different amino acid (assuming the canonical genetic code), leading to a null expectation of R = 116 α / (276 β) = 0.42 α/β. Thus, the observation of roughly equal 4 indicates a bias of over 2-fold. Kumar (1996) estimates 2-fold to 5-fold rate biases in vertebrate mitochondrial genes (excluding 3 rd positions). Other estimates may be found in work cited by Rosenberg, et al. (2003) , but there is not (to our knowledge) a systematic contemporary review of this issue.