Effect of the assignment of ancestral CpG state on the estimation of nucleotide substitution rates in mammals.

ABSTRACT:

Background

Molecular evolutionary studies in mammals often estimate nucleotide substitution rates within and outside CpG dinucleotides separately. Frequently, in alignments of two sequences, the division of sites into CpG and non-CpG classes is based simply on the presence or absence of a CpG dinucleotide in either sequence, a procedure that we refer to as CpG/non-CpG assignment. Although it likely that this procedure is biased, it is generally assumed that the bias is negligible if species are very closely related.

Results

Using simulations of DNA sequence evolution we show that assignment of the ancestral CpG state based on the simple presence/absence of the CpG dinucleotide can seriously bias estimates of the substitution rate, because many true non-CpG changes are misass

SUBMITTER: Gaffney DJ 

PROVIDER: S-EPMC2576242 | biostudies-literature | 2008 Sep

REPOSITORIES: biostudies-literature