However, there has been recent concern over high rates of false inference of positive selection with LRTs, particularly when applied to relatively small alignments with little sequence divergence [ 14- 17].
Conversely, nucleotide diversity values calculated for species within each clade were relatively small, implying that homogenizing forces diminished sequence divergence locally within each separate cluster of 5S rDNA variants in each species.
Among these methods, REL is the most powerful for detecting sites under selection particularly when dealing with small sample size of sequences or low sequence divergence.
The error rate is relatively low, but errors are more common at interspecies SNP sites than elsewhere, and the error rate increases sharply with the small added sequence divergence from chimpanzee to gorilla.
Despite a small mean sequence divergence of 1.53% between the sister species, 25.1% of 18,115 observed amino acid substitutions were inferred by α statistics to be driven by positive selection.
In some cases, novel function may come about with only a small level of sequence divergence of the protein coding region.
Although caution must still be exercised in PCR-based studies, the small size and sequence divergence of these chicken pesudogenes from mitochondrial copies indicates that they may be less of a concern in mtDNA-based studies of birds relative to primates and plants.
We identified 184 human gene duplicate pairs belonging to small gene families (≤5 members) with low synonymous sequence divergence of 10%% or less (K S ≤ 0.1) (Additional file 1: Table S1).
In many comparative studies of chloroplast protein coding genes, the distance value for rps7 gene sequence was mainly small indicating low levels of sequence divergence [ 88, 89].
The genomes are mosaics of large regions identical to S288c interspersed with small regions of high sequence divergence (Fig. 1).
Even small regions of clustered sequence divergence (with multiple substitutions or indels) can dramatically reduce the rate of gene conversion for a region of a gene [ 34, 35].
