Furthermore, evolutionary interpretations have been hampered in both organisms by low DNA sequence diversity of a small number of selected loci.
Thus, the primordial functional evolution of proteins may have proceeded from a population with only a small degree of sequence diversity.
Previous efforts to characterize germ cell promoters have emphasized their relatively small size and sequence diversity and have identified many site-specific transcription factors possibly involved in their regulation.
One of the most remarkable findings of these studies is that relatively small degrees of sequence diversity, e.g., 10 different random sequence for esterase activity, are sufficient to allow Darwinian selection of random polypeptides composed of about 140 amino acid residues [17].
These findings are compatible with previous findings with subtype B that sequence diversity is smaller among R5 virus V3s [26] [28].
We also used haplotype frequencies to measure differentiation, which has been shown to be more reliable than sequence diversity for smaller sample sizes [25] but results for both statistics were similar for antigens with smaller sample sizes (lsa1, glurp, pfs48/45).
On the other hand, sequencing of mixtures of two SIV strains with known nucleotide differences showed that the effects of apparent artifacts on the overall pattern of sequence diversity were small compared with that of known differences.
The limited functional diversity of the smallest sequence neighborhoods we examine likely results from this sparsity.
Recent culture-independent molecular biologic approaches based on the sequence diversity of the small subunit rRNA (16S rRNA and18S rRNA) gene have overcome these limitations.
The reason that we used more stringent parameters for the analysis of 16S sequences is that the SILVA database covers a wider range of sequence diversity [ 18], is smaller and better curated than NCBI-NR, and thus it is easier to obtain high-scored alignments.
