Low diversity and biased substitution patterns in the mitochondrial DNA control region of sperm whales: implications for estimates of time since common ancestry

The mitochondrial DNA (mtDNA) control region was sequenced in 37 spermwhales from a large part of the global range of the species. Nucleotidediversity was several-fold lower than that reported for control regions ofabundant and outbred mammals, but similar to that for populations known tohave experienced bottlenecks. Relative neck tests did not suggest that thelow diversity is due to a lower substitution rate in sperm whale mtDNA.Rather, it is more likely that demographic factors have reduced diversity.The pattern of nucleotide substitutions was examined by cladistic methods,facilitated by the apparent monophyly of lineages from the SouthernHemisphere, as defined by a single base pair deletion. Substitutions werenonrandom in nature, confined to a few "hot spots," and parallelsubstitutions constituted a majority of the inferred changes. Thesubstitution pattern fitted a negative binomial distribution better than aPoisson distribution, and the bias in number of substitutions among siteswas considerably higher than previously reported for the mtDNA controlregion of any species. A novel method of estimating time since commonancestry was developed, which utilizes the transition/transversion ratio Rand the number of substitutions inferred from a parsimony analysis. Usingthis method, we estimated the age of sperm whale mtDNA diversity to beabout 6,000-25,000 years, and when the uncertainty of R was accounted for,a range of about 1,000- 100,000 years was obtained.