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

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Abstract
The mitochondrial DNA (mtDNA) control region was sequenced in 37 sperm whales from a large part of the global range of the species. Nucleotide diversity was several-fold lower than that reported for control regions of abundant and outbred mammals, but similar to that for populations known to have experienced bottlenecks. Relative neck tests did not suggest that the low 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 Southern Hemisphere, as defined by a single base pair deletion. Substitutions were nonrandom in nature, confined to a few "hot spots," and parallel substitutions constituted a majority of the inferred changes. The substitution pattern fitted a negative binomial distribution better than a Poisson distribution, and the bias in number of substitutions among sites was considerably higher than previously reported for the mtDNA control region of any species. A novel method of estimating time since common ancestry was developed, which utilizes the transition/transversion ratio R and the number of substitutions inferred from a parsimony analysis. Using this method, we estimated the age of sperm whale mtDNA diversity to be about 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.

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