Mutations drive evolution and thus knowing how often they occur is fundamental to studying biology. Several methods are available to estimate mutation rates, among which phylogenetic estimates are the most common. In essence, this method consists of counting the number of differences in the DNA sequences between two related species. An annual mutation rate is obtained by dividing the number of differences by the years since the two species split. This kind of estimation relies on several assumptions and uncertainties, which makes it difficult to later compare mutation rates among species. In contrast, direct estimations of mutation rates offer an apple-to-apple comparison between different species and rely on fewer assumptions.

 

Direct estimations of nuclear mutation rates are based on sequencing the entire nuclear genome of “trios”, i.e. a mother, her offspring, and the father. We can subsequently identify mutations in the offspring’s genome that are absent in both parents. Dividing the number of detected mutations by the size of the genome yields an estimate of the mutation rate across one single generation. The main difficulty in this approach is locating the trios. While this is straightforward in captive species with known families, it's an entirely different matter in most wild species. 

 

Baleen whales include the largest and longest-living mammals on Earth. The lower body’s energy use in these gigantic mammals was thought to lead to lower mutation rates relative to smaller mammals, such as humans, which, in turn, might be the reason for the lower incidence of cancer in baleen whales. They travel extensive distances, undertaking some of the longest seasonal migrations among mammals. The large annual ranges and the fact that they do not form family groups make it challenging to sample from complete trios.

 

We identified trios of whales solely using genetic analyses, used in human forensic and paternity testing. We first compared every female whale against all other individuals to see if the female could be the mother of a second whale. If that was the case, we then searched for a male that could be the father among all the males. Surprisingly, this worked very well and we managed to find many complete trios even though we had never observed the whales together in the field. We then selected a few complete trios and sequenced their genomes to estimate the mutation rate directly.

 

We also estimated the mutation rate for the mitochondrial DNA, which is a widely used genetic marker. Our mitochondria are inherited from our mother and contain their own genome. Although mitochondrial mutation rates are several hundred times higher than nuclear rates, the mitochondrial genome is 100,000 times smaller. This means that the chances of detecting a mutation between a single mother and her offspring are extremely low. 

 

We used a shortcut by analyzing individuals with two different mitochondrial genomes, called heteroplasmy. The mitochondria contain multiple, usually identical, mitochondrial genomes. When a new mutation occurs in one copy of the genome, the new mutation coexists with the “original” mitochondrial genome. Both versions are transmitted to the female’s offspring until one copy is lost. The frequency of heteroplasmy in a population and how quickly and often this turnover in the mitochondrial genome happens can be used to estimate the mutation rate in the mitochondrial genome.

 

In our study, we were very fortunate to have access to field observations and genetic data collected during the last four decades from which we could infer a large pedigree of humpback whales in which we found multi-generational maternal lineages, some with mitochondrial heteroplasmies. We used these to estimate the mitochondrial mutation rate. 

 

Our results were quite surprising as both the nuclear and the mitochondrial mutation rates in the gigantic baleen whales were very similar to other smaller-bodied mammals with similar generation times, such as large primates, orcas, and bottlenose dolphins. The similarities did not end there. Most mutations originated from the fathers, with more mutations from older fathers, which has been observed in humans as well. 

 

The estimate of the mitochondrial mutation rate was over ten times higher than the older phylogenetic estimates. This had a large impact on the results in earlier studies; for example, our estimate of the mutation rate suggests that the pre-whaling number of humpback whales in the North Atlantic was overestimated by ~85%.

 

In summary, this study showed that mutation rates can readily be estimated directly in wild populations with very limited prior knowledge thanks to the sustained long-term ecological research effort by our collaborators. Despite their massive sizes and long lives, we show that baleen whales have mutation rates similar to those of smaller animals. This finding has profound implications from cancer research to conservation, highlighting the need for these studies on wild species.