Wild μ: Mutation rate estimates, challenges and applications

Mutations are the engine of evolution, making mutation rate (μ) estimates essential for understanding evolutionary processes and a key parameter in population genetics. Most μ estimates are inferred from the number of observed changes among homologous DNA sequences in phylogenies with known divergence times. However, this approach presents several sources of error and uncertainties. Direct μ estimates, while presenting fewer uncertainties, require extensive pedigree data and have been applied largely to model or captive species, relegating wild organisms to phylogenetic estimations.

Baleen whales encompass the largest and longest-living mammals making them ideal subjects for μ research. However, their ocean-wide distributions and large migrations pose challenges for data collection. From heteroplasmy discovery to genetic-based parentage inference, this thesis developed and tested bioinformatic and molecular tools to obtain the necessary data to perform direct estimates of nuclear and mitochondrial μ in several baleen whale species. The resulting μ estimates were employed to challenge previous debates centred around phylogenetic μ estimates, from explaining low cancer rates in whales to the calculation of pre-whaling population abundances. For wild organisms with non-standard life cycles, such as diatoms, the challenges are far greater with μ estimates often completely lacking despite their crucial ecological roles. This thesis explored the potential estimation of μ and its application in diatom’s demographic history inferences, highlighting the importance of further research in this underexplored field.

Overall, this PhD thesis showed the feasibility of directly estimating μ in wild and difficult-to-study species and the wide-ranging impacts on ecological and evolutionary research.