ARTICLE Using pre- and postexploitation samples to assess the impact of commercial whaling on the genetic characteristics of eastern North Pacific gray and humpback whales and to compare methods used to infer historic demography Stephanie L. Béland 1 | Brenna A. Frasier 1 | James D. Darling 2 | Timothy R. Frasier 1 1 Department of Biology, Saint Mary's University, Halifax, Nova Scotia, Canada 2 Director, Pacific Wildlife Foundation, Vancouver, British Columbia, Canada Correspondence Timothy R. Frasier, Department of Biology, Saint Mary's University, 923 Robie Street, Halifax, Nova Scotia B3H 3C3, Canada. Email: timothy.frasier@smu.ca Funding information Clayoquot Biosphere Trust; Jamie's Whaling Station; Remote Passages Marine Excursions; Saint Mary's University Faculty of Graduate Studies and Research Abstract Many species of whales went through recent bottlenecks due to commercial whaling. These declines were rapid and recent relative to the life spans and generation times of these species, raising questions regarding to what degree commercial whaling influenced the genetic characteristics of these populations. We analyzed mitochondrial and nuclear DNA from pre- and postwhaling samples from two populations that have arguably shown the greatest degree of recovery: eastern North Pacific gray and humpback whales. We also compare the performance of different methods to test for historic bottlenecks and infer past demography based on genetic data. We found substantially higher levels of genetic diversity in gray than in humpback whales (for both time periods), likely due to recent connec- tivity between Atlantic and Pacific gray whale populations. Other than mitochondrial diversity in humpback whales, levels of diversity were not lower in contemporary samples relative to prewhaling samples, indicating that commercial whaling had a minimal impact on metrics of genetic diver- sity themselves. However, it did have large impacts on the patterns of diversity, as evidenced by all coalescent-based methods showing clear evidence of a bottleneck for both Received: 25 July 2018 Revised: 27 June 2019 Accepted: 7 September 2019 DOI: 10.1111/mms.12652 Mar Mam Sci. 2019;1–23. wileyonlinelibrary.com/journal/mms © 2019 Society for Marine Mammalogy 1