Genomic histories shaped by whaling and 16,000 years of isolation

The reproducing population of the Eastern North Pacific fin whale population was reduced 99% during the 20th-century whaling period, whereas the Gulf of California population remained small and isolated for 16,000 years. This contrasting histories have affected the genomes of both populations.
Published in Ecology & Evolution
Genomic histories shaped by whaling and 16,000 years of isolation

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The 19th and 20th Century whaling had a severe impact on most baleen whale species, with several of them coming close to extinction. Among them, fin whales (Balaenoptera physalus) were perhaps the most affected. It has been reported that in the North Pacific alone, industrial whaling operations caught almost 76,000 (Rocha et al. 2016), which would represent a 60% - 70% population reduction (Allen 1977). However, the actual number of killed fin whales may have been higher because, in the early days of whaling, between 30% to 50% of the killed whales were lost at sea (IWC 2017). Additionally, whales are known for their long migrations between feeding and breeding grounds, but there is a fin whale population that seems to break this pattern. This group of fin whales spends the whole year in the Gulf of California (or Sea of Cortés) in Mexico, it consists of only 300 to 600 individuals (Jiménez et al. 2019) and was not affected by whaling. It seems that the Gulf's highly productive waters provide them with the necessary resources for their survival, making it unnecessary for them to migrate out into the Eastern North Pacific. Surprisingly, even though the populations of fin whales in the Gulf and the Pacific are only 200 to 400 kilometers apart, individuals from the Pacific also rarely enter the Gulf. This is surprising, considering that the fin whale is the second-largest animal on the planet and that smaller whale species make larger migrations.

Satellite image of the Gulf of California

In our study, we aimed to sequence whole genomes of fin whales together with simulation analyses to assess the effects of whaling and isolation on the genetic diversity of the Eastern North Pacific and Gulf of California populations. Additionally, we explored the conservation implications of our findings and propose actions to improve the conservation of both populations.

To achieve our goals, we implemented a collaborative effort. Dr. Eric Archer at the Southwest Fisheries Science Center (SWFSC-NOAA) provided 30 fin whale DNA samples from Eastern North Pacific (from Alaska to California) and Dr. Jorge Urban from Universidad Autónoma de Baja California Sur in Mexico, contributed 20 samples from the Gulf of California population. Interestingly, I collected some of these Gulf samples and extracted their DNA during my internship at Dr. Urban's laboratory while I was an undergraduate student. Little did I know that years later I would analyze the whole genome of those samples. This project holds a special significance for me personally, as it represents the journey of my academic career - from collecting samples in the field to extracting their DNA in the laboratory, and ultimately analyzing whole genomes using bioinformatic tools. Very few people can claim to have studied the genomes of the second largest animal on our planet after having interacted with them up close in the field, and I am grateful to be one of those few fortunate individuals.

Fin whale in the Gulf of California

We found that the effective size (individuals that actually reproduce in a population) of the Eastern North Pacific population expanded during the last interglacial period (95,000 years ago), from approximately 16,000 to 24,000. Then, about 52 to 26 years ago the population dramatically decreased to around 300 effective individuals. Since the average year of collection for the Eastern North Pacific samples was 2006 (1999 – 2017), this drastic reduction corresponds to a period between the years 1954 and 1980, which is the period in which the fin whale population was at its lowest numbers due to whaling activities (Rocha et al. 2014; Mizroch et al. 2009). Therefore, this result shows the magnitude of the impact that whaling had on the effective size of the Eastern North Pacific population.

Despite the severe reduction in effective population size, our study reveals that the Eastern North Pacific population has managed to retain most of its genetic diversity, and there is no evidence of accumulation of damaging genetic variants that could reduce its fitness. This is mainly due to the fact that the population reduction is very recent and has only lasted for two or three generations. Our computer simulations show that if the population remains small for 20 generations, then we will observe a reduction in genetic diversity. Therefore, it is crucial to maintain the whaling moratorium that was implemented in 1985 to allow the population to continue recovering.

We discovered that the Gulf of California population separated from the Eastern North Pacific population around 16,000 years ago during the Last Glacial Maximum. Since then, the Gulf population has had a small effective size, with an average of only 114 individuals. Moreover, the Gulf population has also been mostly isolated, with only 0.36 individuals migrating from the Eastern North Pacific population to the Gulf and being able to reproduce. Therefore, it could be said that this occurs once every 75 years. This isolation has resulted in a loss of genetic diversity in the Gulf of California population and an increase in inbreeding. However, this inbreeding is not recent but is historical, probably due to the isolation of the population for thousands of years. Our computer simulations, combined with empirical analysis, suggest that this small population size, limited migration, and historical inbreeding have likely led to the accumulation of weakly damaging genetic variants in the Gulf population. However, these factors have also allowed it to eliminate or purge strongly damaging variants. Hence, it is possible that the overall health of the population has not deteriorated significantly yet.

Fin whale traveling in the Gulf of California

Finally, our simulation analyses show that the migration into the Gulf, even if limited, has aided the population in maintaining some level of genetic diversity and has prevented further accumulation of harmful genetic variations. This result demonstrates that it is crucial to maintain the existing limited migration between the Eastern North Pacific and Gulf of California fin whales to ensure the long-term survival of the Gulf population.

We believe that our study demonstrates how genomic research can be utilized to guide conservation and management efforts for fin whale populations, as well as marine mammals in general. For instance, it may help reassess the recovery objectives for the Eastern North Pacific population and reevaluate the endangered status of the Gulf of California population.


Allen, K. R. 1977. Updated estimates of fin whale stocks. Reports of the International Whaling Commission 27: 221.

International Whaling Commission. 2017. Report of the Sub-Committee on the Revised Management Procedure. Journal of Cetacean Research and Management 18(Suppl.): 123-173.

Jiménez, M. E. L., Palacios, D.M., Legorreta, A. J., Urbán, J. R. & Mate, B. R. 2019. Fin whale movements in the Gulf of California, Mexico, from satellite telemetry. PLoS ONE, 14:e0209324.

Mizroch, S. A., Rice, D. W., Zwiefelhofer, D., Waite, J. & Perryman, W. L. 2009. Distribution and movements of fin whales in the North Pacific Ocean. Mammal Review 39:193–227.

Rocha, R. C., Clapham, P. J. & Ivashchenko, Y. V. 2014. Emptying the oceans: a summary of industrial whaling catches in the 20th century. Marine Fisheries Review, 76:37–48.



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