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Mitochondrial structure despite nuclear panmixia: sex-specific dispersal dictates population structure in sperm whales

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Abstract

Marine mammals have high potential for dispersal, yet behavioral or environmental constraints can limit gene flow. This is true for the endangered sperm whale, Physeter macrocephalus, which has a global distribution and long-distance migrations. While previous studies revealed mitochondrial population structure with weak nuclear structure globally, genomic approaches examining this pattern have been limited. Understanding connectivity is critical for the management of this species due to population declines relative to pre-whaling numbers and increased recent anthropogenic stressors. We investigated connectivity between two regions, the U.S. Gulf of Mexico and the western North Atlantic Ocean, using reduced representation genomic and mitochondrial control region sequencing of 73 sperm whales. Relatedness decreased with geographic distance, likely due to the presence of social groups and familial structure. Nuclear markers showed no population structure (FST = 0.001–0.008), while mitochondrial structure was high (FST = 0.36–0.65), consistent with male-biased dispersal and female philopatry. Female-only analyses showed higher differentiation for mitochondrial but not nuclear markers; male-only analyses revealed no structure. Across all samples, genetic diversity (nuclear: 0.0014; mitochondrial: 0.0017) and effective population size (Ne = 460) were low. Given this low diversity and evidence for partitioning of genetic variation, we recommend managers treat these two regions as distinct to preserve existing variation and promote resilience of this species. These results illustrate that despite the increased power of a genomic approach, it is essential to consider the biology of the species at hand and leverage both mitochondrial and nuclear markers to understand the genetic structure of threatened species.

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Fig. 1: Collection sites for all samples.
Fig. 2: Pairwise relatedness between all individuals colored by the population origin of each individual.
Fig. 3: Nuclear panmixia across populations.
Fig. 4: Measures of genetic diversity for nuclear markers.
Fig. 5: mtDNA population structure across all individuals and subsets by sex.

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Data availability

Raw genomic data can be found on NCBI under bioproject PRJNA1189584. Code to run all analyses and metadata for samples, including NCBI accessions for mitochondrial data, can be found on Zenodo: https://doi.org/10.5281/zenodo.14715105.

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Acknowledgements

We thank Nicole Phillips for assistance with processing samples in the laboratory and Laura Dias, Jesse Wicker, and Wayne Hoggard for contributing to sample collection. Funding for sample collection was provided by the Bureau of Ocean Energy Management IA M09PG00014 and M11PG00041. This work made use of the Sedna high-performance computing cluster hosted at and administered within NOAA Fisheries, which has been funded by NOAA Fisheries' advanced technologies strategic initiatives. The scientific results and conclusions, as well as any views or opinions expressed herein, are those of the author(s) and do not necessarily reflect those of NOAA or the Department of Commerce.

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Authors and Affiliations

  1. Marine Mammal and Turtle Division, Southeast Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Miami, FL, USA

    Reid S. Brennan, Anthony Martinez & Lance P. Garrison

  2. Marine Mammal and Turtle Division, Southeast Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Lafayette, LA, USA

    Lynsey A. Wilcox Talbot, Nicole L. Vollmer & Patricia E. Rosel

  3. HDR, 701 Independence Circle, Virginia Beach, VA, USA

    Dan Engelhaupt

  4. Cooperative Institute for Marine and Atmospheric Studies, Rosenstiel School for Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL, USA

    Nicole L. Vollmer

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RSB conducted the analysis, made figures, and wrote the manuscript. LAWT conducted lab work and analyzed the mitochondrial data, while LAWT, NLV, and PER conceptualized the project and helped to interpret results. AM, LPG, and DE collected samples. All authors helped to revise the manuscript.

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Correspondence to Reid S. Brennan.

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The authors declare no competing interests.

Research ethics statement

This research was carried out, in part, under the auspices of the Cooperative Institute for Marine and Atmospheric Studies (CIMAS), a Cooperative Institute of the University of Miami and the National Oceanic and Atmospheric Administration, cooperative agreement #NA20OAR4320472. Biopsy sampling was conducted under NMFS MMPA permits 738, 779-1339, 779-1633, and 14450.

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Brennan, R.S., Wilcox Talbot, L.A., Martinez, A. et al. Mitochondrial structure despite nuclear panmixia: sex-specific dispersal dictates population structure in sperm whales. Heredity (2026). https://doi.org/10.1038/s41437-026-00824-x

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