Gray whale spyhopping | Sam Beebe
A new Frontiers in Marine Science publication presents high-quality reference genomes for 18 cetacean species across eight of the 14 whale, dolphin, and porpoise families. This work, led by Dr. Phillip Morin at NOAA’s Southwest Fisheries Science Center, was launched in 2020 with funding from NOAA and Revive & Restore. At the time, only 3 high-quality cetacean genomes were available. Since then, Dr. Morin and his colleagues have formed the Cetacean Genomes Project (CGP), which now coordinates resources and generates reference-quality genomes for cetacean species, and sparked widespread enthusiasm to support cetacean genome initiatives and research.
The 18 “platinum-standard” genomes presented in the publication meet Vertebrate Genomes Project quality standards and provide unprecedented resolution compared to earlier draft assemblies. They also reveal important biological insights that directly inform conservation efforts. For example, the authors found that cetaceans have remarkably conserved chromosome organization, with most species maintaining 22 ancestral chromosome groups largely intact over millions of years of evolution. By comparing these high-quality genomes to previous draft assemblies, the team showed dramatic improvements in capturing repetitive DNA sequences and complex gene regions. For example, the new assemblies contain 7.5% more repetitive elements on average, revealing recent bursts of transposable element activity that were invisible in earlier genome versions.
The genomic analyses revealed warnings for the genetic health of some endangered species (Fig. 1). The critically endangered vaquita (Phocoena sinus) and Rice’s whale (Balaenoptera ricei) showed extensive runs of homozygosity (genomic regions with reduced genetic diversity), indicating severe population bottlenecks. Rice’s whale displayed an unusual pattern of alternating high and low genetic diversity across its genome, possibly reflecting past hybridization events. Historical demographic reconstructions using these genomes revealed that many cetacean species experienced population declines coinciding with past climate changes, particularly around the last glacial maximum. This provides crucial context for understanding current population vulnerabilities.
Figure 1: Genome-wide heterozygosity (variants/bp) in cetaceans based on non-overlapping 1Mb windows, from reads mapped to the reference genome followed by removal of repeats. **Reference genome species. IUCN Red List status as of April 2023. Courtesy of Morin et al., 2025.
The study also examined immune system genes (Major Histocompatibility Complex), finding that high-quality genomes revealed significantly more immune gene copies than draft assemblies detected. This is critical for conservation because immune gene diversity directly affects disease resistance in wild populations.
These reference genomes create essential infrastructure for modern conservation genetics. They enable more accurate assessment of genetic health in wild populations, better detection of hybridization between species, and improved understanding of adaptive potential in the face of environmental change. Additionally, the genomes facilitate population monitoring through improved genetic markers and provide baselines for detecting genetic changes over time. Perhaps most importantly, these resources enable conservationists to move beyond simple measures of genetic diversity to more sophisticated assessments of extinction risk, recovery potential, and adaptive capacity, all crucial for prioritizing limited conservation resources in our rapidly changing oceans.
Revive & Restore is proud to have funded the creation of five of the reference genomes presented in this publication, including the gray whale, North Atlantic right whale, pygmy sperm whale, Blainville’s beaked whale, and false killer whale. With this publication, Dr. Morin and his colleagues have demonstrated precisely why high-quality reference genomes are invaluable in enhancing conservation efforts for endangered species.
