This Wild Genomes project sequenced five whale species that represent evolutionary diversity across the cetacean phylogeny. In building publicly available reference genomes, this project provides genomic resources for population-level studies and help to reveal taxonomy, demographic history, inbreeding, local adaptation, and potential responses to climate change.
Cetaceans are a unique branch of marine mammals that includes whales, dolphins, and porpoises. For centuries, humans have directly impacted cetaceans through targeted hunting, fisheries bycatch, and habitat degradation.
These animals are particularly challenging to study due to their aquatic habitats and broad distributions, rendering traditional monitoring methods used for terrestrial species impossible. As such, genetics and genomic studies provide critical, otherwise inaccessible insights into their evolutionary and demographic histories, population structure, and health.
Out of 94 recognized cetacean species, only 3 high-quality reference genomes were available as of 2020. This project, led by PIs Phillip Morin (NOAA), Erich Jarvis (Rockefeller University), and Oliver Ryder (San Diego Zoo Wildlife Alliance), generated reference-level genome assemblies for 5 additional species from across the cetacean family tree, with the goal of improving infrastructure for cetacean genomics research and conservation.
With funding from Revive & Restore and NOAA, the team succeeded in sequencing and assembling reference-quality genomes for 5 species of highest conservation concern
- Gray whale (Eschrichtius robustus)—IUCN Endangered
- False killer whale (Pseudorca crassidens)—IUCN Near Threatened
- Blainville’s beaked whale (Mesoplodon densirostris)—IUCN data deficient
- North Atlantic right whale (Eubalaena glacialis)—IUCN and ESA Endangered
- Pygmy sperm whale (Kogia breviceps)—IUCN Least Concern
Principal Investigator: Phillip Morin (NOAA)
Co-PIs: Erich Jarvis (Rockefeller University) and Oliver Ryder (San Diego Zoo Wildlife Alliance)
The gray whale sampled for genome sequencing in this project, including the crossbow dart as it hits the whale. The dart takes a small (~1cm) skin biopsy and bounces off the whale, then floats on the surface to be picked up by the biopsier.
Photo: Cene Bryant, biopsy taken by Jeff Jacobsen, under SWFSC Marine Mammal Permit #14097
The team chose these species based on several criteria:
First, they needed ultra-high-quality tissue available for sequencing the genome and RNA for annotation. This is a surprisingly difficult criterion to meet, because they don’t have the option to obtain sufficient tissues on request. They have to rely on samples obtained from freshly dead animals that were necropsied within 24 hours of death and appropriately stored, or skin biopsies from live animals that were collected specifically for cell culture. Second, species were chosen to represent 5 of the 14 families in the suborder cetacea, to try to maximize the representation of cetacean species. Third, the team tried to select species that were of the highest conservation concern, for faster potential application of the genomic data and related studies to conservation management.
PI Phil Morin reflected: “I’ve been amazed at the number of different research projects that have been proposed or started already based on these and other cetacean genomes that have been completed since we initiated this project.”
As a direct result of the team’s efforts to identify appropriate cetacean samples for sequencing, they developed collaborations to provide samples and sequence 8 additional species representing 7 different genera and 1 additional family. All of these are publicly available through the US NCBI and European Nucleotide Archive (ENA) databases, and most have been annotated. This team is continuing to develop additional resources with several more species genomes currently in process.
The Cetacean Genomes Project has become an affiliated project with the Earth Biogenomes Project.
A North Atlantic right whale and its calf. Credit: Clearwater Marine Aquarium Research Institute, taken under NOAA permit #20556-01
Fibroblasts from the gray whale sample used to generate the reference genome for this species. The sample was collected in 2016 near Crescent City, CA, and cells were cultured by Susanne Meyer at UCSB.
Photo: Susanne Meyer, UCSB
These reference genomes are already being leveraged for a range of research projects, including:
- Comparative analyses on cetacean genome organization, patterns of genome-wide heterozygosity, and historical demography
- Population genomics of the critically endangered Rice’s whale (mutational load, demographic history, and inbreeding)
- Genetic marker development for population structure analysis of false killer whales and beaked whales impacted by Naval Sonar
- Evolution of gene families of interest for conservation (e.g. globin genes and MHC gene families), adaptation to the aquatic environment, and other life-history characteristics of cetaceans (e.g. reproductive age, lifespan)
- Evolution of cetacean genome structure
- Detection of genes involved in speciation and divergent evolution.
According to Morin, these reference genomes are being used “as the backbone for phylogenetic, population and comparative genomics studies, enabling increasingly sophisticated (and more robust) applications in evolutionary and conservation genetics.”
A biopsy dart just after it hit the side of a false killer whale from the endangered main Hawaiian Islands population, taking a small skin plug. Credit: Robin Baird, taken under NMFS Permit #26596
Revive & Restore is honored to have supported this project, and we look forward to hearing about how these new genomic resources continue to enable conservation actions and management decisions. Special thanks to the partners that fund Wild Genomes:
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