Multi-species and multi-tissue methylation clocks for age estimation in toothed whales and dolphins

• Published in: Communications biology Vol. 4; no. 1; p. 642
• Main Authors: Robeck, Todd R., Fei, Zhe, Lu, Ake T., Haghani, Amin, Jourdain, Eve, Zoller, Joseph A., Li, Caesar Z., Steinman, Karen J., DiRocco, Stacy, Schmitt, Todd, Osborn, Steve, Van Bonn, Bill, Katsumata, Etsuko, Mergl, June, Almunia, Javier, Rodriguez, Magdalena, Haulena, Martin, Dold, Christopher, Horvath, Steve
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 31.05.2021; Nature Publishing Group; Nature Portfolio
• Subjects: 45/43; 631/158/672; 631/208/176/1988; Age; Age determination; Age Factors; Aging; Aging - genetics; Aging - physiology; Animals; Biology; Biomedical and Life Sciences; Cetacea; CpG islands; Deoxyribonucleic acid; DNA; DNA - genetics; DNA fingerprinting; DNA methylation; DNA Methylation - genetics; Dolphins & porpoises; Dolphins - genetics; Dolphins - metabolism; Epigenesis, Genetic - genetics; Epigenetics; Epigenomics - methods; Genome; Genomes; Life Sciences; Odontoceti; Phylogeny; Skin; Species; Whales - genetics; Whales - metabolism; Wildlife conservation
• ISSN: 2399-3642; 2399-3642
• DOI: 10.1038/s42003-021-02179-x

The development of a precise blood or skin tissue DNA Epigenetic Aging Clock for Odontocete (OEAC) would solve current age estimation inaccuracies for wild odontocetes. Therefore, we determined genome-wide DNA methylation profiles using a custom array (HorvathMammalMethyl40) across skin and blood samples (n = 446) from known age animals representing nine odontocete species within 4 phylogenetic families to identify age associated CG dinucleotides (CpGs). The top CpGs were used to create a cross-validated OEAC clock which was highly correlated for individuals (r = 0.94) and for unique species (median r = 0.93). Finally, we applied the OEAC for estimating the age and sex of 22 wild Norwegian killer whales. DNA methylation patterns of age associated CpGs are highly conserved across odontocetes. These similarities allowed us to develop an odontocete epigenetic aging clock (OEAC) which can be used for species conservation efforts by provide a mechanism for estimating the age of free ranging odontocetes from either blood or skin samples. Todd Robeck and Zhe Fei et al. use DNA methylation profiling to develop an epigenetic clock to measure age in odontocete species, including toothed whales and dolphins. The clocks were highly accurate and represent a valuable tool to help in wildlife conservation efforts.