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

Todd R Robeck; Zhe Fei; Ake T Lu; Amin Haghani; Eve Jourdain; Joseph A Zoller; Caesar Z Li; Karen J Steinman; Stacy DiRocco; Todd Schmitt; Steve Osborn; Bill Van Bonn; Etsuko Katsumata; June Mergl; Javier Almunia; Magdalena Rodriguez; Martin Haulena; Christopher Dold; Steve Horvath

doi:10.1038/s42003-021-02179-x

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

Commun Biol. 2021 May 31;4(1):642. doi: 10.1038/s42003-021-02179-x.

Authors

Todd R Robeck^#¹, Zhe Fei^#², Ake T Lu³, Amin Haghani³, Eve Jourdain⁴, Joseph A Zoller², Caesar Z Li², Karen J Steinman⁵, Stacy DiRocco⁶, Todd Schmitt⁷, Steve Osborn⁸, Bill Van Bonn⁹, Etsuko Katsumata¹⁰, June Mergl¹¹, Javier Almunia¹², Magdalena Rodriguez¹³, Martin Haulena¹⁴, Christopher Dold¹⁵, Steve Horvath^{16

17}

Affiliations

¹ Zoological Operations, SeaWorld Parks and Entertainment, Orlando, FL, USA. [email protected].
² Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA.
³ Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
⁴ Norwegian Orca Survey, Andenes, Norway.
⁵ Species Preservation Laboratory, SeaWorld San Diego, San Diego, CA, USA.
⁶ SeaWorld Orlando, Orlando, FL, USA.
⁷ SeaWorld San Diego, San Diego, CA, USA.
⁸ SeaWorld San Antonio, San Antonio, TX, USA.
⁹ John G. Shedd Aquarium, Chicago, IL, USA.
¹⁰ Kamogawa Sea World, Kamogawa, Chiba, Japan.
¹¹ Marineland of Canada, Niagara Falls, ON, Canada.
¹² Loro Parque Fundación, SA, Avenida Loro Parque, Puerto de la Cruz, Santa Cruz de Tenerife, Spain.
¹³ Miami Seaquarium, Miami, FL, USA.
¹⁴ Vancouver Aquarium, Vancouver, Canada.
¹⁵ Zoological Operations, SeaWorld Parks and Entertainment, Orlando, FL, USA.
¹⁶ Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA. [email protected].
¹⁷ Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA. [email protected].

^# Contributed equally.

Abstract

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Age Factors
Aging / genetics*
Aging / physiology
Animals
DNA / genetics
DNA Methylation / genetics
Dolphins / genetics
Dolphins / metabolism*
Epigenesis, Genetic / genetics
Epigenomics / methods
Genome
Phylogeny
Whales / genetics
Whales / metabolism*

Substances

DNA