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

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

doi:10.1038/s42003-021-02179-x

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.

Highlights

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
This study describes the construction of a accurate (r = 0.94 Leave One Sample Out Cross Validation (LOOCV)) odontocete DNAm epigenetic clock that was developed using blood and skin samples from eight species within four families of odontocetes
The Leave One Species Out Cross-Validation (LOSOCV) crossvalidation analysis indicated that the chronological age of an animal from any species of odontocete can be predicted with a high degree of accuracy

Summary

Introduction

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. 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. Long-term photo identification studies have produced the most robust and accurate data concerning life history of a few populations of odontocetes, these studies face limitations[2,3,4,5], for example, inaccuracies can arise when attempting to use population level biological statistics to define ages of individual animals that were mature prior to the onset of these studies[3,6]. Accuracy and debate exist concerning the ability to count growth layers as teeth wear differentially based on feeding strategies or with age[11,12,13,14,15,16,17,18]

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