Epigenetic models developed for plains zebras predict age in domestic horses and endangered equids

Brenda Larison,Christopher B Kaelin,Todd R Robeck,Steve Horvath,Matteo Pellegrini,Gregory S Barsh,Bernard Wooding,Dewey Maddox,Joseph A Zoller,Caesar Z Li,Gabriela M Pinho,Carrie J Finno,Colin Farrell,Amin Haghani

doi:10.1038/s42003-021-02935-z

Abstract

Effective conservation and management of threatened wildlife populations require an accurate assessment of age structure to estimate demographic trends and population viability. Epigenetic aging models are promising developments because they estimate individual age with high accuracy, accurately predict age in related species, and do not require invasive sampling or intensive long-term studies. Using blood and biopsy samples from known age plains zebras (Equus quagga), we model epigenetic aging using two approaches: the epigenetic clock (EC) and the epigenetic pacemaker (EPM). The plains zebra EC has the potential for broad application within the genus Equus given that five of the seven extant wild species of the genus are threatened. We test the EC’s ability to predict age in sister taxa, including two endangered species and the more distantly related domestic horse, demonstrating high accuracy in all cases. By comparing chronological and estimated age in plains zebras, we investigate age acceleration as a proxy of health status. An interaction between chronological age and inbreeding is associated with age acceleration estimated by the EPM, suggesting a cumulative effect of inbreeding on biological aging throughout life.

Highlights

Effective conservation and management of threatened wildlife populations require an accurate assessment of age structure to estimate demographic trends and population viability
We further show that inbreeding associated age acceleration increases with age, suggesting that inbreeding may have a cumulative effect on age acceleration througout life
We developed both an epigenetic clock (EC) and an epigenetic pacemaker (EPM)

Summary

Introduction

Effective conservation and management of threatened wildlife populations require an accurate assessment of age structure to estimate demographic trends and population viability. Epigenetic aging models are promising developments because they estimate individual age with high accuracy, accurately predict age in related species, and do not require invasive sampling or intensive long-term studies. We develop epigenetic models for a wild equid (plains zebras, Equus quagga) using both blood and remote biopsy samples collected from known-age individuals in a captive-bred population. Besides their high accuracy, four other features of epigenetic aging models should make them attractive for wildlife managers. We aim to test the performance of the EC developed for plains zebras to predict age in domestic horses (E. caballus) and two threatened species: Grevy’s zebras (E. grevyi) and Somali asses (E. africanus somaliensis)

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