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

Cytosine methylation patterns have not yet been thoroughly studied in horses. Here, we profile n = 333 samples from 42 horse tissue types at loci that are highly conserved between mammalian species using a custom array (HorvathMammalMethylChip40). Using the blood and liver tissues from horses, we develop five epigenetic aging clocks: a multi-tissue clock, a blood clock, a liver clock and two dual-species clocks that apply to both horses and humans. In addition, using blood methylation data from three additional equid species (plains zebra, Grevy’s zebras and Somali asses), we develop another clock that applies across all equid species. Castration does not significantly impact the epigenetic aging rate of blood or liver samples from horses. Methylation and RNA data from the same tissues define the relationship between methylation and RNA expression across horse tissues. We expect that the multi-tissue atlas will become a valuable resource.

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“…S6D ). Overall, these results from this equine EWAS of age are consistent with those in humans and other mammalian species 28 – 31 .…”

Section: Resultssupporting

confidence: 86%

DNA methylation aging and transcriptomic studies in horses

et al. 2022

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“…Currently, the blood clock is more accurate than the multi-tissue clock; however, a skin-specific clock can be produced with additional samples and compared with the multi-tissue clock to see which is most accurate for future use. The recently published odontocete clock produced an R 2 of 0.81 for a skin-only clock with a mean absolute error of 7.76 years [7]. We hypothesize that a more accurate species-specific skin clock with an error equivalent to the multi-tissue clock of approximately 2 years can be created with an increased skin sample size.…”

Section: Discussionmentioning

confidence: 89%

“…The initial application for chronological age estimation of bottlenose dolphins (Tursiops truncatus) focused on two cytosine-phosphate-guanine sites (CpG) (of 17 screened) producing an R 2 of 0.74 and a root mean squared error of 5.14 years when estimating chronological age [6]. Similarly, for nine odontocete species combined, a median absolute age prediction error of 2.57 years was produced using 142 CpG sites [7]. Creating species-specific epigenetic clocks with a wide range of known age animals improves the accuracy of age estimation [8].…”

Section: Introductionmentioning

confidence: 99%

Accurate Epigenetic Aging in Bottlenose Dolphins (Tursiops truncatus), an Essential Step in the Conservation of at-Risk Dolphins

Barratclough

Smith

Gomez

et al. 2021

JZBG

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Epigenetics, specifically DNA methylation, allows for the estimation of animal age from blood or remotely sampled skin. This multi-tissue epigenetic age estimation clock uses 110 longitudinal samples from 34 Navy bottlenose dolphins (Tursiops truncatus), identifying 195 cytosine-phosphate-guanine sites associated with chronological aging via cross-validation with one individual left out in each fold (R2 = 0.95). With a median absolute error of 2.5 years, this clock improves age estimation capacity in wild dolphins, helping conservation efforts and enabling a better understanding of population demographics.

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“…Age might be difficult to determine, in particular in wild populations, which might need to be considered during the study design. Cytosine methylation clocks provide some promise for determining the age of wild animals that are not part of tagged or monitored populations (for example, see Robeck et al, 2021 ; Wilkinson et al, 2021 ). Additional data collected on individuals sampled will depend on the specific question under study, but information about size dimorphisms and overall physical health would be helpful.…”

Section: Opportunities For Research Into Sex Differences In Agingmentioning

confidence: 99%