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SC/69A/SM/02
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Resource ID
20062
Access
Open
Document Number
SC/69A/SM/02
Full Title
Epigenetic aging of Hector’s and Māui dolphins: progress report to the New Zealand Department of Conservation
Author
Keith M. Hernandez, Kaimyn O’Neill, Steve Horvath, Ellie Bors, Rochelle Constantine, Kristina Hillock, Anton Van Helden, Wendi Roe, Debbie Steel, C. Scott Baker
Authors Summary
This report details progress on using DNA methylation data to develop an epigenetic clock for aging Hector’s and Māui dolphins (Cephalorhynchus hectori hectori and C. h. maui). Specifically, the report includes a review of tooth growth layer counts from calibration samples, and provides preliminary age estimates for a subset of samples based on the odontocete epigenetic aging clock (OEAC, Robeck et al. 2021) and a beluga-specific (Delphinapterus leucas) clock (Bors et al. 2021). The next steps for this project are to use the methods in Bors et al. (2021) to develop and validate a species-specific epigenetic model to estimate the age of Hector’s and Māui dolphins using skin samples collected with a biopsy dart.
Publisher
IWC
Publication Year
2023
Abstract
The age of an individual is an essential parameter for population dynamics, but is difficult to determine without lethal sampling. DNA methylation, the addition of methyl groups throughout the genome, is increasingly applied to develop statistical models known as “epigenetic clocks” to estimate age from minimally invasive samples. This report describes initial stages in developing an epigenetic clock for aging Hector’s and Māui dolphins (Cephalorhynchus hectori hectori and
C. h. maui). Following preliminary efforts as reported in O’Neill et al. (2021), the New Zealand Department of Conservation – Te Papa Atawhai contracted for a revised count of tooth growth layers in the samples intended to provide a calibration of the epigenetic clock. On the basis of this review (Betty et al. 2022), the samples available for the calibration were grouped into two confidence categories: “strict”, with n = 31 samples, and “relaxed”, with n = 48 samples. Methylation was measured in these calibration individuals using a custom mammalian array targeting 37,554 sites throughout the genome. Applying p-value filtering to CpG sites from this revised calibration dataset reduced nearly 30,000 potential CpG sites to at least 4,800 sites for modelling. Pearson’s correlation analyses of methylation ratios with known sexes and revised growth layer counts identified thousands of CpG sites with significant correlations. A preliminary analysis with both subsets of individuals with published epigenetic clocks (Bors et al. 2021, Robeck et al. 2021) produced age estimates that were generally overestimates relative to the estimated age from tooth growth layers. Next steps for this project are to use the methods in Bors et al. (2021) to develop and validate epigenetic models to predict the age of Hector’s and Māui dolphins using skin samples collected with a biopsy dart.