Epigenetic aging of Māui and Hector's dolphins

The age of an individual is an essential demographic parameter but is difficult to estimate without long-term monitoring or invasive sampling. Epigenetic approaches are increasingly used to age organisms, including non-model organisms such as cetaceans. Māui dolphins (Cephalorhynchus hectori maui) are a critically endangered subspecies endemic to Aotearoa New Zealand, and the age structure of this population is important for informing conservation. Here we present an epigenetic clock for aging Māui and Hector's dolphins (C. h. hectori) developed from methylation data using DNA from tooth aged individuals (n = 48). Based on this training dataset, the optimal model required only eight methylation sites, provided an age correlation of 0.95, and had a median absolute age error of 1.54 years. A leave-one-out cross-validation analysis with the same parameters resulted in an age correlation of 0.87 and median absolute age error of 2.09 years. To improve age estimate, we included previously pub..., , , # Epigenetic aging of Māui and Hector's dolphins

The files linked here accompany the article by Hernandez et al., \"Using epigenetic clocks to investigate changes in the age structure of critically endangered Māui dolphins.\" Included here are the R code for the epigenetic clock construction and accompanying analyses and the files needed to replicate this work. Supplementary material is available from the journal website.

## Description of the data and file structure

The methylation data is structured to where each row is a cytosine-guanine dinucleotide (CpG) site in the methylation array, and each column is an individual sample, as indicated by the variable Basename and ExternalSampleID. Metadata are structured to where each row is an individual sample, and the columns are associated metadata variables. Missing data are indicated by NAs. Individuals with a \"no\" in the CanBeUsedForAging variable or DOC_Cat \"red\" were excluded from epigenetic clock development as these individuals wer...