Data from: Genome-wide DNA methylation patterns predict age in the zebra shark (Stegostoma tigrinum) and provide insight into the evolution of vertebrate aging
Data files
Apr 07, 2026 version files 22.72 KB
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README.md
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zebrashark_factors_dryad.csv
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zs_growth_r.csv
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Abstract
Epigenomic changes are a hallmark of aging, and DNA methylation (DNAm) has emerged as the most reliable molecular marker of an individual’s age. Genome-wide patterns of age-associated hypo- and hypermethylation have been applied to generate predictive models (i.e., “epigenetic clocks”) capable of estimating chronological age in an increasingly diverse set of species including many mammals, a few birds, a reptile, and several bony fishes. Elasmobranchs (sharks, skates, and rays) are underrepresented in comparative investigations of epigenetic aging despite exhibiting exceptional life history variation, occupying a key basal position in the vertebrate phylogeny, and encompassing a large proportion of threatened species lacking accurate, non-lethal age determination methods. Here, we characterize epigenome-wide aging signals in the zebra shark (Stegostoma tigrinum), a long-lived elasmobranch of conservation concern, from whole-genome enzymatic methyl-sequencing of whole blood. Using a cohort of 51 known-age aquarium-bred individuals, we develop several epigenetic clock models capable of predicting chronological age with a median absolute error of 1.03-1.99 yrs (3.32-6.42% of lifespan) based on the methylation status of as few as ten cytosines. We further apply our models to 19 individuals of unknown age originating from the wild. By profiling the broader age-associated methylome we demonstrate that these patterns not only predict age with high accuracy but also exhibit striking similarities in their genomic distributions to those observed in mammals pointing to conservation of the processes underlying epigenetic aging across vertebrates.
Dataset DOI: 10.5061/dryad.dr7sqvbbb
Description of the data and file structure
These data were generated as part of a study to characterize genome-wide DNA methylation patterns associated with age in blood cells of aquarium-kept zebra sharks (Stegostoma tigrinum) ranging in age from 0 – 30 years. Methylation data was generated from blood cell genomic DNA using the NEBNext Enzymatic Methyl-Seq (EM-Seq) kit (Catalog #E720S) according to manufacturer instructions. Sequencing of methyl-seq libraries was performed by the University of Florida Interdisciplinary Center for Biotechnology Research with either Illumina NovaSeq 6000 S4 or NovaSeq X Plus. Code and scripts associated with the project are available at https://github.com/slbock/elasmo_dnam_aging
Files and variables
File: zebrashark_factors_dryad.csv
Description: Sample metadata for all individuals included in study.
Variables
- gn.number: unique sample identifier
- sex: biological sex as determined by morphology
- type.c: categorical code indicating whether individual was born in captivity (‘c’ a.k.a. aquarium bred) or captured in the wild prior to being brought into human care (‘w’ a.k.a. wild-caught)
- est.age: Estimated or known age in years calculated as the difference between sample date and either birth date or date at aquarium acquisition
- mature.kl: categorical code indicating whether an individual was sexually mature
- institution: institution where individual was housed at time of sampling
- sample.date: date on which blood sample was taken
- orig.date: birth date for aquarium-bred individuals or date of aquarium acquisition for wild-caught individuals
- preservative: preservative in which blood sample was kept prior to genomic DNA extraction – either RNAlater, ethanol (EtOH), or none
- flag: indicating aquarium-bred samples where the precise day of birth was not known
Abbreviations
- F: female
- M: male
- c: captive (aquarium-bred)
- w: wild-caught prior to being brought into aquarium
File: zs_growth_r.csv
Description: Repeated total length data for aquarium-bred zebra sharks used to construct von Bertalanffy growth curve.
Variables
- inst: institution where individual was housed and measured
- id: institution-specific individual identifier
- id_r: unique individual identifier used in analysis
- hatch.date: date individual was hatched (if known by institution); format is MM/DD/YY
- measure.date: date individual was measured; format is MM/DD/YY
- age.days: age at measurement in days
- length.cm: total length of individual in centimeters
- sex: biological sex as determined by morphology
- outcome: current status of individual
Abbreviations
- F: female
- M: male
- NA: data not available from originating aquarium
Code/software
Code and scripts associated with the project are available at https://github.com/slbock/elasmo_dnam_aging
Access information
Other publicly accessible locations of the data:
- Raw sequencing reads for whole-genome enzymatic methyl-sequencing libraries are publicly available in the NCBI Sequence Read Archive (SRA) under the BioProject PRJNA1422842.