Age prediction of green turtles with an epigenetic clock

Mayne, Benjamin; Mustin, Walter; Baboolal, Vandanaa; Casella, F.; Ballorain, Katia; Barret, Mathieu; Vanderklift, Mathew A.; Tucker, Anton D.; Korbie, Darren; Jarman, Simon; Berry, Oliver

doi:10.1111/1755-0998.13621

Cited by 24 publications

(27 citation statements)

References 68 publications

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“…Thus, the 193 positively and 160 negatively correlated CpGs become hypermethylated and hypomethylated with age, respectively. Subsequently, additional epigenetic clocks have been developed for several vertebrates (De Paoli-Iseppi et al, 2019), mostly mammals, but also birds, a marine turtle (Mayne et al, 2022) and fishes (Table 1). More recently, epigenetic clocks have also been developed in an invertebrate, the European lobster (Fairfield et al, 2021), and in a tree, the loblolly pine (Gardner et al, 2022), suggesting that agedependent DNA methylation changes may be a universal phenomenon in eukaryotes.…”

Section: Vertebrate Epigenetic Clocksmentioning

confidence: 99%

Age estimation in fishes using epigenetic clocks: Applications to fisheries management and conservation biology

Piferrer

Anastasiadi

2023

Front. Mar. Sci.

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The distribution of age classes is a key demographic parameter of populations and thus proper age estimation is crucial for fisheries management and for conservation biology. Age estimation in fishes has traditionally relied on the analysis of growth marks in hard structures such as otoliths. However, besides being lethal this method is time-consuming, can have low accuracy in some species and cannot be applied in others. Thus, there is a need for the development of new methods. DNA methylation is an epigenetic modification consisting in the addition of a methyl group in cytosine-guanine loci. Aging is associated with changes in DNA methylation. Among a background of global and weak genome hypomethylation, there are some loci in which age-associated DNA methylation changes are of a “clock-like” nature and thus predictable. Chronological age estimators built from DNA methylation are termed ‘epigenetic clocks’. Epigenetic clocks have been developed in the last ten years for many species, notably vertebrates, including already several fish species. Here, we review the piscine epigenetic clocks built so far and outline the major considerations to be taken into account for the development of new epigenetic clocks for additional species, which include the number of samples to be collected and tissues to be targeted. The steps on how to develop such a clock and the techniques available to do so are also discussed. Next, we focus on the features of epigenetic clocks as measuring devices, considering aspects such as accuracy, precision and reproducibility. Finally, we discuss the possibility of developing a multi-species piscine epigenetic clock and how processing automation can greatly reduce the cost per sample. One important knowledge gap is to determine how environmental changes, especially temperature and food availability, may affect the tick rate of piscine epigenetic clocks. Improved age prediction through the use of piscine epigenetic clocks can contribute to better fisheries management practices in a context of overexploited fish stocks worldwide, and in the estimation of age classes in endangered species.

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Section: Vertebrate Epigenetic Clocksmentioning

confidence: 99%

Age estimation in fishes using epigenetic clocks: Applications to fisheries management and conservation biology

Piferrer

Anastasiadi

2023

Front. Mar. Sci.

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“…However, the animals' status as critically endangered means that sacrificing large numbers of animals to obtain vertebral samples is problematic (30). Addressing this uncertainty is likely to involve further development and refinement of nonlethal age estimation (31)(32)(33).…”

Section: Discussionmentioning

confidence: 99%

Rapid assessment of adult abundance and demographic connectivity from juvenile kin pairs in a critically endangered species

et al. 2022

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The viability of spatially structured populations depends on the abundance and connectivity between subpopulations of breeding adults. Yet, for many species, both are extremely difficult to assess. The speartooth shark is a critically endangered elasmobranch inhabiting tropical rivers with only three adults ever recorded in Australia. Close-kin mark-recapture models, informed by sibling pairs among 226 juveniles, were developed to estimate adult abundance and connectivity in two Australian river systems. Sixty-eight sibling pairs were found, and adult abundance was estimated at 892 for the Adelaide River and 1128 for the Alligator Rivers. We found strong evidence for female philopatry, with most females returning to the same river to pup. Adelaide River males appear largely philopatric, whereas Alligator Rivers males are highly connected to the Adelaide River. From only 4 years of sampling, our results demonstrate that juvenile-only kin pairs can inform simultaneous estimates of abundance and connectivity in a rare and threatened species.

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“…Since the development of the first epigenetic clock in humans [ 17 ], DNA methylation age predictors have also been expanded to numerous other species, including mammals (e.g., rodents [ 18–23 ]), birds [ 24 ], reptiles [ 25 ], fish [ 26 ], and invertebrates [ 27 ], just to name a few. However, amphibians have not yet been extensively examined in ageing studies, despite the fact that Xenopus has many unique features as a model organism for ageing biology.…”

Section: Introductionmentioning

confidence: 99%

Age-associated DNA methylation changes in Xenopus frogs

et al. 2023

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Age-associated changes in DNA methylation have been characterized across various animals, but not yet in amphibians, which are of particular interest because they include widely studied model organisms. In this study, we present clear evidence that the aquatic vertebrate species Xenopus tropicalis displays patterns of age-associated changes in DNA methylation. We have generated whole-genome bisulfite sequencing (WGBS) profiles from skin samples of nine frogs representing young, mature, and old adults and characterized the gene- and chromosome-scale DNA methylation changes with age. Many of the methylation features and changes we observe are consistent with what is known in mammalian species, suggesting that the mechanism of age-related changes is conserved. Moreover, we selected a few thousand age-associated CpG sites to build an assay based on targeted DNA methylation analysis (TBSseq) to expand our findings in future studies involving larger cohorts of individuals. Preliminary results of a pilot TBSeq experiment recapitulate the findings obtained with WGBS setting the basis for the development of an epigenetic clock assay. The results of this study will allow us to leverage the unique resources available for Xenopus to study how DNA methylation relates to other hallmarks of ageing.

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Age prediction of green turtles with an epigenetic clock

Cited by 24 publications

References 68 publications

Age estimation in fishes using epigenetic clocks: Applications to fisheries management and conservation biology

Age estimation in fishes using epigenetic clocks: Applications to fisheries management and conservation biology

Rapid assessment of adult abundance and demographic connectivity from juvenile kin pairs in a critically endangered species

Age-associated DNA methylation changes in Xenopus frogs

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