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

Barratclough, Ashley; Smith, Cynthia R.; Gomez, Forrest M.; Photopoulou, Theoni; Takeshita, Ryan; Pirotta, Enrico; Thomas, Len; McClain, Abby M.; Parry, Celeste; Zoller, Joseph A.; Horvath, Steve; Schwacke, Lori H.

doi:10.20944/preprints202107.0075.v1

Cited by 3 publications

(5 citation statements)

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“…This study presents a robust and accurate ( r = 0.86, MAE = 2.1) epigenetic clock for the aging of Indo‐Pacific bottlenose dolphins based on skin tissue. To date, five other epigenetic clocks exist for odontocetes, using skin and/or blood samples: three for common bottlenose dolphins (Barratclough et al, 2021; Beal et al, 2019; Robeck, Fei, Haghani, et al, 2021), one for belugas (Bors et al, 2021), and one multi‐species odontocete clock, which was cross‐validated with nine species (Robeck, Fei, Lu, et al, 2021). While Beal et al (2019) used a pyrosequencing approach based on 13 CpG sites correlated with age, the remaining clocks were built using the HorvathMammalMethylChip40 with 37,492 CpG sites, as we did here.…”

Section: Discussionmentioning

confidence: 99%

“…Multi‐species clocks effectively estimate age and sex of individual members of various species simultaneously and, thus, facilitate conservation efforts by enabling the investigation of population viability of multiple species with a single tool (Robeck, Fei, Lu, et al, 2021). Nevertheless, accuracy of age predictions can be improved with species‐specific clocks (Field et al, 2018; Zhang et al, 2019), several of which currently exist for odontocetes, including belugas (Bors et al, 2021) and common bottlenose dolphins (Barratclough et al, 2021; Beal et al, 2019; Robeck, Fei, Haghani, et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

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An epigenetic DNA methylation clock for age estimates in Indo‐Pacific bottlenose dolphins (Tursiops aduncus)

Peters

Gerber

Scheu

et al. 2022

Evolutionary Applications

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Knowledge of an animal's chronological age is crucial for understanding and predicting population demographics, survival and reproduction, but accurate age determination for many wild animals remains challenging. Previous methods to estimate age require invasive procedures, such as tooth extraction to analyse growth layers, which are difficult to carry out with large, mobile animals such as cetaceans. However, recent advances in epigenetic methods have opened new avenues for precise age determination. These ‘epigenetic clocks’ present a less invasive alternative and can provide age estimates with unprecedented accuracy. Here, we present a species‐specific epigenetic clock based on skin tissue samples for a population of Indo‐Pacific bottlenose dolphins ( Tursiops aduncus ) in Shark Bay, Western Australia. We measured methylation levels at 37,492 cytosine‐guanine sites (CpG sites) in 165 samples using the mammalian methylation array. Chronological age estimates with an accuracy of ±1 year were available for 68 animals as part of a long‐term behavioral study of this population. Using these samples with known age, we built an elastic net model with Leave‐One‐Out‐Cross‐Validation, which retained 43 CpG sites, providing an r = 0.86 and median absolute age error (MAE) = 2.1 years (5% of maximum age). This model was more accurate for our data than the previously published methylation clock based on skin samples of common bottlenose dolphins ( T. truncatus : r = 0.83, MAE = 2.2) and the multi‐species odontocete methylation clock ( r = 0.68, MAE = 6.8), highlighting that species‐specific clocks can have superior performance over those of multi‐species assemblages. We further developed an epigenetic sex estimator, predicting sex with 100% accuracy. As age and sex are critical parameters for the study of animal populations, this clock and sex estimator will provide a useful tool for extracting life history information from skin samples rather than long‐term observational data for free‐ranging Indo‐Pacific bottlenose dolphins worldwide.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

An epigenetic DNA methylation clock for age estimates in Indo‐Pacific bottlenose dolphins (Tursiops aduncus)

Peters

Gerber

Scheu

et al. 2022

Evolutionary Applications

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“…Previous studies have reported on epigenetic clocks for cetacean species, including humpback whales (Polanowski et al 2014; Beal et al 2019; Bors et al 2020; Tanabe et al 2020; Barratclough et al 2021; Robeck et al 2021). In prior work on humpback whales (Polanowski et al 2014), CpG sites were selected for based on their association with age in other species.…”

Section: Discussionmentioning

confidence: 99%

“…Several DNA methylation-based age predictors, referred to as epigenetic clocks, have been developed for humans, mice and other mammals (Bocklandt et al 2011; Hannum et al 2013; Horvath 2013). Epigenetic clocks have also been developed for several cetacean species, including minke whales, Balaenoptera acutorostrata (Tanabe et al 2020), humpback whales, Megaptera novaeangliae (Polanowski et al 2014), bottlenose dolphins, Tursiops truncatus (Beal et al 2019; Barratclough et al 2021; Robeck et al 2021), beluga whales, Delphinapterus leucas (Bors et al 2020), and more generally odontocetes (Robeck et al 2021).…”

Section: Introductionmentioning

confidence: 99%

DNA methylation age studies of humpback whales

Horvath

Haghani²,

Zoller

et al. 2022

Preprint

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Several previous studies have described epigenetic clocks for whale and dolphin species. Here we present a novel and highly robust epigenetic clock for the humpback whale based on methylation levels measured using the Mammalian Methylation Array platform. Skin samples were obtained from 76 individuals that had been studied since their birth year and known to range in age from <1 to 39.5 years. The humpback whale clock provided a highly accurate estimate of chronological age (R=0.96, median error 2.2 years) according to a leave-one-out cross validation analysis. We applied this clock to an independent set of samples from humpback whales of unknown exact age but with sighting histories that were as long as or longer than the upper 20% of the available known-age range. Although there was a strong correlation with minimum age (R=0.89), the clock underestimated age in these older animals by a median error of at least 7.8 years. Finally, we applied the humpback clock to publicly available methylation data from beluga whales. In this data set from a different species, the humpback clock provided an age correlation of R=0.78. While a DNAm age estimator has previously been described for humpback whales, this is the first such clock shown to apply to another cetacean species as well. Our humpback whale clock built from well-studied population lends itself for understanding humpback populations that otherwise lack age data.

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“…These changes in DNA methylation are linked to age‐related mechanisms and developmental milestones that often result in changes in gene expression (Gladyshev, 2016 ; Hannum et al, 2013 ; López‐Otín et al, 2013 ). Although largely focused on mammalian species (Barratclough et al, 2021 ; Beal et al, 2019 ; Bors et al, 2021 ; Fei et al, 2021 ; Horvath & Raj, 2018 ; Polanowski et al, 2014 ; Robeck et al, 2021 ; Stubbs et al, 2017 ; Tanabe et al, 2020 ), accurate clocks have been developed for other taxa including birds and fishes (Anastasiadi & Piferrer, 2020 ; De Paoli‐Iseppi et al, 2019 ; Mayne et al, 2020 ).…”

Section: Introductionmentioning

confidence: 99%

Age group DNA methylation differences in lemon sharks (Negaprion brevirostris): Implications for future age estimation tools

Beal

Hackerott

Feldheim

et al. 2022

Ecology and Evolution

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Overfishing constitutes the most important threat to elasmobranchs including sharks, skates, and rays (Dulvy et al., 2014), making fisheries management critical for their conservation. Consequently, the characterization of demographic information is of utmost importance to model the sustainability of populations under fishing pressure. Age information is a critical parameter of these models, which is unfortunately not available for most species due (among other reasons) to the lack of physiological and morphological traits that can be accurately used as proxies of chronological age in elasmobranchs. Particularly in the case of sharks, body length has been largely used to infer age and

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

Cited by 3 publications

References 11 publications

An epigenetic DNA methylation clock for age estimates in Indo‐Pacific bottlenose dolphins (Tursiops aduncus)

An epigenetic DNA methylation clock for age estimates in Indo‐Pacific bottlenose dolphins (Tursiops aduncus)

DNA methylation age studies of humpback whales

Age group DNA methylation differences in lemon sharks (Negaprion brevirostris): Implications for future age estimation tools

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