Age estimation by DNA methylation in the Antarctic minke whale

Tanabe, Atsushi; Shimizu, Ryo; Osawa, Yui; Suzuki, Maroh; Ito, Saki; Goto, Mutsuo; Pastene, Luis A.; Fujise, Yoshihiro; Sahara, Hiroeki

doi:10.1007/s12562-019-01371-7

Cited by 22 publications

(30 citation statements)

References 16 publications

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“…In total, nine CpG sites were successfully assayed through pyrosequencing: three for TET2 ( TET2_CpG + 16 , TET2_CpG + 21 , TET2_CpG + 31 ), three for CDKN2A ( CDKN2A_CpG + 297 , CDKN2A_CpG + 303 , CDKN2A_CpG + 309 ), and three for GRIA2 ( GRIA2_CpG + 202 , GRIA2_CpG + 188 , GRIA2_CpG + 183 ). We were not able to obtain results for the fourth site of TET2 ( TET2_CpG + 58 ) or CDKN2A ( CDKN2A_CpG + 327 ), but we obtained two additional sites in the GRIA2 gene ( GRIA2_CpG + 188 and GRIA2_CpG + 183 ) that have been previously analyzed in minke whales (Tanabe et al, 2020).…”

Section: Resultsmentioning

confidence: 83%

“…More promising was the analysis of the methylation levels of selected genes, which in humpback whales appeared to provide high accuracy in age determinations (Polanowski et al, 2014; Riekkola et al, 2018). However, two of the three genes used in this study were later investigated in Antarctic minke whales and provided dissimilar results (Goto et al, 2020; Tanabe et al, 2020), thus suggesting differences between closely related species.…”

Section: Introductionmentioning

confidence: 94%

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CpG methylation frequency of TET2, GRIA2, and CDKN2A genes in the North Atlantic fin whale varies with age and between populations

García‐Vernet

Martín

Peinado

et al. 2021

Marine Mammal Science

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Recovery rates for baleen whales that were decimated by exploitation vary between species and populations. Age determination is critical for the understanding of recovery trends and population structure, but determining age in free‐ranging individuals remains challenging. Recent research has suggested that the methylation level of some genes in skin samples may provide age determinations with accuracy. We selected nine CpG sites from three genes (TET2, CDKN2A, and GRIA2) and analyzed them in 40 skin samples from known‐age individuals pertaining to two different populations of fin whales from the North Atlantic. We observed significant correlations with age in five CpG sites. We used three of these CpG sites to perform an epigenetic age estimation. Predictions had a standard deviation of 2.94, but regression between observed and predicted ages showed a clear underestimation for older fin whales. For further development, we suggest: (1) screening for new CpG sites associated with age that exhibit higher variability between individuals, and (2) including older animals whenever the sampling allows it. We also observed subtle, but significant differences between the two populations studied in one of the CpG sites (TET2_CpG + 21). We attributed these differences to genetic differences or to the dissimilar environments that affect both populations.

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Section: Resultsmentioning

confidence: 83%

Section: Introductionmentioning

confidence: 94%

CpG methylation frequency of TET2, GRIA2, and CDKN2A genes in the North Atlantic fin whale varies with age and between populations

García‐Vernet

Martín

Peinado

et al. 2021

Marine Mammal Science

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“…In an attempt to improve upon age estimations of wild cetaceans, two DNA methylation or epigenetic aging clocks directed at individual species have been published for the humpback whale 39 , Antarctic minke whale 40 , and the bottlenose dolphin 1 . DNA methylation is a well-studied epigenetic modification which refers to the transfer of a methyl (CH3) group from S-adenosyl methionine (SAM) to the fifth position of cytosine nucleotides, forming 5-methylcytosine (5mC) 41 .…”

Section: Introductionmentioning

confidence: 99%

Multi-species and multi-tissue methylation clocks for age estimation in toothed whales and dolphins

Robeck

Fei

et al. 2021

Commun Biol

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The development of a precise blood or skin tissue DNA Epigenetic Aging Clock for Odontocete (OEAC) would solve current age estimation inaccuracies for wild odontocetes. Therefore, we determined genome-wide DNA methylation profiles using a custom array (HorvathMammalMethyl40) across skin and blood samples (n = 446) from known age animals representing nine odontocete species within 4 phylogenetic families to identify age associated CG dinucleotides (CpGs). The top CpGs were used to create a cross-validated OEAC clock which was highly correlated for individuals (r = 0.94) and for unique species (median r = 0.93). Finally, we applied the OEAC for estimating the age and sex of 22 wild Norwegian killer whales. DNA methylation patterns of age associated CpGs are highly conserved across odontocetes. These similarities allowed us to develop an odontocete epigenetic aging clock (OEAC) which can be used for species conservation efforts by provide a mechanism for estimating the age of free ranging odontocetes from either blood or skin samples.

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“…In humans, clocks have been designed using varying numbers of CpG sites, from one site (e.g., an age predictor based on a CpG in the ELOVL2 gene; Garagnani et al, 2012) to several hundred sites (e.g., 353 sites; Horvath, 2013). Epigenetic clocks have also been developed for other species including the mouse (Meer et al, 2018; Petkovich et al, 2017; Stubbs et al, 2017; Thompson et al, 2018), chimpanzee (Ito et al, 2018), bat (Wright et al, 2018), canid (Ito et al, 2017; Thompson et al, 2017), humpback whale (Polanowski et al, 2014), minke whale (Tanabe et al, 2020), and bottlenose dolphin (Beal et al, 2019). Accurate age estimates can be valuable for conservation efforts and species management.…”

Section: Introductionmentioning

confidence: 99%

An epigenetic clock to estimate the age of living beluga whales

Bors

Baker

Wade

et al. 2021

Evolutionary Applications

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DNA methylation data facilitate the development of accurate molecular estimators of chronological age or “epigenetic clocks.” We present a robust epigenetic clock for the beluga whale, Delphinapterus leucas, developed for an endangered population in Cook Inlet, Alaska, USA. We used a custom methylation array to measure methylation levels at 37,491 cytosine–guanine sites (CpGs) from skin samples of dead whales (n = 67) whose chronological ages were estimated based on tooth growth layer groups. Using these calibration data, a penalized regression model selected 23 CpGs, providing an R2 = 0.92 for the training data; and an R2 = 0.74 and median absolute age error = 2.9 years for the leave one out cross‐validation. We applied the epigenetic clock to an independent dataset of 38 skin samples collected with a biopsy dart from living whales between 2016 and 2018. Age estimates ranged from 11 to 27 years. We also report sex correlations in CpG data and describe an approach of identifying the sex of an animal using DNA methylation. The epigenetic estimators of age and sex presented here have broad applications for conservation and management of Cook Inlet beluga whales and potentially other cetaceans.

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Age estimation by DNA methylation in the Antarctic minke whale

Cited by 22 publications

References 16 publications

CpG methylation frequency of TET2, GRIA2, and CDKN2A genes in the North Atlantic fin whale varies with age and between populations

CpG methylation frequency of TET2, GRIA2, and CDKN2A genes in the North Atlantic fin whale varies with age and between populations

Multi-species and multi-tissue methylation clocks for age estimation in toothed whales and dolphins

An epigenetic clock to estimate the age of living beluga whales

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