Epigenetic clock and methylation studies in elephants

Prado, Natalia A.; Brown, Janine L.; Zoller, Joseph A.; Haghani, Amin; Yao, Mingjia; Bagryanova, Lora; Campana, Michael G.; Maldonado, Jesús E.; Raj, Kenneth; Schmitt, Dennis L.; Robeck, Todd R.; Horvath, Steve

doi:10.1111/acel.13414

Cited by 48 publications

(58 citation statements)

References 37 publications

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“…The fact that one can build such multispecies clocks reflects the technical properties of the mammalian methylation array platform (which focuses on conserved CpGs) [ 35 ] and biological properties of epigenetic aging effects that are highly conserved across mammals. Similar multispecies clocks have been constructed for many different mammalian species [ 36 – 41 ].…”

Section: Discussionmentioning

confidence: 99%

Methylation studies in Peromyscus: aging, altitude adaptation, and monogamy

et al. 2021

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DNA methylation-based biomarkers of aging have been developed for humans and many other mammals and could be used to assess how stress factors impact aging. Deer mice (Peromyscus) are long-living rodents that have emerged as an informative model to study aging, adaptation to extreme environments, and monogamous behavior. In the present study, we have undertaken an exhaustive, genome-wide analysis of DNA methylation in Peromyscus, spanning different species, stocks, sexes, tissues, and age cohorts. We describe DNA methylation-based estimators of age for different species of deer mice based on novel DNA methylation data generated on highly conserved mammalian CpGs measured with a custom array. The multi-tissue epigenetic clock for deer mice was trained on 3 tissues (tail, liver, and brain). Two human-Peromyscus clocks accurately measure age and relative age, respectively. We present CpGs and enriched pathways that relate to different conditions such as chronological age, high altitude, and monogamous behavior. Overall, this study provides a first step towards studying the epigenetic correlates of monogamous behavior and adaptation to high altitude in Peromyscus. The human-Peromyscus epigenetic clocks are expected to provide a significant boost to the attractiveness of Peromyscus as a biological model.

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Section: Discussionmentioning

confidence: 99%

Methylation studies in Peromyscus: aging, altitude adaptation, and monogamy

et al. 2021

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“…These epigenetic clocks, while they can predict chronological age (Jasinska et al, 2021;Lu et al, 2021;Prado et al, 2021;Raj et al, 2021;Schachtschneider et al, 2021), have also been shown to be elevated in inbred individuals, suggesting that inbreeding can lead to aging at a faster rate compared to non-inbred individuals (Larison et al, 2021). Likewise, metabolic syndrome in humans (i.e., hypertension, obesity) also results in increased epigenetic aging (Lee & Park, 2020;Nannini et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

“…Differential methylation patterns in wild and captive populations have been associated with phenotypic traits such as body size in sheep ( Ovis ammon ) (Cao et al, 2015) and lynx ( Lynx canadensis ) (Meröndun et al, 2019), pigmentation levels in rabbits ( Oryctolagus cuniculus ) (Chen et al, 2021) and breeding success in barn swallows ( Hirundo rustica ) (Saino et al, 2017). In addition, the rate of DNAm, particularly hypermethylation, on specific CpG sites changes throughout an individual’s lifetime, making it possible to age individuals based on their methylation levels (Horvath, 2013; Lu et al, 2021; Prado et al, 2021; Wilkinson et al, 2021). These epigenetic clocks , while they can predict chronological age (Jasinska et al, 2021; Lu et al, 2021; Prado et al, 2021; Raj et al, 2021; Schachtschneider et al, 2021), have also been shown to be elevated in inbred individuals, suggesting that inbreeding can lead to aging at a faster rate compared to non-inbred individuals (Larison et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

“…In addition, the rate of DNAm, particularly hypermethylation, on specific CpG sites changes throughout an individual’s lifetime, making it possible to age individuals based on their methylation levels (Horvath, 2013; Lu et al, 2021; Prado et al, 2021; Wilkinson et al, 2021). These epigenetic clocks , while they can predict chronological age (Jasinska et al, 2021; Lu et al, 2021; Prado et al, 2021; Raj et al, 2021; Schachtschneider et al, 2021), have also been shown to be elevated in inbred individuals, suggesting that inbreeding can lead to aging at a faster rate compared to non-inbred individuals (Larison et al, 2021). Likewise, metabolic syndrome in humans (i.e., hypertension, obesity) also results in increased epigenetic aging (Lee & Park, 2020; Nannini et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

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Epigenetics and island-mainland divergence in an insectivorous small mammal

Cossette

Stewart

Haghani

et al. 2022

Preprint

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Geographically isolated populations, including island-mainland populations, tend to exhibit phenotypic variation in many species. The so-called island syndrome occurs when different environmental pressures lead to insular divergence from mainland populations. This phenomenon can be seen in an island population of Nova Scotia masked shrews (Sorex cinereus), which have developed a specialized feeding habit and digestive enzyme compared to their mainland counterparts. Epigenetic modifications, such as DNA methylation (DNAm), can impact phenotypes by altering gene expression without changing the DNA sequence. Here, we used a de novo masked shrew genome assembly and epigenome-wide assay to investigate morphological and DNA methylation patterns between island and mainland populations. Island shrews were morphologically and epigenetically different than their mainland counterparts, exhibiting a smaller body size; remarkably, the gene ontology analyses mirrored these phenotypes including genes for the digestive enzyme phenotypes. Moreover, island shrews appeared to age faster than their mainland counterparts. This study provides an example counter to the prevailing island syndrome morphological patterns, along with novel epigenomic insight into the drivers of island-mainland divergence in mammals.

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Age is not just a number: How incorrect ageing impacts close‐kin mark‐recapture estimates of population size

Petersma,

Thomas,

Harris

et al. 2024

Ecology and Evolution

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Population size is a key parameter for the conservation of animal species. Close‐kin mark‐recapture (CKMR) relies on the observed frequency and type of kinship among individuals sampled from the population to estimate population size. Knowledge of the age of the individuals, or a surrogate thereof, is essential for inference with acceptable precision. One common approach, particularly in fish studies, is to measure animal length and infer age using an assumed age‐length relationship (a ‘growth curve’). We used simulation to test the effect of misspecifying the length measurement error and the growth curve on population size estimation. Simulated populations represented two fictional shark species, one with a relatively simple life history and the other with a more complex life history based on the grey reef shark (Carcharhinus amblyrhynchos). We estimated sex‐specific adult abundance, which we assumed to be constant in time. We observed small median biases in these estimates ranging from 1.35% to 2.79% when specifying the correct measurement error standard deviation and growth curve. CI coverage was adequate whenever the growth curve was correctly specified. Introducing error via misspecified growth curves resulted in changes in the magnitude of the estimated adult population, where underestimating age negatively biased the abundance estimates. Over‐ and underestimating the standard deviation of length measurement error did not introduce a bias and had negligible effect on the variance in the estimates. Our findings show that assuming an incorrect standard deviation of length measurement error has little effect on estimation, but having an accurate growth curve is crucial for CKMR whenever ageing is based on length measurements. If ageing could be biased, researchers should be cautious when interpreting CKMR results and consider the potential biases arising from inaccurate age inference.

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Epigenetic clock and methylation studies in elephants

Abstract: This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

Cited by 48 publications

References 37 publications

Methylation studies in Peromyscus: aging, altitude adaptation, and monogamy

Methylation studies in Peromyscus: aging, altitude adaptation, and monogamy

Epigenetics and island-mainland divergence in an insectivorous small mammal

Age is not just a number: How incorrect ageing impacts close‐kin mark‐recapture estimates of population size

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