Epigenetic models developed for plains zebras predict age in domestic horses and endangered equids

Larison, Brenda; Pinho, Gabriela Medeiros de; Haghani, Amin; Zoller, Joseph A.; Li, Caesar Z.; Finno, Carrie J.; Farrell, Colin; Kaelin, Christopher B.; Barsh, Greg; Wooding, Bernard; Robeck, Todd R.; Maddox, Dewey; Pellegrini, Matteo; Horvath, Steve

doi:10.1038/s42003-021-02935-z

Cited by 35 publications

(41 citation statements)

References 112 publications

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“…We tested whether phenotypic divergence occurred via epigenetic modifications, specifically DNA methylation, which alter gene expression without changing the DNA sequence (Razin & Riggs, 1980). Over 29,000 probes aligned to our genome, consistent with other mammalian studies (Larison et al, 2021; Pinho et al, 2021; Schachtschneider et al, 2021; Sugrue et al, 2021), and a robust epigenetic clock was generated (Figure 1). The differential methylation between island-mainland populations showed a remarkable overlap between enriched pathways and measured phenotypic differences.…”

Section: Discussionsupporting

confidence: 84%

“…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%

“…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%

“…Epigenetic clocks can also be used to predict demographic trends for conservation efforts (Prado et al, 2021) and have been shown to be elevated in inbred individuals, suggesting that inbreeding can lead to aging at a faster rate (Larison et al, 2021). Likewise, metabolic syndrome in humans (i.e., 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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Section: Discussionsupporting

confidence: 84%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

Self Cite

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“…Marttila et al 11 observed that age-associated DNA hypermethylation seems to originate from programmed developmental changes while DNA hypomethylation could result from environmental in uences 11 . Furthermore, DNAm pro les in several species have been demonstrated to predict individuals' biological age, known as epigenetic clocks [12][13][14][15][16][17][18][19][20][21][22][23] . Recently, Caulton et al 13 reported a prediction accuracy of 0.95 for epigenetic clocks based on DNAm in a dairy herd.…”

Section: Introductionmentioning

confidence: 99%

DNA methylation profile in beef cattle is influenced by additive genetics and age

Ribeiro¹,

Sanglard²,

Wijesena³

et al. 2022

Preprint

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DNA methylation (DNAm) has been considered a promising indicator of biological age in mammals and could be useful to increase the accuracy of phenotypic prediction in livestock. The objectives of this study were to estimate the heritability and age effects of site-specific DNAm (DNAm level) and cumulative DNAm across all sites (DNAm load) in beef cattle. Blood samples were collected from cows ranging from 217 to 3,192 days (0.6 to 8.7 years) of age (n = 136). All animals were genotyped, and DNAm was obtained using the Infinium array HorvathMammalMethylChip40. Genetic parameters for DNAm were obtained from an animal model based on the genomic relationship matrix, including the fixed effects of age and breed composition. Heritability estimates of DNAm levels ranged from 0.18 to 0.72, with a similar average across all regions and chromosomes. Heritability estimate of DNAm load was 0.45. The average age effect on DNAm level varied among genomic regions. The DNAm level across the genome increased with age in the promoter and 5' UTR and decreased in the exonic, intronic, 3’ UTR, and intergenic regions. In addition, DNAm level increased with age in regions enriched in CpG and decreased in regions deficient in CpG. Results suggest DNAm profiles are influenced by both genetics and the environmental effect of age in beef cattle.

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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 models developed for plains zebras predict age in domestic horses and endangered equids

Cited by 35 publications

References 112 publications

Epigenetics and island-mainland divergence in an insectivorous small mammal

Epigenetics and island-mainland divergence in an insectivorous small mammal

DNA methylation profile in beef cattle is influenced by additive genetics and age

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

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