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

Epigenetics, specifically DNA methylation, allows for the estimation of animal age from blood or remotely sampled skin. This multi-tissue epigenetic age estimation clock uses 110 longitudinal samples from 34 Navy bottlenose dolphins (Tursiops truncatus), identifying 195 cytosine-phosphate-guanine sites associated with chronological aging via cross-validation with one individual left out in each fold (R2 = 0.95). With a median absolute error of 2.5 years, this clock improves age estimation capacity in wild dolphins, helping conservation efforts and enabling a better understanding of population demographics.

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

10.20944/preprints202107.0075.v1 ◽

2021 ◽

Author(s):

Ashley Barratclough ◽

Cynthia R. Smith ◽

Forrest M. Gomez ◽

Theoni Photopoulou ◽

Ryan Takeshita ◽

...

Keyword(s):

Tursiops Truncatus ◽

Cross Validation ◽

Bottlenose Dolphins ◽

Absolute Error ◽

Population Demographics ◽

Chronological Aging ◽

Essential Step ◽

Epigenetic Aging ◽

Estimation Capacity ◽

Median Absolute Error

Epigenetics, specifically DNA methylation, allows for estimation of animal age from blood or remotely sampled skin. This multi tissue epigenetic aging clock uses 110 longitudinal samples from 34 Navy bottlenose dolphins (Tursiops truncatus), identifying 195 cytosine-phosphate-guanine sites associated with chronological aging via leave-one-individual-out-cross-validation (R2=0.95). With a median absolute error of 2.5 years this clock improves age estimation capacity in wild dolphins, expanding conservation efforts, enabling better understanding of population demographics.

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The combined effect of obesity and aging on human sperm DNA methylation signatures: inclusion of BMI in the paternal germ line age prediction model

Scientific Reports ◽

10.1038/s41598-020-71979-8 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Albert Salas-Huetos ◽

Emma R. James ◽

Dallin S. Broberg ◽

Kenneth I. Aston ◽

Douglas T. Carrell ◽

...

Keyword(s):

Dna Methylation ◽

Germ Line ◽

Age Groups ◽

Human Sperm ◽

Absolute Error ◽

Epigenetic Aging ◽

Epigenetic Age ◽

Sperm Dna ◽

Epigenetic Age Acceleration ◽

The Impact

Abstract Male aging and obesity have both been shown to contribute to declines in fertility in men. Recent work in aging has shown consistent epigenetic changes to sperm as a man ages. In fact, our lab has built a tool that utilizes DNA methylation signatures from sperm to effectively predict an individual’s age. Herein, we performed this preliminary cohort study to determine if increased BMI accelerates the epigenetic aging in sperm. A total of 96 participants were divided into four age groups (22–24, 30, 40–41, and > 48 years of age) and additionally parsed into two BMI sub-categories (normal and high/obese). We found no statistically significant epigenetic age acceleration. However, it is important to note that within each age category, high BMI individuals were predicted to be older on average than their actual age (~ 1.4 years), which was not observed in the normal BMI group. To further investigate this, we re-trained a model using only the present data with and without BMI as a feature. We found a modest but non-significant improvement in prediction with BMI [r2 = 0.8814, mean absolute error (MAE) = 3.2913] compared to prediction without BMI (r2 = 0.8739, MAE = 3.3567). Future studies with higher numbers of age-matched individuals are needed to definitively understand the impact of BMI on epigenetic aging in sperm.

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Novel epigenetic age estimation in wild-caught Gulf of Mexico reef fishes

Canadian Journal of Fisheries and Aquatic Sciences ◽

10.1139/cjfas-2021-0240 ◽

2021 ◽

Author(s):

D. Nick Weber ◽

Andrew T. Fields ◽

William F. Patterson ◽

Beverly K. Barnett ◽

Christopher M. Hollenbeck ◽

...

Keyword(s):

Dna Methylation ◽

Gulf Of Mexico ◽

Age Estimation ◽

Reef Fishes ◽

Lutjanus Campechanus ◽

Cpg Sites ◽

Epigenetic Aging ◽

Epigenetic Age ◽

Red Grouper ◽

Species Specific

Cutting-edge DNA methylation-based epigenetic aging techniques were applied to Gulf of Mexico northern red snapper (Lutjanus campechanus; n = 10; 1–26 years old) and red grouper (Epinephelus morio; n = 10; 2–14 years old). Bisulfite-converted restriction site-associated DNA sequencing was used to identify CpG sites (cytosines followed by guanines) that exhibit age-correlated DNA methylation, and species-specific epigenetic clocks developed from 100s of CpG sites in each species showed strong agreements between predicted and otolith-derived ages (r2 > 0.99 for both species). Results suggest epigenetic age estimation could provide an accurate and efficient approach to mass-aging fishes in a non-invasive manner.

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Adolescent age estimation using voice features

Biomedical Engineering / Biomedizinische Technik ◽

10.1515/bmt-2018-0082 ◽

2020 ◽

Vol 65 (4) ◽

pp. 429-434

Author(s):

Marcin D. Bugdol ◽

Monika N. Bugdol ◽

Maria J. Bieńkowska ◽

Anna Lipowicz ◽

Agata M. Wijata ◽

...

Keyword(s):

Age Estimation ◽

Cross Validation ◽

Rapid Development ◽

Absolute Error ◽

Regression Method ◽

Chronological Age ◽

Height Measurement ◽

Voice Signal ◽

Selection Operator ◽

Fold Cross Validation

AbstractIn this paper, a method for evaluating the chronological age of adolescents on the basis of their voice signal is presented. For every examined child, the vowels a, e, i, o and u were recorded in extended phonation. Sixty voice parameters were extracted from each recording. Voice recordings were supplemented with height measurement in order to check if it could improve the accuracy of the proposed solution. Predictor selection was performed using the LASSO (least absolute shrinkage and selection operator) algorithm. For age estimation, the random forest (RF) for regression method was employed and it was tested using a 10-fold cross-validation. The lowest absolute error (0.37 year ± 0.28) was obtained for boys only when all selected features were included into prediction. In all cases, the achieved accuracy was higher for boys than for girls, which results from the fact that the change of voice with age is larger for men than for women. The achieved results suggest that the presented approach can be employed for accurate age estimation during rapid development in children.

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Impact of excessive alcohol abuse on age prediction using the VISAGE enhanced tool for epigenetic age estimation in blood

International Journal of Legal Medicine ◽

10.1007/s00414-021-02665-1 ◽

2021 ◽

Author(s):

Danuta Piniewska-Róg ◽

Antonia Heidegger ◽

Ewelina Pośpiech ◽

Catarina Xavier ◽

Aleksandra Pisarek ◽

...

Keyword(s):

Dna Methylation ◽

Alcohol Abuse ◽

Age Estimation ◽

Forensic Genetics ◽

Absolute Error ◽

Control Group ◽

Older Individuals ◽

Alcohol Abusers ◽

Epigenetic Age ◽

Age Prediction

AbstractDNA methylation-based clocks provide the most accurate age estimates with practical implications for clinical and forensic genetics. However, the effects of external factors that may influence the estimates are poorly studied. Here, we evaluated the effect of alcohol consumption on epigenetic age prediction in a cohort of extreme alcohol abusers. Blood samples from deceased alcohol abusers and age- and sex-matched controls were analyzed using the VISAGE enhanced tool for age prediction from somatic tissues that enables examination of 44 CpGs within eight age markers. Significantly altered DNA methylation was recorded for alcohol abusers in MIR29B2CHG. This resulted in a mean predicted age of 1.4 years higher compared to the controls and this trend increased in older individuals. The association of alcohol abuse with epigenetic age acceleration, as determined by the prediction analysis performed based on MIR29B2CHG, was small but significant (β = 0.190; P-value = 0.007). However, the observed alteration in DNA methylation of MIR29B2CHG had a non-significant effect on age estimation with the VISAGE age prediction model. The mean absolute error in the alcohol-abusing cohort was 3.1 years, compared to 3.3 years in the control group. At the same time, upregulation of MIR29B2CHG expression may have a biological function, which merits further studies.

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Age estimation based on 3D post-mortem computed tomography images of mandible and femur using convolutional neural networks

PLoS ONE ◽

10.1371/journal.pone.0251388 ◽

2021 ◽

Vol 16 (5) ◽

pp. e0251388

Author(s):

Cuong Van Pham ◽

Su-Jin Lee ◽

So-Yeon Kim ◽

Sookyoung Lee ◽

Soo-Hyung Kim ◽

...

Keyword(s):

Computed Tomography ◽

Age Estimation ◽

Cross Validation ◽

Absolute Error ◽

Post Mortem ◽

Age Assessment ◽

Computed Tomography Images ◽

Forensic Service ◽

Domain Specific Knowledge ◽

Prediction Approach

Age assessment has attracted increasing attention in the field of forensics. However, most existing works are laborious and requires domain-specific knowledge. Modern computing power makes it is possible to leverage massive amounts of data to produce more reliable results. Therefore, it is logical to use automated age estimation approaches to handle large datasets. In this study, a fully automated age prediction approach was proposed by assessing 3D mandible and femur scans using deep learning. A total of 814 post-mortem computed tomography scans from 619 men and 195 women, within the age range of 20–70, were collected from the National Forensic Service in South Korea. Multiple preprocessing steps were applied for each scan to normalize the image and perform intensity correction to create 3D voxels that represent these parts accurately. The accuracy of the proposed method was evaluated by 10-fold cross-validation. The initial cross-validation results illustrated the potential of the proposed method as it achieved a mean absolute error of 5.15 years with a concordance correlation coefficient of 0.80. The proposed approach is likely to be faster and potentially more reliable, which could be used for age assessment in the future.

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Female reproductive parameters and population demographics of bottlenose dolphins (Tursiops truncatus) in the Shannon Estuary, Ireland

Marine Biology ◽

10.1007/s00227-017-3265-z ◽

2017 ◽

Vol 165 (1) ◽

Cited By ~ 7

Author(s):

Isabel Baker ◽

Joanne O’Brien ◽

Katherine McHugh ◽

Simon Berrow

Keyword(s):

Tursiops Truncatus ◽

Bottlenose Dolphins ◽

Reproductive Parameters ◽

Population Demographics

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Multi-tissue methylation clocks for age estimation in the common bottlenose dolphin

10.1101/2021.05.03.442523 ◽

2021 ◽

Author(s):

Todd R Robeck ◽

Zhe Fei ◽

Amin Haghani ◽

Joseph Alan Zoller ◽

Caesar Z Li ◽

...

Keyword(s):

Age Estimation ◽

Bottlenose Dolphin ◽

Bottlenose Dolphins ◽

Management Strategies ◽

Absolute Error ◽

Accurate Identification ◽

Methylation Array ◽

Common Bottlenose Dolphin ◽

The Common ◽

Methylation Patterns

Accurate identification of individual ages within wild bottlenose dolphins (Tursiops truncatus) is critical for determining population health and the development of population management strategies. As such, we analyzed DNA methylation patterns by applying a custom methylation array (HorvathMammalMethyl40) to both blood (n = 140) and skin samples (n = 87) from known age or approximate age (0 to 57 years) bottlenose dolphins. We present three bottlenose dolphin specific age estimation clocks using combined blood and skin (48 CpGs, R = 0.93, median absolute error = 2.13 years), blood only (64 CpGs, R = 0.97, error= 1.46 years) and skin only (39 CpGs, R = 0.95, error= 2.53). Our sex estimator based on 71 CpGs predicts the sex of any odontocete species with 99.5% accuracy. We characterize individual cytosines that correlate with sex and age in dolphins. The presented epigenetic clocks are expected to be useful for conservation efforts and for studying anthropogenic events.

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