1
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Balard A, Baltazar-Soares M, Eizaguirre C, Heckwolf MJ. An epigenetic toolbox for conservation biologists. Evol Appl 2024; 17:e13699. [PMID: 38832081 PMCID: PMC11146150 DOI: 10.1111/eva.13699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 04/22/2024] [Accepted: 04/24/2024] [Indexed: 06/05/2024] Open
Abstract
Ongoing climatic shifts and increasing anthropogenic pressures demand an efficient delineation of conservation units and accurate predictions of populations' resilience and adaptive potential. Molecular tools involving DNA sequencing are nowadays routinely used for these purposes. Yet, most of the existing tools focusing on sequence-level information have shortcomings in detecting signals of short-term ecological relevance. Epigenetic modifications carry valuable information to better link individuals, populations, and species to their environment. Here, we discuss a series of epigenetic monitoring tools that can be directly applied to various conservation contexts, complementing already existing molecular monitoring frameworks. Focusing on DNA sequence-based methods (e.g. DNA methylation, for which the applications are readily available), we demonstrate how (a) the identification of epi-biomarkers associated with age or infection can facilitate the determination of an individual's health status in wild populations; (b) whole epigenome analyses can identify signatures of selection linked to environmental conditions and facilitate estimating the adaptive potential of populations; and (c) epi-eDNA (epigenetic environmental DNA), an epigenetic-based conservation tool, presents a non-invasive sampling method to monitor biological information beyond the mere presence of individuals. Overall, our framework refines conservation strategies, ensuring a comprehensive understanding of species' adaptive potential and persistence on ecologically relevant timescales.
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Affiliation(s)
- Alice Balard
- School of Biological and Behavioural Sciences Queen Mary University of London London UK
| | | | - Christophe Eizaguirre
- School of Biological and Behavioural Sciences Queen Mary University of London London UK
| | - Melanie J Heckwolf
- Department of Ecology Leibniz Centre for Tropical Marine Research Bremen Germany
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2
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Petersma FT, Thomas L, Harris D, Bradley D, Papastamatiou YP. Age is not just a number: How incorrect ageing impacts close-kin mark-recapture estimates of population size. Ecol Evol 2024; 14:e11352. [PMID: 38840589 PMCID: PMC11150428 DOI: 10.1002/ece3.11352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 04/06/2024] [Accepted: 04/15/2024] [Indexed: 06/07/2024] Open
Abstract
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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Affiliation(s)
- Felix T. Petersma
- Centre for Research into Environmental and Ecological ModellingUniversity of St AndrewsSt AndrewsUK
| | - Len Thomas
- Centre for Research into Environmental and Ecological ModellingUniversity of St AndrewsSt AndrewsUK
| | - Danielle Harris
- Centre for Research into Environmental and Ecological ModellingUniversity of St AndrewsSt AndrewsUK
| | - Darcy Bradley
- Bren School of Environmental Science & ManagementUniversity of CaliforniaSanta BarbaraCaliforniaUSA
| | - Yannis P. Papastamatiou
- Department of Biological Sciences, Institute of EnvironmentFlorida International UniversityNorth MiamiFloridaUSA
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3
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Mayne B, Chandler D, Noune C, Espinoza T, Roberts D, Anderson C, Berry O. Increased scalability and sequencing quality of an epigenetic age prediction assay. PLoS One 2024; 19:e0297006. [PMID: 38743704 PMCID: PMC11093300 DOI: 10.1371/journal.pone.0297006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 12/22/2023] [Indexed: 05/16/2024] Open
Abstract
Epigenetic ageing in a human context, has been used to better understand the relationship between age and factors such as lifestyle and genetics. In an ecological setting, it has been used to predict the age of individual animals for wildlife management. Despite the importance of epigenetic ageing in a range of research fields, the assays to measure epigenetic ageing are either expensive on a large scale or complex. In this study, we aimed to improve the efficiency and sequencing quality of an existing epigenetic ageing assay for the Australian Lungfish (Neoceratodus forsteri). We used an enzyme-based alternative to bisulfite conversion to reduce DNA fragmentation and evaluated its performance relative to bisulfite conversion. We found the sequencing quality to be 12% higher with the enzymatic alternative compared to bisulfite treatment (p-value < 0.01). This new enzymatic based approach, although currently double the cost of bisulfite treatment can increases the throughput and sequencing quality. We envisage this assay setup being adopted increasingly as the scope and scale of epigenetic ageing research continues to grow.
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Affiliation(s)
- Benjamin Mayne
- Environomics Future Science Platform, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Indian Ocean Marine Research Centre, Crawley, Western Australia, Australia
| | - David Chandler
- Australian Genome Research Facility, Perth, WA, Australia
| | | | | | | | - Chloe Anderson
- Environomics Future Science Platform, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Indian Ocean Marine Research Centre, Crawley, Western Australia, Australia
| | - Oliver Berry
- Environomics Future Science Platform, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Indian Ocean Marine Research Centre, Crawley, Western Australia, Australia
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4
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Pozzo LD, Xu Z, Lin S, Wang J, Wang Y, Enechojo OS, Abankwah JK, Peng Y, Chu X, Zhou H, Bian Y. Role of epigenetics in the regulation of skin aging and geroprotective intervention: A new sight. Biomed Pharmacother 2024; 174:116592. [PMID: 38615608 DOI: 10.1016/j.biopha.2024.116592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 04/07/2024] [Accepted: 04/10/2024] [Indexed: 04/16/2024] Open
Abstract
Multiple epigenetic factors play a regulatory role in maintaining the homeostasis of cutaneous components and are implicated in the aging process of the skin. They have been associated with the activation of the senescence program, which is the primary contributor to age-related decline in the skin. Senescent species drive a series of interconnected processes that impact the immediate surroundings, leading to structural changes, diminished functionality, and heightened vulnerability to infections. Geroprotective medicines that may restore the epigenetic balance represent valid therapeutic alliances against skin aging. Most of them are well-known Western medications such as metformin, nicotinamide adenine dinucleotide (NAD+), rapamycin, and histone deacetylase inhibitors, while others belong to Traditional Chinese Medicine (TCM) remedies for which the scientific literature provides limited information. With the help of the Geroprotectors.org database and a comprehensive analysis of the referenced literature, we have compiled data on compounds and formulae that have shown potential in preventing skin aging and have been identified as epigenetic modulators.
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Affiliation(s)
- Lisa Dal Pozzo
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Zhe Xu
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Shan Lin
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Jida Wang
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Ying Wang
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Ogbe Susan Enechojo
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Joseph Kofi Abankwah
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Yanfei Peng
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Xiaoqian Chu
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Huifang Zhou
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China.
| | - Yuhong Bian
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China.
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5
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Qi H, Lim QL, Kinoshita K, Nakajima N, Inoue-Murayama M. A cost-effective blood DNA methylation-based age estimation method in domestic cats, Tsushima leopard cats (Prionailurus bengalensis euptilurus) and Panthera species, using targeted bisulphite sequencing and machine learning models. Mol Ecol Resour 2024; 24:e13928. [PMID: 38234258 DOI: 10.1111/1755-0998.13928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 12/29/2023] [Accepted: 01/03/2024] [Indexed: 01/19/2024]
Abstract
Individual age can be used to design more efficient and suitable management plans in both in situ and ex situ conservation programmes for targeted wildlife species. DNA methylation is a promising marker of epigenetic ageing that can accurately estimate age from small amounts of biological material, which can be collected in a minimally invasive manner. In this study, we sequenced five targeted genetic regions and used 8-23 selected CpG sites to build age estimation models using machine learning methods at only about $3-7 per sample. Blood samples of seven Felidae species were used, ranging from small to big, and domestic to endangered species: domestic cats (Felis catus, 139 samples), Tsushima leopard cats (Prionailurus bengalensis euptilurus, 84 samples) and five Panthera species (96 samples). The models achieved satisfactory accuracy, with the mean absolute error of the most accurate models recorded at 1.966, 1.348 and 1.552 years in domestic cats, Tsushima leopard cats and Panthera spp. respectively. We developed the models in domestic cats and Tsushima leopard cats, which were applicable to individuals regardless of health conditions; therefore, these models are applicable to samples collected from individuals with diverse characteristics, which is often the case in conservation. We also showed the possibility of developing universal age estimation models for the five Panthera spp. using only two of the five genetic regions. We do not recommend building a common age estimation model for all the target species using our markers, because of the degraded performance of models that included all species.
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Affiliation(s)
- Huiyuan Qi
- Wildlife Research Center, Kyoto University, Kyoto, Japan
| | - Qi Luan Lim
- Wildlife Research Center, Kyoto University, Kyoto, Japan
| | | | - Nobuyoshi Nakajima
- Biodiversity Division, National Institute for Environmental Studies, Tsukuba, Ibaraki, Japan
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6
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Hanski E, Joseph S, Raulo A, Wanelik KM, O'Toole Á, Knowles SCL, Little TJ. Epigenetic age estimation of wild mice using faecal samples. Mol Ecol 2024; 33:e17330. [PMID: 38561950 DOI: 10.1111/mec.17330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 02/19/2024] [Accepted: 03/01/2024] [Indexed: 04/04/2024]
Abstract
Age is a key parameter in population ecology, with a myriad of biological processes changing with age as organisms develop in early life then later senesce. As age is often hard to accurately measure with non-lethal methods, epigenetic methods of age estimation (epigenetic clocks) have become a popular tool in animal ecology and are often developed or calibrated using captive animals of known age. However, studies typically rely on invasive blood or tissue samples, which limit their application in more sensitive or elusive species. Moreover, few studies have directly assessed how methylation patterns and epigenetic age estimates compare across environmental contexts (e.g. captive or laboratory-based vs. wild animals). Here, we built a targeted epigenetic clock from laboratory house mice (strain C57BL/6, Mus musculus) using DNA from non-invasive faecal samples, and then used it to estimate age in a population of wild mice (Mus musculus domesticus) of unknown age. This laboratory mouse-derived epigenetic clock accurately predicted adult wild mice to be older than juveniles and showed that wild mice typically increased in epigenetic age over time, but with wide variation in epigenetic ageing rate among individuals. Our results also suggested that, for a given body mass, wild mice had higher methylation across targeted CpG sites than laboratory mice (and consistently higher epigenetic age estimates as a result), even among the smallest, juvenile mice. This suggests wild and laboratory mice may display different CpG methylation levels from very early in life and indicates caution is needed when developing epigenetic clocks on laboratory animals and applying them in the wild.
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Affiliation(s)
- Eveliina Hanski
- University of Oxford, Oxford, UK
- University of Helsinki, Helsinki, Finland
| | | | - Aura Raulo
- University of Oxford, Oxford, UK
- University of Turku, Turku, Finland
| | - Klara M Wanelik
- University of Oxford, Oxford, UK
- University of Surrey, Guildford, UK
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7
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Thavornkanlapachai R, Armstrong KN, Knuckey C, Huntley B, Hanrahan N, Ottewell K. Species-specific SNP arrays for non-invasive genetic monitoring of a vulnerable bat. Sci Rep 2024; 14:1847. [PMID: 38253562 PMCID: PMC10803360 DOI: 10.1038/s41598-024-51461-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 01/05/2024] [Indexed: 01/24/2024] Open
Abstract
Genetic tagging from scats is one of the minimally invasive sampling (MIS) monitoring approaches commonly used to guide management decisions and evaluate conservation efforts. Microsatellite markers have traditionally been used but are prone to genotyping errors. Here, we present a novel method for individual identification in the Threatened ghost bat Macroderma gigas using custom-designed Single Nucleotide Polymorphism (SNP) arrays on the MassARRAY system. We identified 611 informative SNPs from DArTseq data from which three SNP panels (44-50 SNPs per panel) were designed. We applied SNP genotyping and molecular sexing to 209 M. gigas scats collected from seven caves in the Pilbara, Western Australia, employing a two-step genotyping protocol and identifying unique genotypes using a custom-made R package, ScatMatch. Following data cleaning, the average amplification rate was 0.90 ± 0.01 and SNP genotyping errors were low (allelic dropout 0.003 ± 0.000) allowing clustering of scats based on one or fewer allelic mismatches. We identified 19 unique bats (9 confirmed/likely males and 10 confirmed/likely females) from a maternity and multiple transitory roosts, with two male bats detected using roosts, 9 km and 47 m apart. The accuracy of our SNP panels enabled a high level of confidence in the identification of individual bats. Targeted SNP genotyping is a valuable tool for monitoring and tracking of non-model species through a minimally invasive sampling approach.
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Affiliation(s)
- Rujiporn Thavornkanlapachai
- Department of Biodiversity, Conservation and Attractions, Bentley Delivery Centre, Locked Bag 104, Bentley, WA, 6983, Australia.
| | - Kyle N Armstrong
- School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
- South Australian Museum, Adelaide, SA, 5000, Australia
| | - Chris Knuckey
- Biologic Environmental, 24 Wickham Street, East Perth, WA, 6004, Australia
| | - Bart Huntley
- Department of Biodiversity, Conservation and Attractions, Bentley Delivery Centre, Locked Bag 104, Bentley, WA, 6983, Australia
| | - Nicola Hanrahan
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT, 0815, Australia
| | - Kym Ottewell
- Department of Biodiversity, Conservation and Attractions, Bentley Delivery Centre, Locked Bag 104, Bentley, WA, 6983, Australia
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8
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Arai K, Qi H, Inoue-Murayama M. Age estimation of captive Asian elephants (Elephas maximus) based on DNA methylation: An exploratory analysis using methylation-sensitive high-resolution melting (MS-HRM). PLoS One 2023; 18:e0294994. [PMID: 38079426 PMCID: PMC10712859 DOI: 10.1371/journal.pone.0294994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 11/13/2023] [Indexed: 12/18/2023] Open
Abstract
Age is an important parameter for bettering the understanding of biodemographic trends-development, survival, reproduction and environmental effects-critical for conservation. However, current age estimation methods are challenging to apply to many species, and no standardised technique has been adopted yet. This study examined the potential use of methylation-sensitive high-resolution melting (MS-HRM), a labour-, time-, and cost-effective method to estimate chronological age from DNA methylation in Asian elephants (Elephas maximus). The objective of this study was to investigate the accuracy and validation of MS-HRM use for age determination in long-lived species, such as Asian elephants. The average lifespan of Asian elephants is between 50-70 years but some have been known to survive for more than 80 years. DNA was extracted from 53 blood samples of captive Asian elephants across 11 zoos in Japan, with known ages ranging from a few months to 65 years. Methylation rates of two candidate age-related epigenetic genes, RALYL and TET2, were significantly correlated with chronological age. Finally, we established a linear, unisex age estimation model with a mean absolute error (MAE) of 7.36 years. This exploratory study suggests an avenue to further explore MS-HRM as an alternative method to estimate the chronological age of Asian elephants.
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Affiliation(s)
- Kana Arai
- Wildlife Research Center, Kyoto University, Kyoto, Japan
| | - Huiyuan Qi
- Wildlife Research Center, Kyoto University, Kyoto, Japan
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9
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Le Clercq LS, Kotzé A, Grobler JP, Dalton DL. Biological clocks as age estimation markers in animals: a systematic review and meta-analysis. Biol Rev Camb Philos Soc 2023; 98:1972-2011. [PMID: 37356823 DOI: 10.1111/brv.12992] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 06/04/2023] [Accepted: 06/08/2023] [Indexed: 06/27/2023]
Abstract
Various biological attributes associated with individual fitness in animals change predictably over the lifespan of an organism. Therefore, the study of animal ecology and the work of conservationists frequently relies upon the ability to assign animals to functionally relevant age classes to model population fitness. Several approaches have been applied to determining individual age and, while these methods have proved useful, they are not without limitations and often lack standardisation or are only applicable to specific species. For these reasons, scientists have explored the potential use of biological clocks towards creating a universal age-determination method. Two biological clocks, tooth layer annulation and otolith layering have found universal appeal. Both methods are highly invasive and most appropriate for post-mortem age-at-death estimation. More recently, attributes of cellular ageing previously explored in humans have been adapted to studying ageing in animals for the use of less-invasive molecular methods for determining age. Here, we review two such methods, assessment of methylation and telomere length, describing (i) what they are, (ii) how they change with age, and providing (iii) a summary and meta-analysis of studies that have explored their utility in animal age determination. We found that both attributes have been studied across multiple vertebrate classes, however, telomere studies were used before methylation studies and telomere length has been modelled in nearly twice as many studies. Telomere length studies included in the review often related changes to stress responses and illustrated that telomere length is sensitive to environmental and social stressors and, in the absence of repair mechanisms such as telomerase or alternative lengthening modes, lacks the ability to recover. Methylation studies, however, while also detecting sensitivity to stressors and toxins, illustrated the ability to recover from such stresses after a period of accelerated ageing, likely due to constitutive expression or reactivation of repair enzymes such as DNA methyl transferases. We also found that both studied attributes have parentally heritable features, but the mode of inheritance differs among taxa and may relate to heterogamy. Our meta-analysis included more than 40 species in common for methylation and telomere length, although both analyses included at least 60 age-estimation models. We found that methylation outperforms telomere length in terms of predictive power evidenced from effect sizes (more than double that observed for telomeres) and smaller prediction intervals. Both methods produced age correlation models using similar sample sizes and were able to classify individuals into young, middle, or old age classes with high accuracy. Our review and meta-analysis illustrate that both methods are well suited to studying age in animals and do not suffer significantly from variation due to differences in the lifespan of the species, genome size, karyotype, or tissue type but rather that quantitative method, patterns of inheritance, and environmental factors should be the main considerations. Thus, provided that complex factors affecting the measured trait can be accounted for, both methylation and telomere length are promising targets to develop as biomarkers for age determination in animals.
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Affiliation(s)
- Louis-Stéphane Le Clercq
- South African National Biodiversity Institute, P.O. Box 754, Pretoria, 0001, South Africa
- Department of Genetics, University of the Free State, P.O. Box 339, Bloemfontein, 9300, South Africa
| | - Antoinette Kotzé
- South African National Biodiversity Institute, P.O. Box 754, Pretoria, 0001, South Africa
- Department of Genetics, University of the Free State, P.O. Box 339, Bloemfontein, 9300, South Africa
| | - J Paul Grobler
- Department of Genetics, University of the Free State, P.O. Box 339, Bloemfontein, 9300, South Africa
| | - Desiré Lee Dalton
- School of Health and Life Sciences, Teesside University, Middlesbrough, TS1 3BA, UK
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Hernandez KM, O'Neill KB, Bors EK, Steel D, Zoller JA, Constantine R, Horvath S, Baker CS. Using epigenetic clocks to investigate changes in the age structure of critically endangered Māui dolphins. Ecol Evol 2023; 13:e10562. [PMID: 37780090 PMCID: PMC10534197 DOI: 10.1002/ece3.10562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 09/11/2023] [Indexed: 10/03/2023] Open
Abstract
The age of an individual is an essential demographic parameter but is difficult to estimate without long-term monitoring or invasive sampling. Epigenetic approaches are increasingly used to age organisms, including nonmodel organisms such as cetaceans. Māui dolphins (Cephalorhynchus hectori maui) are a critically endangered subspecies endemic to Aotearoa New Zealand, and the age structure of this population is important for informing conservation. Here we present an epigenetic clock for aging Māui and Hector's dolphins (C. h. hectori) developed from methylation data using DNA from tooth aged individuals (n = 48). Based on this training data set, the optimal model required only eight methylation sites, provided an age correlation of .95, and had a median absolute age error of 1.54 years. A leave-one-out cross-validation analysis with the same parameters resulted in an age correlation of .87 and median absolute age error of 2.09 years. To improve age estimation, we included previously published beluga whale (Delphinapterus leucas) data to develop a joint beluga/dolphin clock, resulting in a clock with comparable performance and improved estimation of older individuals. Application of the models to DNA from skin biopsy samples of living Māui dolphins revealed a shift from a median age of 8-9 years to a younger population aged 7-8 years 10 years later. These models could be applied to other dolphin species and demonstrate the ability to construct a clock even when the number of known age samples is limited, removing this impediment to estimating demographic parameters vital to the conservation of critically endangered species.
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Affiliation(s)
| | | | - Eleanor K. Bors
- Marine Mammal InstituteOregon State UniversityOregonNewportUSA
| | - Debbie Steel
- Marine Mammal InstituteOregon State UniversityOregonNewportUSA
| | - Joseph A. Zoller
- Fielding School of Public Health, Department of BiostatisticsUniversity of CaliforniaCaliforniaLos AngelesUSA
| | - Rochelle Constantine
- School of Biological Sciences & Institute of Marine ScienceUniversity of Auckland – Waipapa Taumata RauAucklandNew Zealand
| | - Steve Horvath
- Fielding School of Public Health, Department of BiostatisticsUniversity of CaliforniaCaliforniaLos AngelesUSA
- David Geffen School of Medicine, Department of Human GeneticsUniversity of CaliforniaCaliforniaLos AngelesUSA
- Altos LabsCaliforniaSan DiegoUSA
| | - C. Scott Baker
- Marine Mammal InstituteOregon State UniversityOregonNewportUSA
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11
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Mayne B, Espinoza T, Crook DA, Anderson C, Korbie D, Marshall JC, Kennard MJ, Harding DJ, Butler GL, Roberts B, Whiley J, Marshall S. Accurate, non-destructive, and high-throughput age estimation for Golden perch (Macquaria ambigua spp.) using DNA methylation. Sci Rep 2023; 13:9547. [PMID: 37308782 PMCID: PMC10260977 DOI: 10.1038/s41598-023-36773-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 06/09/2023] [Indexed: 06/14/2023] Open
Abstract
Age structure information of animal populations is fundamental to their conservation and management. In fisheries, age is routinely obtained by counting daily or annual increments in calcified structures (e.g., otoliths) which requires lethal sampling. Recently, DNA methylation has been shown to estimate age using DNA extracted from fin tissue without the need to kill the fish. In this study we used conserved known age-associated sites from the zebrafish (Danio rerio) genome to predict the age of golden perch (Macquaria ambigua), a large-bodied native fish from eastern Australia. Individuals aged using validated otolith techniques from across the species' distribution were used to calibrate three epigenetic clocks. One clock was calibrated using daily (daily clock) and another with annual (annual clock) otolith increment counts, respectively. A third used both daily and annual increments (universal clock). We found a high correlation between the otolith and epigenetic age (Pearson correlation > 0.94) across all clocks. The median absolute error was 2.4 days in the daily clock, 184.6 days in the annual clock, and 74.5 days in the universal clock. Our study demonstrates the emerging utility of epigenetic clocks as non-lethal and high-throughput tools for obtaining age estimates to support the management of fish populations and fisheries.
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Affiliation(s)
- Benjamin Mayne
- Environomics Future Science Platform, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Indian Ocean Marine Research Centre, Crawley, WA, Australia.
| | - Tom Espinoza
- Department of Regional Development, Manufacturing and Water, Brisbane, QLD, Australia
| | - David A Crook
- Department of Primary Industries, Narrandera Fisheries Centre, Narrandera, NSW, Australia
| | - Chloe Anderson
- Environomics Future Science Platform, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Indian Ocean Marine Research Centre, Crawley, WA, Australia
| | - Darren Korbie
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia
| | - Jonathan C Marshall
- Queensland Department of Environment and Science, Brisbane, QLD, Australia
- Australian Rivers Institute and Griffith School of Environment and Science, Griffith University, Nathan, QLD, 4111, Australia
| | - Mark J Kennard
- Australian Rivers Institute and Griffith School of Environment and Science, Griffith University, Nathan, QLD, 4111, Australia
| | - Doug J Harding
- Department of Regional Development, Manufacturing and Water, Brisbane, QLD, Australia
| | - Gavin L Butler
- NSW Department of Primary Industries (Fisheries), Grafton, NSW, Australia
| | - Brien Roberts
- Fisheries Division, Department of Industry, Tourism and Trade, Darwin, NT, Australia
| | - Josh Whiley
- Australian Rivers Institute and Griffith School of Environment and Science, Griffith University, Nathan, QLD, 4111, Australia
| | - Sharon Marshall
- Department of Regional Development, Manufacturing and Water, Brisbane, QLD, Australia
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12
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Larroque J, Balkenhol N. A simulation-based evaluation of methods for estimating census population size of terrestrial game species from genetically-identified parent-offspring pairs. PeerJ 2023; 11:e15151. [PMID: 37070094 PMCID: PMC10105560 DOI: 10.7717/peerj.15151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 03/09/2023] [Indexed: 04/19/2023] Open
Abstract
Estimates of wildlife population size are critical for conservation and management, but accurate estimates are difficult to obtain for many species. Several methods have recently been developed that estimate abundance using kinship relationships observed in genetic samples, particularly parent-offspring pairs. While these methods are similar to traditional Capture-Mark-Recapture, they do not need physical recapture, as individuals are considered recaptured if a sample contains one or more close relatives. This makes methods based on genetically-identified parent-offspring pairs particularly interesting for species for which releasing marked animals back into the population is not desirable or not possible (e.g., harvested fish or game species). However, while these methods have successfully been applied in commercially important fish species, in the absence of life-history data, they are making several assumptions unlikely to be met for harvested terrestrial species. They assume that a sample contains only one generation of parents and one generation of juveniles of the year, while more than two generations can coexist in the hunting bags of long-lived species, or that the sampling probability is the same for each individual, an assumption that is violated when fecundity and/or survival depend on sex or other individual traits. In order to assess the usefulness of kin-based methods to estimate population sizes of terrestrial game species, we simulated population pedigrees of two different species with contrasting demographic strategies (wild boar and red deer), applied four different methods and compared the accuracy and precision of their estimates. We also performed a sensitivity analysis, simulating population pedigrees with varying fecundity characteristics and various levels of harvesting to identify optimal conditions of applicability of each method. We showed that all these methods reached the required levels of accuracy and precision to be effective in wildlife management under simulated circumstances (i.e., for species within a given range of fecundity and for a given range of sampling intensity), while being robust to fecundity variation. Despite the potential usefulness of the methods for terrestrial game species, care is needed as several biases linked to hunting practices still need to be investigated (e.g., when hunting bags are biased toward a particular group of individuals).
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Affiliation(s)
- Jeremy Larroque
- Wildlife Sciences, University of Goettingen, Goettingen, Germany
| | - Niko Balkenhol
- Wildlife Sciences, University of Goettingen, Goettingen, Germany
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13
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Peters KJ, Gerber L, Scheu L, Cicciarella R, Zoller JA, Fei Z, Horvath S, Allen SJ, King SL, Connor RC, Rollins LA, Krützen M. An epigenetic DNA methylation clock for age estimates in Indo-Pacific bottlenose dolphins ( Tursiops aduncus). Evol Appl 2022; 16:126-133. [PMID: 36699128 PMCID: PMC9850008 DOI: 10.1111/eva.13516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 11/22/2022] [Accepted: 11/25/2022] [Indexed: 12/23/2022] Open
Abstract
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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Affiliation(s)
- Katharina J. Peters
- Evolutionary Genetics Group, Department of AnthropologyUniversity of ZurichZurichSwitzerland,School of Earth and EnvironmentUniversity of CanterburyChristchurchNew Zealand,Cetacean Ecology Research Group, School of Natural SciencesMassey UniversityAucklandNew Zealand,Global Ecology, College of Science and EngineeringFlinders UniversityAdelaide, South AustraliaAustralia
| | - Livia Gerber
- Evolutionary Genetics Group, Department of AnthropologyUniversity of ZurichZurichSwitzerland,Evolution & Ecology Research Centre, School of Biological, Earth and Environmental SciencesUniversity of New South WalesSydney, New South WalesAustralia
| | - Luca Scheu
- Evolutionary Genetics Group, Department of AnthropologyUniversity of ZurichZurichSwitzerland
| | - Riccardo Cicciarella
- Evolutionary Genetics Group, Department of AnthropologyUniversity of ZurichZurichSwitzerland
| | - Joseph A. Zoller
- Department of Biostatistics, Fielding School of Public HealthUniversity of California Los AngelesLos Angeles, CaliforniaUSA
| | - Zhe Fei
- Department of Biostatistics, Fielding School of Public HealthUniversity of California Los AngelesLos Angeles, CaliforniaUSA,Department of StatisticsUniversity of CaliforniaRiverside, CaliforniaUSA
| | - Steve Horvath
- Department of Biostatistics, Fielding School of Public HealthUniversity of California Los AngelesLos Angeles, CaliforniaUSA,Department of Human Genetics, David Geffen School of MedicineUniversity of California Los AngelesLos Angeles, CaliforniaUSA,Altos Labs, San Diego Institute of ScienceSan Diego, CaliforniaUSA
| | - Simon J. Allen
- Evolutionary Genetics Group, Department of AnthropologyUniversity of ZurichZurichSwitzerland,School of Biological SciencesUniversity of BristolBristolUK,School of Biological SciencesUniversity of Western AustraliaCrawley, Western AustraliaAustralia
| | - Stephanie L. King
- School of Biological SciencesUniversity of BristolBristolUK,School of Biological SciencesUniversity of Western AustraliaCrawley, Western AustraliaAustralia
| | | | - Lee Ann Rollins
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental SciencesUniversity of New South WalesSydney, New South WalesAustralia
| | - Michael Krützen
- Evolutionary Genetics Group, Department of AnthropologyUniversity of ZurichZurichSwitzerland
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14
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Bock SL, Smaga CR, McCoy JA, Parrott BB. Genome-wide DNA methylation patterns harbour signatures of hatchling sex and past incubation temperature in a species with environmental sex determination. Mol Ecol 2022; 31:5487-5505. [PMID: 35997618 PMCID: PMC9826120 DOI: 10.1111/mec.16670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 08/15/2022] [Accepted: 08/18/2022] [Indexed: 01/11/2023]
Abstract
Conservation of thermally sensitive species depends on monitoring organismal and population-level responses to environmental change in real time. Epigenetic processes are increasingly recognized as key integrators of environmental conditions into developmentally plastic responses, and attendant epigenomic data sets hold potential for revealing cryptic phenotypes relevant to conservation efforts. Here, we demonstrate the utility of genome-wide DNA methylation (DNAm) patterns in the face of climate change for a group of especially vulnerable species, those with temperature-dependent sex determination (TSD). Due to their reliance on thermal cues during development to determine sexual fate, contemporary shifts in temperature are predicted to skew offspring sex ratios and ultimately destabilize sensitive populations. Using reduced-representation bisulphite sequencing, we profiled the DNA methylome in blood cells of hatchling American alligators (Alligator mississippiensis), a TSD species lacking reliable markers of sexual dimorphism in early life stages. We identified 120 sex-associated differentially methylated cytosines (DMCs; FDR < 0.1) in hatchlings incubated under a range of temperatures, as well as 707 unique temperature-associated DMCs. We further developed DNAm-based models capable of predicting hatchling sex with 100% accuracy (in 20 training samples and four test samples) and past incubation temperature with a mean absolute error of 1.2°C (in four test samples) based on the methylation status of 20 and 24 loci, respectively. Though largely independent of epigenomic patterning occurring in the embryonic gonad during TSD, DNAm patterns in blood cells may serve as nonlethal markers of hatchling sex and past incubation conditions in conservation applications. These findings also raise intriguing questions regarding tissue-specific epigenomic patterning in the context of developmental plasticity.
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Affiliation(s)
- Samantha L. Bock
- Eugene P. Odum School of EcologyUniversity of GeorgiaAthensGeorgiaUSA
- Savannah River Ecology LaboratoryAikenSouth CarolinaUSA
| | - Christopher R. Smaga
- Eugene P. Odum School of EcologyUniversity of GeorgiaAthensGeorgiaUSA
- Savannah River Ecology LaboratoryAikenSouth CarolinaUSA
| | - Jessica A. McCoy
- Department of BiologyCollege of CharlestonCharlestonSouth CarolinaUSA
| | - Benjamin B. Parrott
- Eugene P. Odum School of EcologyUniversity of GeorgiaAthensGeorgiaUSA
- Savannah River Ecology LaboratoryAikenSouth CarolinaUSA
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15
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Mayne B, Mustin W, Baboolal V, Casella F, Ballorain K, Barret M, Vanderklift MA, Tucker AD, Korbie D, Jarman S, Berry O. Age prediction of green turtles with an epigenetic clock. Mol Ecol Resour 2022; 22:2275-2284. [DOI: 10.1111/1755-0998.13621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 03/29/2022] [Accepted: 04/11/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Benjamin Mayne
- Environomics Future Science Platform Indian Oceans Marine Research Centre Commonwealth Scientific and Industrial Research Organisation (CSIRO) Crawley Western Australia Australia
| | - Walter Mustin
- Cayman Turtle Conservation and Education Centre Grand Cayman KY1‐1301 Cayman Islands
| | - Vandanaa Baboolal
- Cayman Turtle Conservation and Education Centre Grand Cayman KY1‐1301 Cayman Islands
| | - Francesca Casella
- Cayman Turtle Conservation and Education Centre Grand Cayman KY1‐1301 Cayman Islands
| | - Katia Ballorain
- Centre d'Etude et de Découverte des Tortues Marines (CEDTM) 19 Cité des Frangipaniers 97424 Piton Saint‐Leu, La Réunion France
| | - Mathieu Barret
- Kélonia l’observatoire des tortues marines 46 Rue Général de Gaulle 97436 Saint‐Leu, La Réunion France
| | - Mathew A. Vanderklift
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Oceans and Atmosphere Crawley Western Australia Australia
| | - Anton D. Tucker
- Department of Biodiversity, Conservation and Attractions Marine Science Program Kensington Western Australia Australia
| | - Darren Korbie
- Australian Institute for Bioengineering and Nanotechnology The University of Queensland Brisbane Queensland Australia
| | - Simon Jarman
- School of Biological Sciences University of Western Australia 35 Stirling Highway Perth Western Australia Australia
| | - Oliver Berry
- Environomics Future Science Platform Indian Oceans Marine Research Centre Commonwealth Scientific and Industrial Research Organisation (CSIRO) Crawley Western Australia Australia
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16
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Hibernation slows epigenetic ageing in yellow-bellied marmots. Nat Ecol Evol 2022; 6:418-426. [PMID: 35256811 PMCID: PMC8986532 DOI: 10.1038/s41559-022-01679-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 01/20/2022] [Indexed: 01/02/2023]
Abstract
Species that hibernate generally live longer than would be expected based solely on their body size. Hibernation is characterized by long periods of metabolic suppression (torpor) interspersed by short periods of increased metabolism (arousal). The torpor–arousal cycles occur multiple times during hibernation, and it has been suggested that processes controlling the transition between torpor and arousal states cause ageing suppression. Metabolic rate is also a known correlate of longevity; we thus proposed the ‘hibernation–ageing hypothesis’ whereby ageing is suspended during hibernation. We tested this hypothesis in a well-studied population of yellow-bellied marmots (Marmota flaviventer), which spend 7–8 months per year hibernating. We used two approaches to estimate epigenetic age: the epigenetic clock and the epigenetic pacemaker. Variation in epigenetic age of 149 samples collected throughout the life of 73 females was modelled using generalized additive mixed models (GAMM), where season (cyclic cubic spline) and chronological age (cubic spline) were fixed effects. As expected, the GAMM using epigenetic ages calculated from the epigenetic pacemaker was better able to detect nonlinear patterns in epigenetic ageing over time. We observed a logarithmic curve of epigenetic age with time, where the epigenetic age increased at a higher rate until females reached sexual maturity (two years old). With respect to circannual patterns, the epigenetic age increased during the active season and essentially stalled during the hibernation period. Taken together, our results are consistent with the hibernation–ageing hypothesis and may explain the enhanced longevity in hibernators. Species that hibernate generally have longer lifespans than expected based on their body size. The authors show epigenetic ageing patterns from a natural population of hibernating yellow-bellied marmots consistent with the hypothesis that ageing is suspended during hibernation.
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17
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Siddiqui R, Maciver SK, Khan NA. Gut microbiome-immune system interaction in reptiles. J Appl Microbiol 2022; 132:2558-2571. [PMID: 34984778 DOI: 10.1111/jam.15438] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/12/2021] [Accepted: 12/31/2021] [Indexed: 12/17/2022]
Abstract
Reptiles are ectothermic amniotes in a world dominated by endotherms. Reptiles originated more than 300 million years ago and they often dwell in polluted environments which may expose them to pathogenic micro-organisms, radiation and/or heavy metals. Reptiles also possess greater longevity and may live much longer than similar-sized land mammals, for example, turtles, tortoises, crocodiles and tuatara are long-lived reptiles living up to 100 years or more. Many recent studies have emphasized the pivotal role of the gut microbiome on its host; thus, we postulated that reptilian gut microbiome and/or its metabolites and the interplay with their robust immune system may contribute to their longevity and overall hardiness. Herein, we discuss the composition of the reptilian gut microbiome, immune system-gut microbiome cross-talk, antimicrobial peptides, reptilian resistance to infectious diseases and cancer, ageing, as well the current knowledge of the genome and epigenome of these remarkable species. Preliminary studies have demonstrated that microbial gut flora of reptiles such as crocodiles, tortoises, water monitor lizard and python exhibit remarkable anticancer and antibacterial properties, as well as comprise novel gut bacterial metabolites and antimicrobial peptides. The underlying mechanisms between the gut microbiome and the immune system may hold clues to developing new therapies overall for health, and possible extrapolation to exploit the ancient defence systems of reptiles for Homo sapiens benefit.
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Affiliation(s)
- Ruqaiyyah Siddiqui
- College of Arts and Sciences, American University of Sharjah, Sharjah, United Arab Emirates
| | - Sutherland K Maciver
- Centre for Discovery Brain Science, Edinburgh Medical School, Biomedical Sciences, University of Edinburgh, Edinburgh, UK
| | - Naveed Ahmed Khan
- Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
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18
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Larison B, Pinho GM, Haghani A, Zoller JA, Li CZ, Finno CJ, Farrell C, Kaelin CB, Barsh GS, Wooding B, Robeck TR, Maddox D, Pellegrini M, Horvath S. Epigenetic models developed for plains zebras predict age in domestic horses and endangered equids. Commun Biol 2021; 4:1412. [PMID: 34921240 PMCID: PMC8683477 DOI: 10.1038/s42003-021-02935-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 12/02/2021] [Indexed: 01/09/2023] Open
Abstract
Effective conservation and management of threatened wildlife populations require an accurate assessment of age structure to estimate demographic trends and population viability. Epigenetic aging models are promising developments because they estimate individual age with high accuracy, accurately predict age in related species, and do not require invasive sampling or intensive long-term studies. Using blood and biopsy samples from known age plains zebras (Equus quagga), we model epigenetic aging using two approaches: the epigenetic clock (EC) and the epigenetic pacemaker (EPM). The plains zebra EC has the potential for broad application within the genus Equus given that five of the seven extant wild species of the genus are threatened. We test the EC's ability to predict age in sister taxa, including two endangered species and the more distantly related domestic horse, demonstrating high accuracy in all cases. By comparing chronological and estimated age in plains zebras, we investigate age acceleration as a proxy of health status. An interaction between chronological age and inbreeding is associated with age acceleration estimated by the EPM, suggesting a cumulative effect of inbreeding on biological aging throughout life.
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Affiliation(s)
- Brenda Larison
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095, USA.
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, CA, 90095, USA.
| | - Gabriela M Pinho
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095, USA
| | - Amin Haghani
- Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Joseph A Zoller
- Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Caesar Z Li
- Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Carrie J Finno
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA
| | - Colin Farrell
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA
| | - Christopher B Kaelin
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Gregory S Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Bernard Wooding
- Quagga Project, Elandsberg Farms, Hermon, 7308, South Africa
| | - Todd R Robeck
- Zoological Operations, SeaWorld Parks and Entertainment, 7007 SeaWorld Drive, Orlando, FL, USA
| | - Dewey Maddox
- White Oak Conservation, 581705 White Oak Road, Yulee, FL, 32097, USA
| | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA
| | - Steve Horvath
- Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA.
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA.
- Altos Labs, San Diego, CA, USA.
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19
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Siddiqui R, Maciver S, Elmoselhi A, Soares NC, Khan NA. Longevity, cellular senescence and the gut microbiome: lessons to be learned from crocodiles. Heliyon 2021; 7:e08594. [PMID: 34977412 PMCID: PMC8688568 DOI: 10.1016/j.heliyon.2021.e08594] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/24/2021] [Accepted: 12/09/2021] [Indexed: 12/13/2022] Open
Abstract
Crocodiles are flourishing large-bodied ectotherms in a world dominated by endotherms. They survived the Cretaceous extinction event, that eradicated the dinosaurs who are thought to be their ancestral hosts. Crocodiles reside in polluted environments; and often inhabit water which contains heavy metals; frequent exposure to radiation; feed on rotten meat and considered as one of the hardy species that has successfully survived on this planet for millions of years. Another capability that crocodiles possess is their longevity. Crocodiles live much longer than similar-sized land mammals, sometimes living up to 100 years. But how do they withstand such harsh conditions that are detrimental to Homo sapiens? Given the importance of gut microbiome on its' host physiology, we postulate that the crocodile gut microbiome and/or its' metabolites produce substances contributing to their "hardiness" and longevity. Thus, we accomplished literature search in PubMed, Web of Science and Google Scholar and herein, we discuss the composition of the crocodile gut microbiome, longevity and cellular senescence in crocodiles, their resistance to infectious diseases and cancer, and our current knowledge of the genome and epigenome of these remarkable species. Furthermore, preliminary studies that demonstrate the remarkable properties of crocodile gut microbial flora are discussed. Given the profound role of the gut microbiome in the health of its' host, it is likely that the crocodile gut microbiome and its' metabolites may be contributing to their extended life expectancy and elucidating the underlying mechanisms and properties of these metabolites may hold clues to developing new treatments for age-related diseases for the benefit of Homo sapiens.
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Affiliation(s)
- Ruqaiyyah Siddiqui
- College of Arts and Sciences, American University of Sharjah, University City, Sharjah 26666, United Arab Emirates
| | - Sutherland Maciver
- Centre for Discovery Brain Sciences, Edinburgh Medical School: Biomedical Sciences, University of Edinburgh, Edinburgh, UK
| | - Adel Elmoselhi
- College of Medicine, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Nelson Cruz Soares
- College of Pharmacy, University of Sharjah, Sharjah, 27272, United Arab Emirates
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Naveed Ahmed Khan
- College of Medicine, University of Sharjah, Sharjah, 27272, United Arab Emirates
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20
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Heydenrych MJ, Saunders BJ, Bunce M, Jarman SN. Epigenetic Measurement of Key Vertebrate Population Biology Parameters. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.617376] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The age, sex, and sexual maturity of individual animals are key parameters in assessing wild populations and informing conservation management strategies. These parameters represent the reproductive potential of a population and can indicate recovery rates or vulnerabilities. Natural populations of wild animals are difficult to study; logistically, economically, and due to the impacts of invasive biomonitoring. Genetic and epigenetic analyses offer a low impact, low cost, and information-rich alternative. As epigenetic mechanisms are intrinsically linked with both biological aging and reproductive processes, DNA methylation can be used as a suitable biomarker for population biology study. This review assesses published research utilizing DNA methylation analysis in relation to three key population parameters: age, sex, and sexual maturity. We review studies on wild vertebrates that investigate epigenetic age relationships, with successful age estimation assays designed for mammals, birds, and fish. For both determination of sex and identification of sexual maturity, very little has been explored regarding DNA methylation-based assays. Related research, however, confirms the links between DNA methylation and these processes. Future development of age estimation assays for underrepresented and key conservation taxa is suggested, as is the experimental development and design of DNA methylation-based assays for both sex and sexual maturity identification, further expanding the genomics toolkit for population biology studies.
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21
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Lemaître JF, Rey B, Gaillard JM, Régis C, Gilot-Fromont E, Débias F, Duhayer J, Pardonnet S, Pellerin M, Haghani A, Zoller JA, Li CZ, Horvath S. DNA methylation as a tool to explore ageing in wild roe deer populations. Mol Ecol Resour 2021; 22:1002-1015. [PMID: 34665921 PMCID: PMC9297961 DOI: 10.1111/1755-0998.13533] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 09/24/2021] [Accepted: 10/11/2021] [Indexed: 12/12/2022]
Abstract
DNA methylation‐based biomarkers of ageing (epigenetic clocks) promise to lead to new insights into evolutionary biology of ageing. Relatively little is known about how the natural environment affects epigenetic ageing effects in wild species. In this study, we took advantage of a unique long‐term (>40 years) longitudinal monitoring of individual roe deer (Capreolus capreolus) living in two wild populations (Chizé and Trois‐Fontaines, France) facing different ecological contexts, to investigate the relationship between chronological age and levels of DNA methylation (DNAm). We generated novel DNA methylation data from n = 94 blood samples, from which we extracted leucocyte DNA, using a custom methylation array (HorvathMammalMethylChip40). We present three DNA methylation‐based estimators of age (DNAm or epigenetic age), which were trained in males, females, and both sexes combined. We investigated how sex differences influenced the relationship between DNAm age and chronological age using sex‐specific epigenetic clocks. Our results highlight that old females may display a lower degree of biological ageing than males. Further, we identify the main sites of epigenetic alteration that have distinct ageing patterns between the two sexes. These findings open the door to promising avenues of research at the crossroads of evolutionary biology and biogerontology.
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Affiliation(s)
- Jean-François Lemaître
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université de Lyon, Université Lyon 1, CNRS, Villeurbanne, France
| | - Benjamin Rey
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université de Lyon, Université Lyon 1, CNRS, Villeurbanne, France
| | - Jean-Michel Gaillard
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université de Lyon, Université Lyon 1, CNRS, Villeurbanne, France
| | - Corinne Régis
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université de Lyon, Université Lyon 1, CNRS, Villeurbanne, France
| | - Emmanuelle Gilot-Fromont
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université de Lyon, Université Lyon 1, CNRS, Villeurbanne, France.,Université de Lyon, VetAgro Sup, Marcy-l'Etoile, France
| | - François Débias
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université de Lyon, Université Lyon 1, CNRS, Villeurbanne, France
| | - Jeanne Duhayer
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université de Lyon, Université Lyon 1, CNRS, Villeurbanne, France
| | - Sylvia Pardonnet
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université de Lyon, Université Lyon 1, CNRS, Villeurbanne, France
| | - Maryline Pellerin
- Direction de la Recherche et de l'Appui Scientifique, Office Français de la Biodiversité, Unité Ongulés Sauvages, Gap, France
| | - Amin Haghani
- Human Genetics, David Geffen School of Medicine, University of California, Los Angeles California, USA
| | - Joseph A Zoller
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, California, USA
| | - Caesar Z Li
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, California, USA
| | - Steve Horvath
- Human Genetics, David Geffen School of Medicine, University of California, Los Angeles California, USA.,Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, California, USA
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22
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Qi H, Kinoshita K, Mori T, Matsumoto K, Matsui Y, Inoue-Murayama M. Age estimation using methylation-sensitive high-resolution melting (MS-HRM) in both healthy felines and those with chronic kidney disease. Sci Rep 2021; 11:19963. [PMID: 34620957 PMCID: PMC8497492 DOI: 10.1038/s41598-021-99424-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 09/22/2021] [Indexed: 11/12/2022] Open
Abstract
Age is an important ecological tool in wildlife conservation. However, it is difficult to estimate in most animals, including felines-most of whom are endangered. Here, we developed the first DNA methylation-based age-estimation technique-as an alternative to current age-estimation methods-for two feline species that share a relatively long genetic distance with each other: domestic cat (Felis catus; 79 blood samples) and an endangered Panthera, the snow leopard (Panthera uncia; 11 blood samples). We measured the methylation rates of two gene regions using methylation-sensitive high-resolution melting (MS-HRM). Domestic cat age was estimated with a mean absolute deviation (MAD) of 3.83 years. Health conditions influenced accuracy of the model. Specifically, the models built on cats with chronic kidney disease (CKD) had lower accuracy than those built on healthy cats. The snow leopard-specific model (i.e. the model that resets the model settings for snow leopards) had a better accuracy (MAD = 2.10 years) than that obtained on using the domestic cat model directly. This implies that our markers could be utilised across species, although changing the model settings when targeting different species could lead to better estimation accuracy. The snow leopard-specific model also successfully distinguished between sexually immature and mature individuals.
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Affiliation(s)
- Huiyuan Qi
- Wildlife Research Center, Kyoto University, Kyoto, 606-8203, Japan
| | - Kodzue Kinoshita
- Wildlife Research Center, Kyoto University, Kyoto, 606-8203, Japan
| | - Takashi Mori
- Kyoto Medical Center, Daktari Animal Hospital, Kyoto, 615-8234, Japan
| | - Kaori Matsumoto
- Kyoto Medical Center, Daktari Animal Hospital, Kyoto, 615-8234, Japan
- Miyazaki Prefectural Miyakonojo Livestock Hygiene Service Center, Miyazaki, 889-4505, Japan
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Wanner N, Larsen PA, McLain A, Faulk C. The mitochondrial genome and Epigenome of the Golden lion Tamarin from fecal DNA using Nanopore adaptive sequencing. BMC Genomics 2021; 22:726. [PMID: 34620074 PMCID: PMC8499546 DOI: 10.1186/s12864-021-08046-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 09/29/2021] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND The golden lion tamarin (Leontopithecus rosalia) is an endangered Platyrrhine primate endemic to the Atlantic coastal forests of Brazil. Despite ongoing conservation efforts, genetic data on this species remains scarce. Complicating factors include limitations on sample collection and a lack of high-quality reference sequences. Here, we used nanopore adaptive sampling to resequence the L. rosalia mitogenome from feces, a sample which can be collected non-invasively. RESULTS Adaptive sampling doubled the fraction of both host-derived and mitochondrial sequences compared to sequencing without enrichment. 258x coverage of the L. rosalia mitogenome was achieved in a single flow cell by targeting the unfinished genome of the distantly related emperor tamarin (Saguinus imperator) and the mitogenome of the closely related black lion tamarin (Leontopithecus chrysopygus). The L. rosalia mitogenome has a length of 16,597 bp, sharing 99.68% sequence identity with the L. chrysopygus mitogenome. A total of 38 SNPs between them were identified, with the majority being found in the non-coding D-loop region. DNA methylation and hydroxymethylation were directly detected using a neural network model applied to the raw signal from the MinION sequencer. In contrast to prior reports, DNA methylation was negligible in mitochondria in both CpG and non-CpG contexts. Surprisingly, a quarter of the 642 CpG sites exhibited DNA hydroxymethylation greater than 1% and 44 sites were above 5%, with concentration in the 3' side of several coding regions. CONCLUSIONS Overall, we report a robust new mitogenome assembly for L. rosalia and direct detection of cytosine base modifications in all contexts.
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Affiliation(s)
- Nicole Wanner
- Department of Animal Sciences, University of Minnesota, College of Food, Agricultural, and Natural Resource Sciences, 1988 Fitch Ave., Saint Paul, MN 55108 USA
| | - Peter A. Larsen
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN USA
| | - Adam McLain
- Department of Biology and Chemistry, College of Arts and Sciences, SUNY Polytechnic Institute, Utica, NY USA
| | - Christopher Faulk
- Department of Animal Sciences, University of Minnesota, College of Food, Agricultural, and Natural Resource Sciences, 1988 Fitch Ave., Saint Paul, MN 55108 USA
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24
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Fairfield EA, Richardson DS, Daniels CL, Butler CL, Bell E, Taylor MI. Ageing European lobsters ( Homarus gammarus) using DNA methylation of evolutionarily conserved ribosomal DNA. Evol Appl 2021; 14:2305-2318. [PMID: 34603500 PMCID: PMC8477595 DOI: 10.1111/eva.13296] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 08/15/2021] [Accepted: 08/17/2021] [Indexed: 12/30/2022] Open
Abstract
Crustaceans are notoriously difficult to age because of their indeterminate growth and the moulting of their exoskeleton throughout life. The poor knowledge of population age structure in crustaceans therefore hampers accurate assessment of population dynamics and consequently sustainable fisheries management. Quantification of DNA methylation of the evolutionarily conserved ribosomal DNA (rDNA) may allow for age prediction across diverse species. However, the rDNA epigenetic clock remains to be tested in crustaceans, despite its potential to inform both ecological and evolutionary understanding, as well as conservation and management practices. Here, patterns of rDNA methylation with age were measured across 5154 bp of rDNA corresponding to 355 quality-filtered loci in the economically important European lobster (Homarus gammarus). Across 0- to 51-month-old lobsters (n = 155), there was a significant linear relationship between age and percentage rDNA methylation in claw tissue at 60% of quality-filtered loci (n = 214). An Elastic Net regression model using 46 loci allowed for the accurate and precise age estimation of individuals (R 2 = 0.98; standard deviation = 1.6 months). Applying this ageing model to antennal DNA from wild lobsters of unknown age (n = 38) resulted in predicted ages that are concordant with estimates of minimum size at age in the wild (mean estimated age = 40.1 months; range 32.8-55.7 months). Overall, the rDNA epigenetic clock shows potential as a novel, nonlethal ageing technique for European lobsters. However, further validation is required across a wider range of known-age individuals and tissue types before the model can be used in fisheries management.
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Affiliation(s)
| | | | | | | | - Ewen Bell
- The Centre for Environment, Fisheries and Aquaculture ScienceLowestoftUK
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25
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Accurate Epigenetic Aging in Bottlenose Dolphins (Tursiops truncatus), an Essential Step in the Conservation of at-Risk Dolphins. JOURNAL OF ZOOLOGICAL AND BOTANICAL GARDENS 2021. [DOI: 10.3390/jzbg2030030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
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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26
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Mayne B, Espinoza T, Roberts D, Butler GL, Brooks S, Korbie D, Jarman S. Nonlethal age estimation of three threatened fish species using DNA methylation: Australian lungfish, Murray cod and Mary River cod. Mol Ecol Resour 2021; 21:2324-2332. [PMID: 34161658 PMCID: PMC8518777 DOI: 10.1111/1755-0998.13440] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/16/2021] [Accepted: 06/01/2021] [Indexed: 11/29/2022]
Abstract
Age‐based demography is fundamental to management of wild fish populations. Age estimates for individuals can determine rates of change in key life‐history parameters such as length, maturity, mortality and fecundity. These age‐based characteristics are critical for population viability analysis in endangered species and for developing sustainable harvest strategies. For teleost fish, age has traditionally been determined by counting increments formed in calcified structures such as otoliths. However, the collection of otoliths is lethal and therefore undesirable for threatened species. At a molecular level, age can be predicted by measuring DNA methylation. Here, we use previously identified age‐associated sites of DNA methylation in zebrafish (Danio rerio) to develop two epigenetic clocks for three threatened freshwater fish species. One epigenetic clock was developed for the Australian lungfish (Neoceratodus forsteri) and the second for the Murray cod (Maccullochellapeelii) and Mary River cod (Maccullochellamariensis). Age estimation models were calibrated using either known‐age individuals, ages derived from otoliths or bomb radiocarbon dating of scales. We demonstrate a high Pearson's correlation between the chronological and predicted age in both the Lungfish clock (cor = .98) and Maccullochella clock (cor = .92). The median absolute error rate for both epigenetic clocks was also low (Lungfish = 0.86 years; Maccullochella = 0.34 years). This study demonstrates the transferability of DNA methylation sites for age prediction between highly phylogenetically divergent fish species. Given the method is nonlethal and suited to automation, age prediction by DNA methylation has the potential to improve fisheries and other wildlife management settings.
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Affiliation(s)
- Benjamin Mayne
- Environomics Future Science Platform, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Indian Ocean Marine Research Centre, Crawley, WA, Australia
| | - Thomas Espinoza
- Department of Natural Resources, Mines and Energy, Bundaberg, Qld, Australia
| | | | - Gavin L Butler
- Department of Primary Industries, Grafton Fisheries Centre, Grafton, NSW, Australia
| | - Steven Brooks
- Department of Agriculture, Fisheries and Forestry, Brisbane, Qld, Australia
| | - Darren Korbie
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Qld, Australia
| | - Simon Jarman
- School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia
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27
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Mayne B, Berry O, Jarman S. Optimal sample size for calibrating DNA methylation age estimators. Mol Ecol Resour 2021; 21:2316-2323. [PMID: 34053192 PMCID: PMC8518423 DOI: 10.1111/1755-0998.13437] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 05/13/2021] [Accepted: 05/25/2021] [Indexed: 12/12/2022]
Abstract
Age is a fundamental parameter in wildlife management as it is used to determine the risk of extinction, manage invasive species, and regulate sustainable harvest. In a broad variety of vertebrates species, age can be determined by measuring DNA methylation. Animals with known ages are initially required during development, calibration, and validation of these epigenetic clocks. However, wild animals with known ages are frequently difficult to obtain. Here, we perform Monte‐Carlo simulations to determine the optimal sample size required to create an accurate calibration model for age estimation by elastic net regression modelling of cytosine‐phosphate‐guanine methylation data. Our results suggest a minimum calibration population size of 70, but ideally 134 individuals or more for accurate and precise models. We also provide estimates to the extent a model can be extrapolated beyond a distribution of ages that was used during calibration. The findings can assist researchers to better design age estimation models and decide if their model is adequate for determining key population attributes.
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Affiliation(s)
- Benjamin Mayne
- Environomics Future Science Platform, Indian Ocean Marine Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Crawley, WA, Australia
| | - Oliver Berry
- Environomics Future Science Platform, Indian Ocean Marine Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Crawley, WA, Australia
| | - Simon Jarman
- School of Biological Sciences, The University of Western Australia, Perth, WA, Australia
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28
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Bors EK, Baker CS, Wade PR, O'Neill KB, Shelden KEW, Thompson MJ, Fei Z, Jarman S, Horvath S. An epigenetic clock to estimate the age of living beluga whales. Evol Appl 2021; 14:1263-1273. [PMID: 34025766 PMCID: PMC8127720 DOI: 10.1111/eva.13195] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 12/22/2020] [Accepted: 12/23/2020] [Indexed: 12/20/2022] Open
Abstract
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 R 2 = 0.92 for the training data; and an R 2 = 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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Affiliation(s)
| | - C. Scott Baker
- Marine Mammal InstituteOregon State UniversityNewportORUSA
| | - Paul R. Wade
- Marine Mammal LaboratoryAlaska Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanographic and Atmospheric AdministrationSeattleWAUSA
| | | | - Kim E. W. Shelden
- Marine Mammal LaboratoryAlaska Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanographic and Atmospheric AdministrationSeattleWAUSA
| | - Michael J. Thompson
- Molecular, Cell and Developmental BiologyUniversity of California Los AngelesLos AngelesCAUSA
| | - Zhe Fei
- Department of BiostatisticsSchool of Public HealthUniversity of California‐Los AngelesLos AngelesCAUSA
| | - Simon Jarman
- School of Biological SciencesUniversity of Western AustraliaPerthWAAustralia
| | - Steve Horvath
- Department of BiostatisticsSchool of Public HealthUniversity of California‐Los AngelesLos AngelesCAUSA
- Department of Human GeneticsGonda Research CenterDavid Geffen School of MedicineLos AngelesCAUSA
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29
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Mayne B, Korbie D, Kenchington L, Ezzy B, Berry O, Jarman S. A DNA methylation age predictor for zebrafish. Aging (Albany NY) 2020; 12:24817-24835. [PMID: 33353889 PMCID: PMC7803548 DOI: 10.18632/aging.202400] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 11/30/2020] [Indexed: 12/11/2022]
Abstract
Changes in DNA methylation at specific CpG sites have been used to build predictive models to estimate animal age, predominantly in mammals. Little testing for this effect has been conducted in other vertebrate groups, such as bony fish, the largest vertebrate class. The development of most age-predictive models has relied on a genome-wide sequencing method to obtain a DNA methylation level, which makes it costly to deploy as an assay to estimate age in many samples. Here, we have generated a reduced representation bisulfite sequencing data set of caudal fin tissue from a model fish species, zebrafish (Danio rerio), aged from 11.9-60.1 weeks. We identified changes in methylation at specific CpG sites that correlated strongly with increasing age. Using an optimised unique set of 26 CpG sites we developed a multiplex PCR assay that predicts age with an average median absolute error rate of 3.2 weeks in zebrafish between 10.9-78.1 weeks of age. We also demonstrate the use of multiplex PCR as an efficient quantitative approach to measure DNA methylation for the use of age estimation. This study highlights the potential further use of DNA methylation as an age estimation method in non-mammalian vertebrate species.
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Affiliation(s)
- Benjamin Mayne
- Environomics Future Science Platform, Indian Ocean Marine Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Crawley, Western Australia, Australia
| | - Darren Korbie
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St Lucia, Queensland, Australia
| | - Lisa Kenchington
- Western Australian Zebrafish Experimental Research Centre (WAZERC), University of Western Australia, Perth, Western Australia, Australia
| | - Ben Ezzy
- Western Australian Zebrafish Experimental Research Centre (WAZERC), University of Western Australia, Perth, Western Australia, Australia
| | - Oliver Berry
- Environomics Future Science Platform, Indian Ocean Marine Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Crawley, Western Australia, Australia
| | - Simon Jarman
- School of Biological Sciences, The University of Western Australia, Perth, Western Australia, Australia
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30
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Sävilammi T, Papakostas S, Leder EH, Vøllestad LA, Debes PV, Primmer CR. Cytosine methylation patterns suggest a role of methylation in plastic and adaptive responses to temperature in European grayling ( Thymallus thymallus) populations. Epigenetics 2020; 16:271-288. [PMID: 32660325 DOI: 10.1080/15592294.2020.1795597] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Temperature is a key environmental parameter affecting both the phenotypes and distributions of organisms, particularly ectotherms. Rapid organismal responses to thermal environmental changes have been described for several ectotherms; however, the underlying molecular mechanisms often remain unclear. Here, we studied whole genome cytosine methylation patterns of European grayling (Thymallus thymallus) embryos from five populations with contemporary adaptations of early life history traits at either 'colder' or 'warmer' spawning grounds. We reared fish embryos in a common garden experiment using two temperatures that resembled the 'colder' and 'warmer' conditions of the natal natural environments. Genome-wide methylation patterns were similar in populations originating from colder thermal origin subpopulations, whereas single nucleotide polymorphisms uncovered from the same data identified strong population structure among isolated populations, but limited structure among interconnected populations. This was surprising because the previously studied gene expression response among populations was mostly plastic, and mainly influenced by the developmental temperature. These findings support the hypothesis of the magnified role of epigenetic mechanisms in modulating plasticity. The abundance of consistently changing methylation loci between two warmer-to-colder thermal origin population pairs suggests that local adaptation has shaped the observed methylation patterns. The dynamic nature of the methylomes was further highlighted by genome-wide and site-specific plastic responses. Our findings support both the presence of a plastic response in a subset of CpG loci, and the evolutionary role of methylation divergence between populations adapting to contrasting thermal environments.
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Affiliation(s)
- Tiina Sävilammi
- Department of Biology, University of Turku , Turku, Finland.,Department of Biological and Environmental Science, University of Jyväskylä , Jyväskylä, Finland
| | | | - Erica H Leder
- Department of Biology, University of Turku , Turku, Finland.,Natural History Museum, University of Oslo , Oslo, Norway
| | - L Asbjørn Vøllestad
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo , Oslo, Norway
| | - Paul V Debes
- Organismal & Evolutionary Biology Research Program, Faculty of Biological & Environmental Sciences, University of Helsinki , Helsinki, Finland.,Institute of Biotechnology, University of Helsinki , Helsinki, Finland.,Department of Aquaculture and Fish Biology, Hólar University College , Sauðárkrókur, Iceland
| | - Craig R Primmer
- Organismal & Evolutionary Biology Research Program, Faculty of Biological & Environmental Sciences, University of Helsinki , Helsinki, Finland.,Institute of Biotechnology, University of Helsinki , Helsinki, Finland
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31
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The Role of microRNAs in Organismal and Skin Aging. Int J Mol Sci 2020; 21:ijms21155281. [PMID: 32722415 PMCID: PMC7432402 DOI: 10.3390/ijms21155281] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/11/2020] [Accepted: 07/23/2020] [Indexed: 12/12/2022] Open
Abstract
The aging process starts directly after birth and lasts for the entire lifespan; it manifests itself with a decline in an organism’s ability to adapt and is linked to the development of age-related diseases that eventually lead to premature death. This review aims to explore how microRNAs (miRNAs) are involved in skin functioning and aging. Recent evidence has suggested that miRNAs regulate all aspects of cutaneous biogenesis, functionality, and aging. It has been noted that some miRNAs were down-regulated in long-lived individuals, such as let-7, miR-17, and miR-34 (known as longevity-related miRNAs). They are conserved in humans and presumably promote lifespan prolongation; conversely, they are up-regulated in age-related diseases, like cancers. The analysis of the age-associated cutaneous miRNAs revealed the increased expression of miR-130, miR-138, and miR-181a/b in keratinocytes during replicative senescence. These miRNAs affected cell proliferation pathways via targeting the p63 and Sirtuin 1 mRNAs. Notably, miR-181a was also implicated in skin immunosenescence, represented by the Langerhans cells. Dermal fibroblasts also expressed increased the levels of the biomarkers of aging that affect telomere maintenance and all phases of the cellular life cycle, such as let-7, miR-23a-3p, 34a-5p, miR-125a, miR-181a-5p, and miR-221/222-3p. Among them, the miR-34 family, stimulated by ultraviolet B irradiation, deteriorates collagen in the extracellular matrix due to the activation of the matrix metalloproteinases and thereby potentiates wrinkle formation. In addition to the pro-aging effects of miRNAs, the plausible antiaging activity of miR-146a that antagonized the UVA-induced inhibition of proliferation and suppressed aging-related genes (e.g., p21WAF-1, p16, and p53) through targeting Smad4 has also been noticed. Nevertheless, the role of miRNAs in skin aging is still not fully elucidated and needs to be further discovered and explained.
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32
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Mayne B, Berry O, Jarman S. Redefining life expectancy and maximum lifespan for wildlife management. AUSTRAL ECOL 2020. [DOI: 10.1111/aec.12931] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Benjamin Mayne
- Environomics Future Science Platform; Commonwealth Scientific and Industrial Research Organisation (CSIRO); Indian Ocean Marine Research Centre; The University of Western Australia; 64 Fairway Crawley Western Australia 6009 Australia
| | - Oliver Berry
- Environomics Future Science Platform; Commonwealth Scientific and Industrial Research Organisation (CSIRO); Indian Ocean Marine Research Centre; The University of Western Australia; 64 Fairway Crawley Western Australia 6009 Australia
| | - Simon Jarman
- School of Biological Sciences; The University of Western Australia; Crawley Western Australia Australia
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33
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Ineson KM, O’Shea TJ, Kilpatrick CW, Parise KL, Foster JT. Ambiguities in using telomere length for age determination in two North American bat species. J Mammal 2020. [DOI: 10.1093/jmammal/gyaa064] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
AbstractThe age of an animal, determined by time (chronological age) as well as genetic and environmental factors (biological age), influences the likelihood of mortality and reproduction and thus the animal’s contribution to population growth. For many long-lived species, such as bats, a lack of external and morphological indicators has made determining age a challenge, leading researchers to examine genetic markers of age for application to demographic studies. One widely studied biomarker of age is telomere length, which has been related both to chronological and biological age across taxa, but only recently has begun to be studied in bats. We assessed telomere length from the DNA of known-age and minimum known-age individuals of two bat species using a quantitative PCR assay. We determined that telomere length was quadratically related to chronological age in big brown bats (Eptesicus fuscus), although it had little predictive power for accurate age determination of unknown-age individuals. The relationship was different in little brown bats (Myotis lucifugus), where telomere length instead was correlated with biological age, apparently due to infection and wing damage associated with white-nose syndrome. Furthermore, we showed that wing biopsies currently are a better tissue source for studying telomere length in bats than guano and buccal swabs; the results from the latter group were more variable and potentially influenced by storage time. Refinement of collection and assessment methods for different non-lethally collected tissues will be important for longitudinal sampling to better understand telomere dynamics in these long-lived species. Although further work is needed to develop a biomarker capable of determining chronological age in bats, our results suggest that biological age, as reflected in telomere length, may be influenced by extrinsic stressors such as disease.
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Affiliation(s)
- Katherine M Ineson
- Natural Resources and the Environment, University of New Hampshire, Durham, NH, USA
| | - Thomas J O’Shea
- United States Geological Survey, Fort Collins Science Center, Fort Collins, CO, USA
| | | | - Katy L Parise
- Pathogen & Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Jeffrey T Foster
- Pathogen & Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
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34
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Hoekstra LA, Schwartz TS, Sparkman AM, Miller DAW, Bronikowski AM. The untapped potential of reptile biodiversity for understanding how and why animals age. Funct Ecol 2020; 34:38-54. [PMID: 32921868 PMCID: PMC7480806 DOI: 10.1111/1365-2435.13450] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 09/03/2019] [Indexed: 12/12/2022]
Abstract
1. The field of comparative aging biology has greatly expanded in the past 20 years. Longitudinal studies of populations of reptiles with a range of maximum lifespans have accumulated and been analyzed for evidence of mortality senescence and reproductive decline. While not as well represented in studies of amniote senescence, reptiles have been the subjects of many recent demographic and mechanistic studies of the biology of aging. 2. We review recent literature on reptile demographic senescence, mechanisms of senescence, and identify unanswered questions. Given the ecophysiological and demographic diversity of reptiles, what is the expected range of reptile senescence rates? Are known mechanisms of aging in reptiles consistent with canonical hallmarks of aging in model systems? What are the knowledge gaps in our understanding of reptile aging? 3. We find ample evidence of increasing mortality with advancing age in many reptiles. Testudines stand out as slower aging than other orders, but data on crocodilians and tuatara are sparse. Sex-specific analyses are generally not available. Studies of female reproduction suggest that reptiles are less likely to have reproductive decline with advancing age than mammals. 4. Reptiles share many physiological and molecular pathways of aging with mammals, birds, and laboratory model organisms. Adaptations related to stress physiology coupled with reptilian ectothermy suggest novel comparisons and contrasts that can be made with canonical aging phenotypes in mammals. These include stem cell and regeneration biology, homeostatic mechanisms, IIS/TOR signaling, and DNA repair. 5. To overcome challenges to the study of reptile aging, we recommend extending and expanding long-term monitoring of reptile populations, developing reptile cell lines to aid cellular biology, conducting more comparative studies of reptile morphology and physiology sampled along relevant life-history axes, and sequencing more reptile genomes for comparative genomics. Given the diversity of reptile life histories and adaptations, achieving these directives will likely greatly benefit all aging biology.
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Affiliation(s)
- Luke A Hoekstra
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa, 50010, USA
| | - Tonia S Schwartz
- Department of Biological Sciences, Auburn University, Auburn, Alabama 36849, USA
| | - Amanda M Sparkman
- Department of Biology, Westmont College, Santa Barbara, California, 93108, USA
| | - David A W Miller
- Department of Ecosystem Science and Management, Pennsylvania State University, University Park, PA 16802, USA
| | - Anne M Bronikowski
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa, 50010, USA
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35
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Bell CG, Lowe R, Adams PD, Baccarelli AA, Beck S, Bell JT, Christensen BC, Gladyshev VN, Heijmans BT, Horvath S, Ideker T, Issa JPJ, Kelsey KT, Marioni RE, Reik W, Relton CL, Schalkwyk LC, Teschendorff AE, Wagner W, Zhang K, Rakyan VK. DNA methylation aging clocks: challenges and recommendations. Genome Biol 2019; 20:249. [PMID: 31767039 PMCID: PMC6876109 DOI: 10.1186/s13059-019-1824-y] [Citation(s) in RCA: 410] [Impact Index Per Article: 82.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 09/16/2019] [Indexed: 12/15/2022] Open
Abstract
Epigenetic clocks comprise a set of CpG sites whose DNA methylation levels measure subject age. These clocks are acknowledged as a highly accurate molecular correlate of chronological age in humans and other vertebrates. Also, extensive research is aimed at their potential to quantify biological aging rates and test longevity or rejuvenating interventions. Here, we discuss key challenges to understand clock mechanisms and biomarker utility. This requires dissecting the drivers and regulators of age-related changes in single-cell, tissue- and disease-specific models, as well as exploring other epigenomic marks, longitudinal and diverse population studies, and non-human models. We also highlight important ethical issues in forensic age determination and predicting the trajectory of biological aging in an individual.
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Affiliation(s)
- Christopher G Bell
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK.
| | - Robert Lowe
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK.
| | - Peter D Adams
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.
- Beatson Institute for Cancer Research and University of Glasgow, Glasgow, UK.
| | - Andrea A Baccarelli
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA.
| | - Stephan Beck
- Medical Genomics, Paul O'Gorman Building, UCL Cancer Institute, University College London, London, UK.
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK.
| | - Brock C Christensen
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, NH, USA.
- Department of Molecular and Systems Biology, Geisel School of Medicine, Dartmouth College, Lebanon, NH, USA.
- Department of Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Lebanon, NH, USA.
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
| | - Bastiaan T Heijmans
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands.
| | - Steve Horvath
- Department of Human Genetics, Gonda Research Center, David Geffen School of Medicine, Los Angeles, CA, USA.
- Department of Biostatistics, School of Public Health, University of California-Los Angeles, Los Angeles, CA, USA.
| | - Trey Ideker
- San Diego Center for Systems Biology, University of California-San Diego, San Diego, CA, USA.
| | - Jean-Pierre J Issa
- Fels Institute for Cancer Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA.
| | - Karl T Kelsey
- Department of Epidemiology, Brown University, Providence, RI, USA.
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA.
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK.
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK.
| | - Wolf Reik
- Epigenetics Programme, The Babraham Institute, Cambridge, UK.
- The Wellcome Trust Sanger Institute, Cambridge, UK.
| | - Caroline L Relton
- Medical Research Council Integrative Epidemiology Unit (MRC IEU), School of Social and Community Medicine, University of Bristol, Bristol, UK.
| | | | - Andrew E Teschendorff
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China.
- UCL Cancer Institute, Paul O'Gorman Building, University College London, 72 Huntley Street, London, WC1E 6BT, UK.
| | - Wolfgang Wagner
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen Faculty of Medicine, Aachen, Germany.
| | - Kang Zhang
- Faculty of Medicine, Macau University of Science and Technology, Taipa, Macau.
| | - Vardhman K Rakyan
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK.
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Parrott BB, Bertucci EM. Epigenetic Aging Clocks in Ecology and Evolution. Trends Ecol Evol 2019; 34:767-770. [DOI: 10.1016/j.tree.2019.06.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 06/11/2019] [Accepted: 06/14/2019] [Indexed: 11/16/2022]
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Lonati GL, Howell AR, Hostetler JA, Schueller P, de Wit M, Bassett BL, Deutsch CJ, Ward-Geiger LI. Accuracy, precision, and error in age estimation of Florida manatees using growth layer groups in earbones. J Mammal 2019; 100:1350-1363. [PMID: 31379391 PMCID: PMC6660810 DOI: 10.1093/jmammal/gyz079] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 04/16/2019] [Indexed: 11/18/2022] Open
Abstract
Ages of Florida manatees (Trichechus manatus latirostris) can be estimated by counting annual growth layer groups (GLGs) in the periotic dome portion of the tympanoperiotic complex of their earbones. The Florida Fish and Wildlife Conservation Commission manages an archive of more than 8,700 Florida manatee earbones collected from salvaged carcasses from 1989 to 2017. Our goal was to comprehensively evaluate techniques used to estimate age, given this large sample size and changes to processing protocols and earbone readers over time. We developed new standards for estimating ages from earbones, involving two independent readers to obtain measurements of within- and between-reader precision. To quantify accuracy, precision, and error, 111 earbones from manatees with approximately known ages (first known as calves: “KAC”) and 69 earbones from manatees with minimum known ages (“MKA,” based on photo-identification sighting histories) were processed, and their ages were estimated. There was greater precision within readers (coefficient of variation, CV: 2.4–8.5%) than between readers (CV: 13.1–13.3%). The median of age estimates fell within the true age range for 63.1% of KAC cases and was at least the sighting duration for 75.0% of MKA cases. Age estimates were generally unbiased, as indicated by an average raw error ± SD of −0.05 ± 3.05 years for the KAC group. The absolute error (i.e., absolute value of raw error) of the KAC data set averaged 1.75 ± 2.50 years. Accuracy decreased and error increased with increasing known age, especially for animals over 15 years old, whose ages were mostly underestimated due to increasing levels of resorption (the process of bone turnover that obscures GLGs). Understanding the degree of uncertainty in age estimates will help us assess the utility of age data in manatee population models. We emphasize the importance of standardizing and routinely reviewing age estimation and processing protocols to ensure that age data remain consistent and reliable.
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Affiliation(s)
| | - Amber R Howell
- Florida Fish and Wildlife Conservation Commission, Fish and Wildlife Research Institute, St. Petersburg, FL, USA
| | - Jeffrey A Hostetler
- Florida Fish and Wildlife Conservation Commission, Fish and Wildlife Research Institute, St. Petersburg, FL, USA
| | - Paul Schueller
- Florida Fish and Wildlife Conservation Commission, Fish and Wildlife Research Institute, Gainesville, FL, USA
| | - Martine de Wit
- Florida Fish and Wildlife Conservation Commission, Fish and Wildlife Research Institute, St. Petersburg, FL, USA
| | - Brandon L Bassett
- Florida Fish and Wildlife Conservation Commission, Fish and Wildlife Research Institute, St. Petersburg, FL, USA
| | - Charles J Deutsch
- Florida Fish and Wildlife Conservation Commission, Fish and Wildlife Research Institute, Gainesville, FL, USA
- Correspondent:
| | - Leslie I Ward-Geiger
- Florida Fish and Wildlife Conservation Commission, Fish and Wildlife Research Institute, St. Petersburg, FL, USA
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38
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Bird embryos perceive vibratory cues of predation risk from clutch mates. Nat Ecol Evol 2019; 3:1225-1232. [DOI: 10.1038/s41559-019-0929-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 05/20/2019] [Indexed: 12/25/2022]
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Gavery MR, Nichols KM, Berejikian BA, Tatara CP, Goetz GW, Dickey JT, Van Doornik DM, Swanson P. Temporal Dynamics of DNA Methylation Patterns in Response to Rearing Juvenile Steelhead ( Oncorhynchus mykiss) in a Hatchery versus Simulated Stream Environment. Genes (Basel) 2019; 10:E356. [PMID: 31075961 PMCID: PMC6563097 DOI: 10.3390/genes10050356] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 05/06/2019] [Accepted: 05/07/2019] [Indexed: 12/17/2022] Open
Abstract
Genetic selection is often implicated as the underlying cause of heritable phenotypic differences between hatchery and wild populations of steelhead trout (Oncorhynchus mykiss) that also differ in lifetime fitness. Developmental plasticity, which can also affect fitness, may be mediated by epigenetic mechanisms such as DNA methylation. Our previous study identified significant differences in DNA methylation between adult hatchery- and natural-origin steelhead from the same population that could not be distinguished by DNA sequence variation. In the current study, we tested whether hatchery-rearing conditions can influence patterns of DNA methylation in steelhead with known genetic backgrounds, and assessed the stability of these changes over time. Eyed-embryos from 22 families of Methow River steelhead were split across traditional hatchery tanks or a simulated stream-rearing environment for 8 months, followed by a second year in a common hatchery tank environment. Family assignments were made using a genetic parentage analysis to account for relatedness among individuals. DNA methylation patterns were examined in the liver, a relatively homogeneous organ that regulates metabolic processes and somatic growth, of juveniles at two time points: after eight months of rearing in either a tank or stream environment and after a subsequent year of rearing in a common tank environment. Further, we analyzed DNA methylation in the sperm of mature 2-year-old males from the earlier described treatments to assess the potential of environmentally-induced changes to be passed to offspring. Hepatic DNA methylation changes in response to hatchery versus stream-rearing in yearling fish were substantial, but few persisted after a second year in the tank environment. However, the early rearing environment appeared to affect how fish responded to developmental and environmental signals during the second year since novel DNA methylation differences were identified in the livers of hatchery versus stream-reared fish after a year of common tank rearing. Furthermore, we found profound differences in DNA methylation due to age, irrespective of rearing treatment. This could be due to smoltification associated changes in liver physiology after the second year of rearing. Although few rearing-treatment effects were observed in the sperm methylome, strong family effects were observed. These data suggest limited potential for intergenerational changes, but highlight the importance of understanding the effects of kinship among studied individuals in order to properly analyze and interpret DNA methylation data in natural populations. Our work is the first to study family effects and temporal dynamics of DNA methylation patterns in response to hatchery-rearing.
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Affiliation(s)
- Mackenzie R Gavery
- University of Washington, School of Aquatic and Fishery Sciences, 1122 NE Boat St., Seattle, WA 98105, USA.
| | - Krista M Nichols
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, NOAA, 2725 Montlake Blvd. E., Seattle, WA 98112, USA.
| | - Barry A Berejikian
- Environmental and Fisheries Sciences Division, Northwest Fisheries Science Center, National Marine Fisheries Service, NOAA, 7305 Beach Dr. East, Port Orchard, WA 98366, USA.
| | - Christopher P Tatara
- Environmental and Fisheries Sciences Division, Northwest Fisheries Science Center, National Marine Fisheries Service, NOAA, 7305 Beach Dr. East, Port Orchard, WA 98366, USA.
| | - Giles W Goetz
- University of Washington, School of Aquatic and Fishery Sciences, 1122 NE Boat St., Seattle, WA 98105, USA.
| | - Jon T Dickey
- University of Washington, School of Aquatic and Fishery Sciences, 1122 NE Boat St., Seattle, WA 98105, USA.
| | - Donald M Van Doornik
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, NOAA, 7305 Beach Dr. East, Port Orchard, WA 98366, USA.
| | - Penny Swanson
- Environmental and Fisheries Sciences Division, Northwest Fisheries Science Center, National Marine Fisheries Service, NOAA, 2725 Montlake Blvd. E., Seattle, WA 98112, USA.
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40
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Takeda K, Kobayashi E, Nishino K, Imai A, Adachi H, Hoshino Y, Iwao K, Akagi S, Kaneda M, Watanabe S. Age-related changes in DNA methylation levels at CpG sites in bull spermatozoa and in vitro fertilization-derived blastocyst-stage embryos revealed by combined bisulfite restriction analysis. J Reprod Dev 2019; 65:305-312. [PMID: 31061296 PMCID: PMC6708852 DOI: 10.1262/jrd.2018-146] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Age-associated methylation changes in genomic DNA have been recently reported in spermatozoa, and these changes can contribute to decline in fertility. In a previous study, we analyzed the
genome-wide DNA methylation profiles of bull spermatozoa using a human DNA methylation microarray and identified one CpG site (CpG-1) that potentially reflects age-related methylation
changes. In the present study, cryopreserved semen samples from a Japanese Black bull were collected at five different ages, which were referred to as JD1-5: 14, 19, 28, 54, and 162 months,
respectively, and were used for genome-wide DNA methylation analysis and in vitro fertilization (IVF). Distinct age-related changes in methylation profiles were observed,
and 77 CpG sites were found to be differently methylated between young and adult samples (JD1-2 vs. JD4-5). Using combined bisulfite restriction analysis (COBRA), nine CpG
sites (including CpG-1) were confirmed to exhibit significant differences in their age-dependent methylation levels. Eight CpG sites showed an age-dependent increase in their methylation
levels, whereas only one site showed age-dependent hypomethylation; in particular, these changes in methylation levels occurred rapidly at a young age. COBRA revealed low methylation levels
in some CpG regions in the majority of the IVF blastocyst-stage embryos derived from spermatozoa at JD2-5. Interestingly, bulls with different ages did not show differences in their
methylation levels. In conclusion, our findings indicated that methylation levels at nine CpG sites in spermatozoa changed with increasing age and that some CpG regions were demethylated
after fertilization. Further studies are required to determine whether age-dependent different methylation levels in bull spermatozoa can affect fertility.
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Affiliation(s)
- Kumiko Takeda
- Institute of Livestock and Grassland Science, NARO, Ibaraki 305-0901, Japan
| | - Eiji Kobayashi
- Institute of Livestock and Grassland Science, NARO, Ibaraki 305-0901, Japan
| | - Kagetomo Nishino
- Beef Cattle Institute, Ibaraki Prefectural Livestock Research Center, Ibaraki 319-2224, Japan
| | - Akira Imai
- Hiroshima Prefectural Livestock Technology Research Center, Hiroshima 739-0151, Japan
| | - Hiromichi Adachi
- Hida Beef Cattle Research, Gifu Prefectural Livestock Research Institute, Gifu 506-0101, Japan
| | - Yoichiro Hoshino
- Hida Beef Cattle Research, Gifu Prefectural Livestock Research Institute, Gifu 506-0101, Japan.,Kyoto University, Kyoto 622-0203, Japan
| | - Ken Iwao
- Tottori Prefectural Livestock Research Institute, Tottori 689-2503, Japan
| | - Satoshi Akagi
- Institute of Livestock and Grassland Science, NARO, Ibaraki 305-0901, Japan
| | - Masahiro Kaneda
- Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan
| | - Shinya Watanabe
- Institute of Livestock and Grassland Science, NARO, Ibaraki 305-0901, Japan
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41
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Saino N, Albetti B, Ambrosini R, Caprioli M, Costanzo A, Mariani J, Parolini M, Romano A, Rubolini D, Formenti G, Gianfranceschi L, Bollati V. Inter-generational resemblance of methylation levels at circadian genes and associations with phenology in the barn swallow. Sci Rep 2019; 9:6505. [PMID: 31019206 PMCID: PMC6482194 DOI: 10.1038/s41598-019-42798-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 03/25/2019] [Indexed: 12/16/2022] Open
Abstract
Regulation of gene expression can occur via epigenetic effects as mediated by DNA methylation. The potential for epigenetic effects to be transmitted across generations, thus modulating phenotypic variation and affecting ecological and evolutionary processes, is increasingly appreciated. However, the study of variation in epigenomes and inter-generational transmission of epigenetic alterations in wild populations is at its very infancy. We studied sex- and age-related variation in DNA methylation and parent-offspring resemblance in methylation profiles in the barn swallows. We focused on a class of highly conserved ‘clock’ genes (clock, cry1, per2, per3, timeless) relevant in the timing of activities of major ecological importance. In addition, we considerably expanded previous analyses on the relationship between methylation at clock genes and breeding date, a key fitness trait in barn swallows. We found positive assortative mating for methylation at one clock locus. Methylation varied between the nestling and the adult stage, and according to sex. Individuals with relatively high methylation as nestlings also had high methylation levels when adults. Extensive parent-nestling resemblance in methylation levels was observed. Occurrence of extra-pair fertilizations allowed to disclose evidence hinting at a prevalence of paternal germline or sperm quality effects over common environment effects in generating father-offspring resemblance in methylation. Finally, we found an association between methylation at the clock poly-Q region, but not at other loci, and breeding date. We thus provided evidence for sex-dependent variation and the first account of parent-offspring resemblance in methylation in any wild vertebrate. We also showed that epigenetics may influence phenotypic plasticity of timing of life cycle events, thus having a major impact on fitness.
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Affiliation(s)
- Nicola Saino
- Department of Environmental Science and Policy, University of Milan, via Celoria 26, I-20133, Milan, Italy.
| | - Benedetta Albetti
- Department of Clinical Sciences and Community Health, via S. Barnaba 8, I-20122, Milan, Italy
| | - Roberto Ambrosini
- Department of Environmental Science and Policy, University of Milan, via Celoria 26, I-20133, Milan, Italy
| | - Manuela Caprioli
- Department of Environmental Science and Policy, University of Milan, via Celoria 26, I-20133, Milan, Italy
| | - Alessandra Costanzo
- Department of Environmental Science and Policy, University of Milan, via Celoria 26, I-20133, Milan, Italy
| | - Jacopo Mariani
- Department of Clinical Sciences and Community Health, via S. Barnaba 8, I-20122, Milan, Italy
| | - Marco Parolini
- Department of Environmental Science and Policy, University of Milan, via Celoria 26, I-20133, Milan, Italy
| | - Andrea Romano
- Department of Environmental Science and Policy, University of Milan, via Celoria 26, I-20133, Milan, Italy.,Department of Ecology and Evolution, University of Lausanne, Building Biophore, CH-1015, Lausanne, Switzerland
| | - Diego Rubolini
- Department of Environmental Science and Policy, University of Milan, via Celoria 26, I-20133, Milan, Italy
| | - Giulio Formenti
- Department of Environmental Science and Policy, University of Milan, via Celoria 26, I-20133, Milan, Italy
| | - Luca Gianfranceschi
- Department of Biosciences, University of Milan, via Celoria 26, I-20133, Milan, Italy
| | - Valentina Bollati
- Department of Clinical Sciences and Community Health, via S. Barnaba 8, I-20122, Milan, Italy.
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42
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Guevara EE, Lawler RR. Epigenetic Clocks. Evol Anthropol 2018; 27:256-260. [PMID: 30383910 DOI: 10.1002/evan.21745] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Revised: 07/11/2018] [Accepted: 08/06/2018] [Indexed: 12/15/2022]
Abstract
Recent research has revealed clock-like patterns of epigenetic change across the life span in humans. Models describing these epigenetic changes have been dubbed "epigenetic clocks," and they can not only predict chronological age but also reveal biological age, which measures physiological homeostasis and deterioration over the life span. Comparative studies of the epigenetic clocks of different primate species are likely to provide insights into the evolution of life history schedules, as well as shed light on the physiological and genetic bases of aging and aging-related diseases. Chronological age estimation using clock-based calculators may also offer biological anthropologists a useful tool for applying to forensic and demographic studies.
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Affiliation(s)
- Elaine E Guevara
- Department of Anthropology, Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, District of Columbia.,Department of Anthropology, Yale University, New Haven, Connecticut
| | - Richard R Lawler
- Department of Sociology and Anthropology, James Madison University, Harrisonburg, Virginia
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43
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Mendelsohn AR, Larrick JW. Epigenetic Drift Is a Determinant of Mammalian Lifespan. Rejuvenation Res 2018; 20:430-436. [PMID: 28942711 DOI: 10.1089/rej.2017.2024] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The epigenome, which controls cell identity and function, is not maintained with 100% fidelity in somatic animal cells. Errors in the maintenance of the epigenome lead to epigenetic drift, an important hallmark of aging. Numerous studies have described DNA methylation clocks that correlate epigenetic drift with increasing age. The question of how significant a role epigenetic drift plays in creating the phenotypes associated with aging remains open. A recent study describes a new DNA methylation clock that can be slowed by caloric restriction (CR) in a way that correlates with the degree of lifespan and healthspan extension conferred by CR, suggesting that epigenetic drift itself is a determinant of mammalian lifespan. Genetic transplantation using genomic editing of DNA methylation homeostatic genes from long-lived to short-lived species is one way to potentially demonstrate a causative role for DNA methylation. Whether the DNA methylation clock be reset to youthful state, eliminating the effects of epigenetic drift without requiring a pluripotent cell intermediate is a critical question with profound implications for the development of aging therapeutics. Methods that transiently erase the DNA methylation pattern of somatic cells may be developed that reset this aging hallmark with potentially profound effects on lifespan, if DNA methylation-based epigenetic drift really plays a primary role in aging.
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Affiliation(s)
- Andrew R Mendelsohn
- 1 Regenerative Sciences Institute , Sunnyvale, California.,2 Panorama Research Institute , Sunnyvale, California
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44
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Soulsbury CD, Lipponen A, Wood K, Mein CA, Hoffman JI, Lebigre C. Age- and quality-dependent DNA methylation correlate with melanin-based coloration in a wild bird. Ecol Evol 2018; 8:6547-6557. [PMID: 30038756 PMCID: PMC6053554 DOI: 10.1002/ece3.4132] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 03/16/2018] [Accepted: 03/29/2018] [Indexed: 12/11/2022] Open
Abstract
Secondary sexual trait expression can be influenced by fixed individual factors (such as genetic quality) as well as by dynamic factors (such as age and environmentally induced gene expression) that may be associated with variation in condition or quality. In particular, melanin-based traits are known to relate to condition and there is a well-characterized genetic pathway underpinning their expression. However, the mechanisms linking variable trait expression to genetic quality remain unclear. One plausible mechanism is that genetic quality could influence trait expression via differential methylation and differential gene expression. We therefore conducted a pilot study examining DNA methylation at a candidate gene (agouti-related neuropeptide: AgRP) in the black grouse Lyrurus tetrix. We specifically tested whether CpG methylation covaries with age and multilocus heterozygosity (a proxy of genetic quality) and from there whether the expression of a melanin-based ornament (ultraviolet-blue chroma) correlates with DNA methylation. Consistent with expectations, we found clear evidence for age- and heterozygosity-specific patterns of DNA methylation, with two CpG sites showing the greatest DNA methylation in highly heterozygous males at their peak age of reproduction. Furthermore, DNA methylation at three CpG sites was significantly positively correlated with ultraviolet-blue chroma. Ours is the first study to our knowledge to document age- and quality-dependent variation in DNA methylation and to show that dynamic sexual trait expression across the lifespan of an organism is associated with patterns of DNA methylation. Although we cannot demonstrate causality, our work provides empirical support for a mechanism that could potentially link key individual factors to variation in sexual trait expression in a wild vertebrate.
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Affiliation(s)
| | - Anssi Lipponen
- Department of Biological and Environmental ScienceUniversity of JyväskyläFinland
- A. I. Virtanen Institute for Molecular SciencesUniversity of Eastern FinlandKuopioFinland
| | - Kristie Wood
- The Genome Centre, Barts and The London School of Medicine and DentistryQueen Mary University of LondonLondonUK
| | - Charles A. Mein
- The Genome Centre, Barts and The London School of Medicine and DentistryQueen Mary University of LondonLondonUK
| | - Joseph I. Hoffman
- Department of Animal BehaviourUniversity of BielefeldBielefeldGermany
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45
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Mendelsohn AR, Larrick JW. Telomerase May Paradoxically Accelerate Aging of the DNA Methylome. Rejuvenation Res 2018; 21:168-172. [DOI: 10.1089/rej.2018.2073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Affiliation(s)
- Andrew R. Mendelsohn
- Panorama Research Institute, Sunnyvale, California
- Regenerative Sciences Institute, Sunnyvale, California
| | - James W. Larrick
- Panorama Research Institute, Sunnyvale, California
- Regenerative Sciences Institute, Sunnyvale, California
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46
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Declerck K, Vanden Berghe W. Back to the future: Epigenetic clock plasticity towards healthy aging. Mech Ageing Dev 2018; 174:18-29. [PMID: 29337038 DOI: 10.1016/j.mad.2018.01.002] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Revised: 01/08/2018] [Accepted: 01/10/2018] [Indexed: 12/22/2022]
Abstract
Aging is the most important risk factor for major human lifestyle diseases, including cancer, neurological and cardiometabolic disorders. Due to the complex interplay between genetics, lifestyle and environmental factors, some individuals seem to age faster than others, whereas centenarians seem to have a slower aging process. Therefore, a biochemical biomarker reflecting the relative biological age would be helpful to predict an individual's health status and aging disease risk. Although it is already known for years that cumulative epigenetic changes occur upon aging, DNA methylation patterns were only recently used to construct an epigenetic clock predictor for biological age, which is a measure of how well your body functions compared to your chronological age. Moreover, the epigenetic DNA methylation clock signature is increasingly applied as a biomarker to estimate aging disease susceptibility and mortality risk. Finally, the epigenetic clock signature could be used as a lifestyle management tool to monitor healthy aging, to evaluate preventive interventions against chronic aging disorders and to extend healthy lifespan. Dissecting the mechanism of the epigenetic aging clock will yield valuable insights into the aging process and how it can be manipulated to improve health span.
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Affiliation(s)
- Ken Declerck
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp (UA), Belgium
| | - Wim Vanden Berghe
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp (UA), Belgium.
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