Age estimation in fishes using epigenetic clocks: Applications to fisheries management and conservation biology

Frontiers in Marine Science, Journal Year: 2023, Volume and Issue: 10

Published: Jan. 30, 2023

The distribution of age classes is a key demographic parameter populations and thus proper estimation crucial for fisheries management conservation biology. Age in fishes has traditionally relied on the analysis growth marks hard structures such as otoliths. However, besides being lethal this method time-consuming, can have low accuracy some species cannot be applied others. Thus, there need development new methods. DNA methylation an epigenetic modification consisting addition methyl group cytosine-guanine loci. Aging associated with changes methylation. Among background global weak genome hypomethylation, are loci which age-associated “clock-like” nature predictable. Chronological estimators built from termed ‘epigenetic clocks’. Epigenetic clocks been developed last ten years many species, notably vertebrates, including already several fish species. Here, we review piscine so far outline major considerations to taken into account additional include number samples collected tissues targeted. steps how develop clock techniques available do also discussed. Next, focus features measuring devices, considering aspects accuracy, precision reproducibility. Finally, discuss possibility developing multi-species processing automation greatly reduce cost per sample. One important knowledge gap determine environmental changes, especially temperature food availability, may affect tick rate clocks. Improved prediction through use contribute better practices context overexploited stocks worldwide, endangered

Language: Английский

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Environmental DNA Epigenetics Accurately Predicts the Age of Cultured Fish Larvae

Ecology and Evolution, Journal Year: 2025, Volume and Issue: 15(2)

Published: Feb. 1, 2025

ABSTRACT While acquiring age information is crucial for efficient stock management and biodiversity conservation, traditional aging methods fail to offer a universal, non‐invasive, precise way of estimating wild animal's age. DNA methylation from tissue (tDNA) was recently proposed as method overcome these issues showed more accurate results than telomere‐length‐based assessments. Here, we used environmental (eDNA) the first time template estimation, focusing on larval phase (10–24 days post‐hatch) cultured Dicentrarchus labrax (seabass), species major economic conservation interest. Using third‐generation sequencing, were able directly detect various modification types (e.g., cytosine adenosine in all contexts) across whole genome using amplification‐free nanopore sequencing. However, sites only present mitogenome, which could be specific feature eDNA or consequence better protection within mitochondria. By considering qualitative quantitative about according an objective model selection framework, our epigenetic clock reached cross‐validated accuracy 2.6 (Median Absolute Error). Such performances are higher those previous clocks, notably adult seabass even when scaling MAE range, linked dynamic epigenome during early life stages. Overall, pilot study proposes new determine potential simultaneous assessments, although robust validation preliminary along with methodological developments needed before field applications can envisaged.

Language: Английский

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Epigenetic age estimation in a long-lived, deepwater scorpionfish: insights into epigenetic clock development

Canadian Journal of Fisheries and Aquatic Sciences, Journal Year: 2024, Volume and Issue: 81(5), P. 620 - 631

Published: Feb. 14, 2024

Age estimates are essential for fisheries assessment and management, but deepwater (>200 m) fishes often difficult to age using traditional techniques. Therefore, age-predictive epigenetic clocks were developed a model reef fish, blackbelly rosefish Helicolenus dactylopterus, two tissue types (fin clips muscle; n = 61 individuals; 9−60 years) Δ 14 C-validated consensus estimates. The influence of biological information (length sex) on clock accuracy, the potential developing multi-tissue clock, also assessed. Bisulfite-converted restriction site-associated DNA sequencing (bsRADseq) was used identify CpG sites (cytosines followed by guanines) exhibiting age-correlated methylation, showed strong agreement ( R 2 > 0.98) between predicted ages. Including length sex data enhanced accuracy precision 0.99; mean absolute error < 1 year). Age-associated identified across tissues, performed poorly relative single-tissue clocks. Overall, results demonstrate that accurate precise can be fishes, inclusion may enhance precision.

Language: Английский

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Assessment of Age and Growth in Fishes

Fishes, Journal Year: 2023, Volume and Issue: 8(10), P. 479 - 479

Published: Sept. 26, 2023

Fish are the largest and most diverse group of vertebrates [...]

Language: Английский

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Accurate, non-destructive, and high-throughput age estimation for Golden perch (Macquaria ambigua spp.) using DNA methylation

Scientific Reports, Journal Year: 2023, Volume and Issue: 13(1)

Published: June 12, 2023

Abstract Age structure information of animal populations is fundamental to their conservation and management. In fisheries, age routinely obtained by counting daily or annual increments in calcified structures (e.g., otoliths) which requires lethal sampling. Recently, DNA methylation has been shown estimate using extracted from fin tissue without the need kill fish. this study we used conserved known age-associated sites zebrafish ( Danio rerio ) genome predict golden perch Macquaria ambigua ), a large-bodied native fish eastern Australia. Individuals aged validated otolith techniques across species’ distribution were calibrate three epigenetic clocks. One clock was calibrated (daily clock) another with (annual increment counts, respectively. A third both (universal clock). We found high correlation between (Pearson > 0.94) all The median absolute error 2.4 days clock, 184.6 74.5 universal clock. Our demonstrates emerging utility clocks as non-lethal high-throughput tools for obtaining estimates support management fisheries.

Language: Английский

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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

Molecular Ecology Resources, Journal Year: 2024, Volume and Issue: 24(3)

Published: Jan. 18, 2024

Abstract Individual age can be used to design more efficient and suitable management plans in both situ ex conservation programmes for targeted wildlife species. DNA methylation is a promising marker of epigenetic ageing that accurately estimate from small amounts biological material, which collected minimally invasive manner. In this study, we sequenced five genetic regions 8–23 selected CpG sites build estimation models using machine learning methods at only about $3–7 per sample. Blood samples seven Felidae species were used, ranging big, domestic endangered species: cats ( Felis catus , 139 samples), Tsushima leopard Prionailurus bengalensis euptilurus 84 samples) Panthera (96 samples). The achieved satisfactory accuracy, with the mean absolute error most accurate recorded 1.966, 1.348 1.552 years cats, spp. respectively. We developed applicable individuals regardless health conditions; therefore, these are diverse characteristics, often case conservation. also showed possibility developing universal two regions. do not recommend building common model all target our markers, because degraded performance included

Language: Английский

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The role of DNA methylation in facilitating life history trait diversity in fishes

Reviews in Fish Biology and Fisheries, Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 10, 2024

Language: Английский

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Artificial Intelligence-Based Modeling for Sustainable Management of Fish Genetic Resources: Status and Opportunities

Published: Jan. 1, 2024

Language: Английский

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Noninvasive, epigenetic age estimation in an elasmobranch, the cownose ray (Rhinoptera bonasus)

Scientific Reports, Journal Year: 2024, Volume and Issue: 14(1)

Published: Nov. 1, 2024

Age data are essential for estimating life history parameters and thus critical population assessment, management, conservation. Traditional vertebrae-based age estimation in elasmobranchs can be costly, time intensive, of low accuracy, is by necessity lethal. Herein, epigenetic clocks were developed an elasmobranch, the cownose ray (Rhinoptera bonasus), using aquarium-born individuals (n = 42) with known dates birth (age range: 7-7,878 days or 0-21 years) two tissue types (fin clips whole blood) that sampled a relatively non-invasive manner. Enzymatically-converted restriction site-associated DNA sequencing (ECrad-seq) was used to identify CpG sites exhibited age-correlated methylation. The highly accurate (mean absolute error, MAE, < 0.75 precise (R

Language: Английский

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Aquatic Animal Nutrition: Plant Preparations—‘Ever Tried. Ever Failed. Try Again.’

Published: Jan. 1, 2024

Language: Английский

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