Ageing European lobsters (Homarus gammarus) using DNA methylation of evolutionarily conserved ribosomal DNA

Fairfield, Eleanor, Richardson, David S. ORCID:, Daniels, Carly, Butler, Christopher, Bell, Ewen D. and Taylor, Martin ORCID: (2021) Ageing European lobsters (Homarus gammarus) using DNA methylation of evolutionarily conserved ribosomal DNA. Evolutionary Applications, 14 (9). pp. 2305-2318. ISSN 1752-4563

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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.

Item Type: Article
Additional Information: Acknowledgements: With sincere thanks to Jake Scolding and the staff of the National Lobster Hatchery and Cornwall Inshore Fisheries and Conservation Authority for providing the lobster samples and Emily Putnam, Kai Chang and technicians at Zymo Research for delivering the bisulphite sequencing service. This work was supported by the UKRI Biotechnology and Biological Sciences Research Council Norwich Research Park Biosciences Doctoral Training Partnership [Grant number BB/M011216/1] and the Seafood Innovation Fund [Project numbers FS017 and RD051).
Uncontrolled Keywords: dna methylation,chronological age,epigenetic clock,fisheries,lobster,ribosomal dna,ecology, evolution, behavior and systematics,genetics,agricultural and biological sciences(all) ,/dk/atira/pure/subjectarea/asjc/1100/1105
Faculty \ School: Faculty of Science > School of Biological Sciences
UEA Research Groups: Faculty of Science > Research Groups > Collaborative Centre for Sustainable Use of the Seas
Faculty of Science > Research Groups > Organisms and the Environment
Faculty of Science > Research Centres > Centre for Ecology, Evolution and Conservation
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Depositing User: LivePure Connector
Date Deposited: 16 Sep 2021 11:16
Last Modified: 08 Mar 2024 15:32
DOI: 10.1111/eva.13296


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