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.
Highlights
Knowledge of the age structure of animal populations is fundamental to understanding their ecology, evolution and conservation (Jarman et al, 2015; De Paoli-Iseppi et al, 2017)
RT-Polymerase chain reactions (PCRs) were deemed successful if the following criteria were met: average crossing point (Cp) values were less than 40, duplicate Cp values did not differ by more than one, the plateau phase was reached before the run ended at cycle 45, melting curves were in the expected range for PCR products, and duplicates had calculated primer melting temperatures within 10% of the coefficient of variation (CV)
This study investigated whether patterns of CpG methylation in ribosomal DNA (rDNA) could be used to estimate age in European lobsters
Summary
Knowledge of the age structure of animal populations is fundamental to understanding their ecology, evolution and conservation (Jarman et al, 2015; De Paoli-Iseppi et al, 2017). Many animals lack such characteristics and accurate age estimates are often only attainable through expensive tracking or marking studies (De Paoli-Iseppi et al, 2019) These approaches are not practical for many species, especially those that are long lived or inhabit environments that are difficult to access. Molecular markers of age have generated interest among those looking to develop affordable, accurate, non-lethal and minimally-invasive methods for estimating animal age (Jarman et al, 2015; De Paoli-Iseppi et al, 2017). These involve measuring a feature of an individual’s DNA or RNA, or associated molecules, that changes consistently over time. This study is the first to investigate the applicability of site-specific, DNA methylation-based markers for age estimation in crustaceans
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