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

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 5,154 bp of rDNA corresponding to 355 quality filtered
loci in the economically-important European lobster (Hommarus gammarus).
Across 0–51 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 (R2 = 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, with a mean age of 40.07 months (range 32.8 -
55.65 months).  Overall, the rDNA epigenetic clock shows
potential as a novel, non-lethal 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 an applied scenario.