Ageing the unageable: investigating novel methods of ageing crustaceans

Fairfield, Eleanor (2020) Ageing the unageable: investigating novel methods of ageing crustaceans. Doctoral thesis, University of East Anglia.

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Crustaceans are extremely difficult to age because of their indeterminate and variable growth, and the moulting of their exoskeleton throughout life. The consequent lack of data on the age structure of populations makes it impossible to reliably predict population dynamics and viability for sustainable fisheries management. The aim of this thesis was to investigate whether crustacean age can be estimated using novel, molecular markers. Three potential markers of age were investigated in laboratory-reared cohorts of red cherry shrimp (Neocaridina davidi) and/or the economically-important European lobster (Homarus gammarus). First, genome-wide levels of methylation were quantified using a commercially-available, immunoassay-based kit. While the poor reliability afforded by the kit undermined comparisons, there was low variation in global DNA methylation among age groups of lobsters and shrimp. Second, bisulphite sequencing was used to measure site-specific methylation across 5,154 bp of ribosomal DNA sequence in lobsters that ranged in known age from 0–2 years old. A model based on the ten ‘best’ loci predicted lobster age with high accuracy and precision (ca. 2 months). Finally, the full mitochondrial genomes of lobsters and shrimp were sequenced to high depth using next-generation sequencing. In shrimp, the number of mitochondrial DNA (mtDNA) mutations across 39% of the genome did not differ among seven age groups spanning 54% of the species’ lifespan. Sequencing data from the remaining shrimp mitochondrial genome were confounded by probable co-amplification of nuclear DNA of mitochondrial origin (NUMTs). In lobsters, the entire mitochondrial sequencing dataset was confounded by mis-mapping of reads across a duplicated region and likely co-amplification of NUMTs. A range of bioinformatic approaches aimed at removing erroneous sequencing reads was attempted. After thorough filtering of potential false positives, no difference in the number of mtDNA mutations was observed among six lobster age groups. In summary, mtDNA mutation accumulation and genome-wide methylation (at least when measured using the method adopted in this thesis) can be ruled out as viable markers of crustacean age. Conversely, patterns of loci-specific ribosomal DNA methylation show considerable promise as a future tool for crustacean ageing.

Item Type: Thesis (Doctoral)
Faculty \ School: Faculty of Science > School of Biological Sciences
Depositing User: Chris White
Date Deposited: 21 Apr 2021 12:54
Last Modified: 21 Apr 2021 12:54


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