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Title: Genomic analysis of shifts in life history traits in the Trinidadian guppy, Poecilia reticulata
Author: Perry, Hazel
ISNI:       0000 0004 5915 0951
Awarding Body: Prifysgol Bangor University
Current Institution: Bangor University
Date of Award: 2015
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It is widely accepted that size selective mortality induced by commercial fishing can and does cause changes in life history traits that include shifts in maturation age, growth rate and body size. However, whether these changes are the result of fisheries induced evolution (genetic change) or phenotypic plasticity is still unclear. Moreover, where evolution is rapid, epigenetic or regulatory change has also been found to drive major shifts in life history change. To examine the genetic and phenotypic response to size selective harvesting, a previous study (van Wijk 2011a) subjected guppies to divergent size-specific selection. Following selection, a significant difference in both body size and age at maturation was identified as well as signatures of selection at five candidate loci. The project described here utilised these selection lines to examine the genome wide factors contributing to such life history shifts. To assess the genome wide response to size selective harvesting, RAD sequencing was employed to identify and type large numbers of SNPs in individuals from the selection lines, as well as individuals from the generation prior to selection. Significant and consistent signs of selection were identified at 37 SNPs, the majority of which were located on the sex chromosome. The results showed that, in addition to previously observed genetic change, additional regions of the guppy genome responded to, and were associated with, observed phenotypic shifts. Variation in the level of predation in wild populations creates variation in life history traits similar to those seen after size selective harvesting. We therefore examined the 37 SNPs identified by the RAD sequencing of the selected lines in 18 populations of wild guppy. No consistent signs of selection were identified in these wild populations, suggesting that the genetic architecture underpinning variation in life history traits in the guppy varies in different populations. To determine the role of epigenetic change the focus has been on DNA methylation. In order to assess the levels of DNA methylation a technique known as methylation sensitive AFLP has been used. Using this technique, comparisons of the level of DNA methylation between both the selection lines and the before and after selection fish were made as well as comparisons in the levels of DNA methylation between a range of tissue types from the guppy. Results showed that patterns of DNA methylation differ significantly between different tissues in the guppy. Genome wide patterns of genome wide methylation did not differ significantly between the selection lines, however locus-specific variation in DNA methylation was identified.
Supervisor: Carvalho, Gary Sponsor: Not available
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
EThOS ID:  DOI: Not available