Beyond 2020 >> Work packages >> Genetic Architecture

Genetic Architecture

Responses in the genetic architecture of sentinel species (eel and stickleback) to climate variability.

The tasks in this work package are designed to examine evolutionary responses to climate variability in respect of sex determination and ecotype in eel and the fitness effects of hybridisation on
population sympatry, productivity and ecosystem engineering in respect of stickleback. There is also a large project enabling element in this work package for other work packages providing material for biogeochemical analyses (DKIT; DCU; NUIM), metagenomics (UCD; QUB) and microbiome (UoG) studies.

WT 1 The Burrishoole eel population will be sampled at different ages, ecotypes, stages of sexual development, life history stages and times of the year from different locations within the Burrishoole ecosystem complex and the samples passed on to QUB for exploratory genomic analysis (genome, transcriptome, epigenome). Laboratory protocols (e.g. library construction and bioinformatics pipeline for subsequent analyses) and associated infrastructure (e.g. Qubit fluorimeter for DNA quantitation, Advanced Analytical Fragment Analyser for quantitative and qualitative analysis of DNA/RNA inputs before NGS library preparation and quantification of resulting libraries, illumina MiSeq and Nexseq500 – medium and high throughput platforms for next generation sequencing, will be put in place. Genome-wide signatures of DNA methylation data (i.e. epigenome profiles) will be generated using the methylated DNA immune-precipitation sequencing (MeDIP-Seq) approach using a Diagenode platform (Diagenode IP-star) and related essay kits following manufactures protocols, which include NGS library preparation.

WT 2 A reciprocal transfer common garden experiment will be established to assess the relative fitness of stickleback F1 hybrids relative to parental types in contrasting (semi-natural) freshwater and salt water environments. Samples collected at different stages of the experiment will be provided to QUB to facilitate parentage assignment of sampled animals and to undertake genome wide scans of experimental fish to identify those areas affected by and resistant to hybridisation.

WT 3 As part of this WT we will design a programme of seasonal biological and environmental sampling will be undertaken to provide material for biogeochemical, metagenomics, microbiome investigations. In respect of the metagenomic paleo- studies long sediment cores will be recovered using a Tapper corer and will be radiometrically (14C, 210Pb, 137Cs) dated. The core samples will be preserved for eDNA analysis in a -80 oC freezer. The
collection and dating of the cores will be co-ordinated by Dr Catherine Dalton of Mary I Institute, Limerick. Note 14C dating cannot be applied to organic material that is younger than ~200 years. The sediment cores will be collected on a once off basis in month 6.

WT 4 The aerobic scope of eel, stickleback, trout and salmon will be estimated by acquiring measurements of standard metabolic rate (SMR) and maximum metabolic rate (MMR) using flow respirometry of fish at different times of the year and from different ecosystems in order to get estimate of capacity of fish species to utilise food items at different times of the year and inform on bio-energetic potential of fish to use utilise food items. Aerobic scope in candidate fish will commence in month 3 and continue on a biannual basis until the end of the project in month 48.

This work package will deliver three radio-carbon dated cores D4: temporally explicit profile of variation in aquatic biodiversity including eDNA salmon and trout proxies from Loughs, Furnace, Feeagh and Bunaveela D4.2; a taxonomic profile (baseline) of contemporaneous food webs associated with the fish communities in Loughs, Furnace, Feeagh and Bunaveela D7.1; eel genome, transcriptome and epigenome genotypes D7.2; a common garden experiment for stickle back with estimates of ecotype fitness in contrasting environments D7.3; seasonally relevant biological and environmental samples collected from the Burrishoole ecosystem complex D7.4; Measures of aerobic scope for a variety of fish species, sympatric populations, ecotypes D7.5.