Molecular aquatic studies

Question 1

What is an example of a simple molecular tool?

Answer 1

CO1 region Conserved mtDNA in aerobic organism. Evolves fast and is easy to amplify.

650bp sequence is effective as a universal DNA barcode.

Question 2

Describe the next molecular tool

Answer 2

Multi-locus genotype data from variable genetic markers
Discovery via broad sequencing. Developed to targeted amplification via specific primers
Intra-specific or closely related species. Shared alleles link individuals to populations/families

Question 3

Describe different population levels

Answer 3

One population: panmixia
Two: broad scale structure
Three: finescale structure

Question 4

Give an example of multi-locus genotype data

Answer 4

Microsatellites replaced by SNPs for population analysis.
Many alleles per locus = greater exclusion probability = great for relatedness.
Biparental inheritenace means one allele per locus per parent.

Question 5

Describe the next method of molecular tools

Answer 5

Whole genome sequencing
Creates an index of genes and their known purposes, however there is a variety in resource quality.
Can be used as a reference and can pinpoint where variants occur - structureal variation.

Quantify RNA and align back to genomic region to asses up- and down-regulation of genes

Question 6

Describe genetic assignment tools

Answer 6

Restriction site associated DNA sequencing
sbf1 restriction enzyme cuts DNA.
Sequences include many thousands of SNP loci; diversity in allele frequencies can depict wide-range population structure.

Filtering of SNPs with allele frequencies is associated to differentiation.
Develop loci into genotyping assays. Fluorescent tagged alleles provide image-based definition between genotypes after PCR.
Reolution power increases with multi-locus genotype

Rapid. RADseq more expensive.

Question 7

Describe the american lobster case study

Answer 7

~30M live american lobster imported to Europe. Introduced accidentally and via deliberate release. Competition and invasiveness = threat.

Predict: introgression -> a pre-mating barrier prevents hybridisation

SNPs amplify in American lobser, several loci fixed for European minor allele. American females caught with fertilised eggs.

Clear assignment as hybrids

Question 8

Describe restocking across a genetic break case study

Answer 8

Hatchery restocking of lobsters and viability of attempts to restore and conserve stocks while sustaining fisheries for them.
Release after benthic settlement behaviours have been acquired.

Corsica restocked, but their fate couldn’t be properly monitored. Fishery landings started to pick up.

Juveniles had been reared on French atlantic coast. Released inot Med. SNP assays showed origin. 11 of the stock were Atlantic descent. 50 years after release, gained evidence that they worked

Question 9

Describe the dutch lobster mystery

Answer 9

Oostershelde stocks very ustable. Small fleet. Landings variable.
Mystery lobsters are here, because dominated by sedimentary habitat and sparsely dispersed along adjacent lowland.
RADseq

Looked like isolation by distance. Dutch lobsters are a total distinct stock. Divergent in neutral and outlier SNPs. Lower rates of diversity, private alleles. No shared ancestry with other stocks = no larval exchange. Role of genetic drift and local adaptation.
Historic texts foud a lobster shipwreck 1700. Shore stabilisation helped to increase abundance. Found event, plus subsequent stock collapse, explains the low diversity. Hypoxia events.

Question 10

Describe evolutionary responses to human impacts

Answer 10

Cornwall has a long mining history. Leaching = acute pollution with heavy metals in rivers. Biodiversity is drastically reduced.
Metal loads toxic to most higher vertebrates, but some healthy brown trout persists.

1. Measure long-term averages of metal loads in the rivers
2. RADseq. Genome wide-SNPs.
   Fish in all polluted rivers differentiated. Diversity was majorly reduced in the most polluted river (more fixed alleles). SNPs under selection, aligned to genome and associated to genes in metal homeostasis.
3. Fish to lab, systems flushed of residual metals. Metal loads calculated in key tissues. Cadmium and copper are higher in trout from metal environments.
4. Amplification of RNA via qPCR, then abundance of transcripts counted. Identify differentially expressed genes. Up or down regulated between different habitats.