The genomic signatures of adaptation in invasive and nuisance seaweed spreads

The overarching aim of this CASE studentship is to apply quantitative population genomic approaches to understand environmental adaptation in native and invasive species of the ecologically important green seaweed, Ulva spp. The studentship will be based in Durham and Newcastle; the student will also have 3-6 months’ CASE placement with the Durham Heritage Coast organization, which is responsible for coastal ecosystem management and invasive species monitoring along the north-east English coastline.
Green seaweeds have historically been some of the most common and productive seaweed species along UK and European coastlines. However, they are also increasingly associated with nuisance algal blooms (the annual ‘green tides’ of the southern English coast) and with the spread of invasive species from Asia, carried into UK waters as shipping ballast (cf. Smetacek and Zingone 2013 paper in further reading). The Durham PI has recently led the genome sequencing consortium for the model green species, Ulva mutabilis, together with labs in Gent, Belgium, and Jena, Germany. This studentship will now build on this work to investigate how genome variation in green seaweeds worldwide can explain their ability to form nuisance blooms and/or to become invasive.
Specific aims are:
a) To combine whole-genome polymorphism data with environmental datasets to identify loci under selection in invasive and bloom-forming green seaweeds and, therefore, to identify possible candidate genes responsible for invasive behaviour
b) To modify and test the candidate genes identified as being under selection using recently-developed CRISPR approaches (with our European colleagues in Gent and Jena)
c) To develop and encourage the student as an independent researcher
Methodology and skills
Prior work (as part of the PI’s BBSRC-funded SuBBSea and NERC-funded Ulva Genome projects) has generated a high quality (long read) reference genome and RADseq data from ~300 Ulva individuals sampled worldwide; these include bloom-forming and invasive individuals. We are also developing macroalgal gene editing techniques (CRISPR) with European colleagues and can maintain Ulva species in lab culture.
Very little is known about adaptation and selection in seaweed genomes, so the student will develop a bioinformatics pipeline (STACKS/Floragenex) to identify single nucleotide polymorphisms (= SNPs) from the RADseq data; the location of these SNPs (coding or non-coding) will be inferred from the Ulva reference genome. Genome-wide association scans (Q-Q plots) will give preliminary links between behavior (blooms/invasives) and genotype before more powerful tests are applied (single point/haplotype analysis). The focus during this work will be on scanning for selection (identifying sweeps, etc.) using well-established genetic tools (cf. publications by Dr Kapralov), but combining these with environmental data collected for each sample in collaboration with the CASE partner (Durham Heritage Coast) to highlight associations between haplotypes and the ability of individuals to form blooms or spread as invasives.
These scans for selection will inform the identification of candidate adaptive loci; predictions will be tested by CRISPR gene editing of cultured Ulva spp. and growth experiments to establish gene function; this later work will be expected to involve short-term visits (1-2 months) to labs in Belgium or Germany.
Further: http://www.iapetus.ac.uk/wp-content/uploads/2017/11/IAP-17-84-Bothwell-Durham.pdf