Fish adaptation to depth: alternative splicing in the twilight zone?

Project Description

One of the most exciting reasons to study fish biology is the range of environments they inhabit and the broad range of adaptations to those environments they have evolved. Of particular interest is their adaptation to depth, because deep water environments make up so much of the planet. Deep water offers a range of challenges to fish - increased hydrostatic pressure, lack of available oxygen, and reduced light, particularly at certain wavelengths. Understanding genomic adaptations to depth offers key insights into how certain species have been able to occupy these extreme environmental niches but not others. Haplochromine cichlids are particularly useful in this regard. Between 800-1000 species have evolved in Lake Malawi (LM) over the last 2-5 million years, including about 15 deep water taxa (Diplotaxodon spp.) found between 50 -200 m. Recently, a number of key genomic adaptations in 4 Diplotaxodon species were identified, including in the lens clarity protein BSFP2 (Hahn et al. 2017). A substitution in the first intron of this gene was found which is unique to deep water Diplotaxodon, and is also found in other unrelated deep water species in LM. Evidence from other taxa demonstrates this substitution likely plays a role in alternative splicing of 8 exons in the gene, and this in turn affects lens clarity, allowing more light to penetrate the lens in deeper water environments.

We plan to use this internship to develop PCR primers in different exons which will be able to detect alternative splicing when used to amplify cDNA from eye tissue. I will learn how to extract DNA and mRNA from eye tissue, synthesize and PCR amplify cDNA, including PCR optimisation, and then analyse sequence data to identify splice variants. We already have eye tissue from the relevant species in RNAlater, and we maintain stocks of live Diplotaxodon limnothrissa in the aquaria here in case more tissue is needed.

As a result of this internship, I will have first hand experience of a number of lab skills important for evolutionary and ecological genetics, and with the support of my supervisor, I will be able to place this into the wider context of relevance for fish adaptation to depth. I hope to confirm the evolutionary mechanism by which fish eye lenses have adapted to depth by modulating eye lens clarity.