Identifying the signatures of natural selection operating on DNA sequences is a cornerstone of our understanding of adaption, evolution and the processes that shape patterns of biodiversity across the globe.
Traditionally such analysis has focussed on the types and rates of synonymous and non-synonymous mutations that accumulate in the in protein coding DNA sequences, with technologies such as RNAseq being exploited to facilitate assessment across the genome of a broad range of species.
There is, however, growing recognition that RNA structure acts as a direct effector of fundamental biological processes, and thus is itself a target for natural selection and a factor that can constrain or promote underlying sequence polymorphism. Recently, RNAseq technology has been expanded to allow for quantitative measurement of genome-wide RNA secondary structure at single nucleotide resolution, and as such interrogate both sources of information contained within RNA.
This exciting PhD opportunity will identify the footprints of RNA adaptation, encompassing both sequence and structural variation, from across the transcriptomes of multiple species of deep-ocean amphipods that vary in their bathymetric ranges. A focus on structural adaptation in relation to hydrostatic pressure is especially interesting and important given that every single aqueous phase biochemical and metabolic process that an organism can undertake is accompanied by a volume change in the associated interacting molecules. As such, biochemical reactions are extremely sensitive to ambient pressure, with dramatic drop offs in biochemical efficiency at greater than a few atmospheres of pressure. Deep-ocean species must therefore have accumulated effective genetic structural adaptations that regulate the volume changes associated with biochemical processing to maintain activity and efficiency and thrive at extreme hydrostatic pressures.
The project will exploit a globally unique and valuable set of amphipod RNA and DNA samples collected from multiple littoral, bathyal, abyssal and ocean trench populations. High-throughput sequencing technologies such as RNAseq and StructureSEQ will be used to target rRNA homologues and transcriptome-wide mRNA molecules to test multiple hypotheses of predicted signatures of purifying selection for genes associated with large aqueous phase volume change in deep sea species, transposable element disruption, increases in GC content and GC codon bias to maximise molecular stability with depth and pressure, increases in hairpin versus loop secondary structure configurations with increasing depth, and parallel and convergent evolution for polymorphisms that minimise physico-chemical changes in molecules across deep sea species.
The student will gain multidisciplinary training in state-of-the-art laboratory techniques including RNAseq characterisation, bioinformatics, statistical and evolutionary analyses, and physico-chemical modelling. The project will provide the very first holistic insights into the evolutionary mechanisms enabling adaptation to extreme marine environments.