In search of selection: A comparative genome and transcriptome study of sibling New Zealand Chiton species (Sypharochiton pelliserpentis & S. sinclairi)

Abstract

Our understanding of macro-evolutionary processes that drive speciation is now being centred on understanding divergences between populations and species at the DNA level. However, DNA sequence evolution is a complex process that is characterised by multiple factors, such as positive selection, purifying selection, and random drift. By being able to identify what factors are influencing sequence evolution, inferences can be made about the speciation process, and potentially provide evidence for species-specific adaptations to ecosystem pressures. Sypharochiton pelliserpentis and Sypharochiton sinclairi are two closely related chiton species in New Zealand, occupying two distinct niches along the intertidal reef. S. sinclairi, occupies the stable subtidal zone, whereas S. pelliserpentis occupies the dynamic, higher intertidal zone. To survive the increased exposure and repeated emersion, S. pelliserpentis has likely acquired some adaptive advantages, with two potential pathways being those associated with heat stress or desiccation resistance. This thesis aimed to identify candidate genes that may help explain observed ecological differences between sibling species, through assembling three chiton genomes and transcriptomes, and comparing orthologous sequences for evidence of positive selection. Tests of dN/dS ratios, using Chiton glaucus as an outgroup species, were performed on orthologous protein coding sequences extracted from transcriptome data, in order to identify potential candidates. Examination of orthologues resolved 1255 gene sequences shared between the species. Using dN/dS ratios, MLE p (Maximum likelihood probability), LRT (Likelihood ratios tests), and transcriptome annotations, around 56 unique genes were identified as potential candidates under selection in the S. pelliserpentis lineage, based on four models of positive selection implemented in CODEML. FK506-binding protein 4, which has an associated function in heat stress, showed strong signs of positive selection, and one protein, Calmodulin, was identified by all four models of positive selection. Further comparative studies, such as analysis of differential expression, and stress tolerance experiments, are proposed to more confidently identify candidate genes in S. pelliserpentis. This study identified a number of potential candidate genes that may help explain the observed ecological differences between the two sibling species, while also providing valuable new genomic and transcriptomic resources for future comparative studies of these species.