Assessing the evolutionary and physiological resilience of southern African marine species

Thesis (PhD)--Stellenbosch University, 2021.ENGLISH ABSTRACT: Assessing the genomic basis of local adaptation and critical thermal limits is essential for anticipating species persistence and distribution under climate change. Environmental gradients are associated with genomic and physiological differences between populations. South Africa's two ocean regime creates a thermal gradient, which delimits distinct bioregions between its cold-temperate west coast, warm-temperate south coast and warmsubtropical east coast. Three co-distributed key rocky shore invertebrate species representing different phyla were selected for a multi-species approach. The objectives of this dissertation were to 1) identify selectively neutral genomic loci and neutral population structure, 2) determine putatively adaptive loci and adaptive population structure, 3) explore functional annotations and 4) measure critical thermal limits (CTmin, CTmax). Pooled RAD-Seq (ezRAD) was utilised to identify selectively neutral shared and populationspecific single nucleotide polymorphisms (SNPs) in six populations of shore crab Cyclograpsus punctatus (CP), granular limpet Scutellastra granularis (SG), and Cape sea urchin Parechinus angulosus (PA). Population-specific SNPs were detected in all populations. Nucleotide diversity indices (Tajima.s pi, Watterson.s theta)) appear heightened in PA's northern west coast population compared to the remaining sites. Estimated pairwise FST values range from 0.043-0.055 (CP), 0.044-0.066 (SG) to 0.039-0.089 (PA). Selectively neutral genomic population structure indicates instances of intraspecific subdivisions present in all populations. All species populations harbour unique SNPs, yet increased nucleotide diversity is only detected in PA. The empirical FST-method, BayeScan and BayeScEnv identified overall 1102 outliers under positive selection, of which 69 (CP), 11 (SG) and 27 (PA) could be functionally annotated. Candidate loci are involved in various cellular functions including membrane transport, vesicle signalling, protein folding/modification and cytoskeleton function. Identified loci related to energy cycling might point to selection on metabolic capacity to counter environmental stressors. Environmental differentiation of sea surface temperature (SST), salinity and air temperature could be associated with several putative outliers. There is no isolation-by-distance (IBD), but isolation-by-environment (IBE) suggests salinity variation to account for 48% of genomic variation in P. angulosus and SST and air temperature for 45% in S. granularis. Outlier-based population structure indicates possible intraspecific subdivision in some species. Critical thermal limits (CTmin, CTmax) were investigated with thermal tolerance trials and compared to local min/max environmental temperature for warming and cooling tolerance. Across populations, mean CTmin ranges from -1.5-0.6°C (CP), -0.4-3.2°C (SG) to 5-10.9°C (PA). Mean CTmax ranges from 43.8-46.1°C (CP), 34.4-35.7°C (SG) to 28.9-32.4°C (PA). West coast crabs have significantly higher CTmax than east coast crabs. CTmin is negatively and thermal breadth positively correlated with body mass (CP, PA). Significant regional differences in mass were detected (SG, PA). Warming and cooling tolerance appears sufficient, requiring further investigation within situ microhabitat data. East coast rocky shore populations likely face future warm-edge range contractions, whereas the south coast might experience distributional shifts depending on local thermal conditions. The west coast is an anchor for rocky shore species in South Africa and represents a possible climate change refugium. Strategic recognition in regional marine conservation management is warranted.Doctora