Browsing by Author "Nielsen, Erica Spotswood"

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    Complex signatures of genomic variation of two non-model marine species in a homogeneous environment
    (BioMed Central, 2018-05-09) Nielsen, Erica Spotswood; Henriques, Romina; Toonen, Robert J.; Knapp, Ingrid S. S.; Guo, Baocheng; Von der Heyden, Sophie
    Background: Genomic tools are increasingly being used on non-model organisms to provide insights into population structure and variability, including signals of selection. However, most studies are carried out in regions with distinct environmental gradients or across large geographical areas, in which local adaptation is expected to occur. Therefore, the focus of this study is to characterize genomic variation and selective signals over short geographic areas within a largely homogeneous region. To assess adaptive signals between microhabitats within the rocky shore, we compared genomic variation between the Cape urchin (Parechinus angulosus), which is a low to mid-shore species, and the Granular limpet (Scutellastra granularis), a high shore specialist. Results: Using pooled restriction site associated DNA (RAD) sequencing, we described patterns of genomic variation and identified outlier loci in both species. We found relatively low numbers of outlier SNPs within each species, and identified outlier genes associated with different selective pressures than those previously identified in studies conducted over larger environmental gradients. The number of population-specific outlier loci differed between species, likely owing to differential selective pressures within the intertidal environment. Interestingly, the outlier loci were highly differentiated within the two northernmost populations for both species, suggesting that unique evolutionary forces are acting on marine invertebrates within this region. Conclusions: Our study provides a background for comparative genomic studies focused on non-model species, as well as a baseline for the adaptive potential of marine invertebrates along the South African west coast. We also discuss the caveats associated with Pool-seq and potential biases of sequencing coverage on downstream genomic metrics. The findings provide evidence of species-specific selective pressures within a homogeneous environment, and suggest that selective forces acting on small scales are just as crucial to acknowledge as those acting on larger scales. As a whole, our findings imply that future population genomic studies should expand from focusing on model organisms and/or studying heterogeneous regions to better understand the evolutionary processes shaping current and future biodiversity patterns, particularly when used in a comparative phylogeographic context.
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    Integrating genetics into marine conservation planning in South Africa
    (Stellenbosch : Stellenbosch University, 2017-03) Nielsen, Erica Spotswood; Von der Heyden, Sophie; Beger, Maria; Henriques, Romina; Stellenbosch University. Faculty of Science. Dept. of Botany and Zoology.
    ENGLISH ABSTRACT: The mounting threats to biodiversity and global alteration of habitat and species distributions make it increasingly necessary to consider evolutionary patterns in conservation decision-making. Yet there is no clear-cut guidance on how genetic features can be incorporated into conservation planning processes, with several genetic metrics with different ecological and evolutionary relevance to choose from. Genetic patterns also differ between species, but the potential trade-offs amongst different genetic objectives for multiple species in conservation planning are currently understudied. Therefore, the first chapter of this thesis compares spatial conservation prioritizations derived from two metrics of both genetic diversity (nucleotide and haplotype diversity) and genetic isolation (private haplotypes and local genetic differentiation) for five marine species. The results from Chapter One show that conservation plans based solely on habitat representation noticeably differ from those additionally including genetic data, and that all four genetic metrics select similar conservation priority areas. The second chapter builds on the findings of Chapter One by comparing conservation solutions from three marker types (mitochondrial DNA, neutral nuclear DNA, and adaptive nuclear DNA) for the two most genetically distinct species from the multi-species data set. Next generation sequencing was used to identify single nucleotide polymorphism (SNP) variation in both the Cape urchin (P. angulosus) and the Granular limpet (S. granularis), both of which showed high levels of genomic diversity and signals of adaptation to local ecotypes. When comparing the genetic variation between the mitochondrial DNA (mtDNA) and SNP markers within a spatial conservation framework, the solutions show a wide range of spatial priorities, yet the spatial similarities between the different marker types are not consistent across the different species approaches. Largely, the findings from this project suggest that selected species and genetic marker(s) chosen will alter all conservation solutions. Importantly, increasing the amount of genetic information leads to more distinct conservation priorities, resulting in a clearer picture of community-level evolutionary hotspots within the planning region.
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    Using multi-species seascape genomics to conserve areas of evolutionary importance
    (Stellenbosch : Stellenbosch University, 2021-04) Nielsen, Erica Spotswood; Von der Heyden, Sophie; Henriques, Romina; Beger, Maria; Stellenbosch University. Faculty of Science. Dept. of Botany and Zoology.
    ENGLISH ABSTRACT: Understanding the environmental footprints on species and genetic biodiversity is a key concern in molecular ecology and conservation genetics. As species are increasingly under pressure from anthropogenic climate change, understanding how rapid environmental changes will influence intra- and interspecific diversity is essential if we are to conserve functioning ecosystems. This PhD thesis used the unique environmental backdrop of the South African coastline to infer how environmental variables over space and time shape multiple facets of biological variation. Specifically, this thesis utilised seascape genomic analyses to test the strong environmental gradients within South Africa against the molecular variation of three rocky intertidal species: Cape urchin (Parechinus angulosus), Common shore crab (Cyclograpsus punctatus), and Granular limpet (Scutellastra granularis). The first chapter evaluated which contemporary seascape features most strongly correlate with neutral and adaptive intraspecific diversity across species. Here, the results show that gene-environment relationships are species-specific, with the crab showing less population differentiation, strongly influenced by sea-surface salinity, and the urchin and limpet showing a west-east population differentiation predominantly influenced by sea-surface and air temperature. Chapter Two tested the relative influence of historical climatic stability versus contemporary species distributions in shaping patterns of neutral diversity of the three species. The results from this chapter indicate that historical climatic refugia since the Last Glacial Maximum are potentially stronger predictors of contemporary molecular diversity hotspots than the species’ current distribution. The third research chapter evaluated the vulnerability of the three study species with regards to future climatic change, both at two time-points and under two emission scenarios. Here, the results highlight how future responses to global change will likely differ among species, as well as among populations within each species. In the final chapter, the patterns uncovered in the three data chapters, pertaining to genomic diversity and vulnerability, climatic stability, and adaptive potential, are combined in a conservation planning framework to identify areas of evolutionary importance, which can be thought of as priority areas for forward-thinking conservation action. As a whole, this thesis used novel ecological and evolutionary models to understand the spatio-temporal interplay between species, genes, and environment, and used this information to guide conservation action within South Africa.