Shared genomic outliers across two divergent population clusters of a highly threatened seagrass

The seagrass, Zostera capensis, occurs across a broad stretch of coastline and wide environmental gradients in estuaries and sheltered bays in southern and eastern Africa. Throughout its distribution, habitats are highly threatened and poorly protected, increasing the urgency of assessing the genomic variability of this keystone species. A pooled genomic approach was employed to obtain SNP data and examine neutral genomic variation and to identify potential outlier loci to assess differentiation across 12 populations across the ∼9,600 km distribution of Z. capensis. Results indicate high clonality and low genomic diversity within meadows, which combined with poor protection throughout its range, increases the vulnerability of this seagrass to further declines or local extinction. Shared variation at outlier loci potentially indicates local adaptation to temperature and precipitation gradients, with Isolation-by-Environment significantly contributing towards shaping spatial variation in Z. capensis. Our results indicate the presence of two population clusters, broadly corresponding to populations on the west and east coasts, with the two lineages shaped only by frequency differences of outlier loci. Notably, ensemble modelling of suitable seagrass habitat provides evidence that the clusters are linked to historical climate refugia around the Last Glacial Maxi-mum. Our work suggests a complex evolutionary history of Z. capensis in southern and eastern Africa that will require more effective protection in order to safeguard this important ecosystem engineer into the future

Vulnerability, resilience and adaptation: the future for the seagrass, Zostera capensis

Thesis (PhD)--Stellenbosch University, 2018.ENGLISH ABSTRACT: The seagrass Zostera capensis forms a vital component of southern African estuarine systems as it provides critical ecosystem services which support biodiversity, estuary functioning and economically important fishery industries. This intertidal seagrass is restricted to estuaries and sheltered bays, and appears to rely chiefly on vegetative reproduction, limiting its dispersal capacity along the often-harsh coastlines of southern Africa. As such, these isolated and highly clonal populations are likely to be more vulnerable to the impacts of global change, the effects of which are likely to cascade through the ecosystem. South African estuaries are both highly threatened and poorly protected, and little is known about the standing of the southern-east African coastline in this regard, increasing the urgency of assessing the status of this keystone estuarine species. A genomic approach can provide a cost-effective, comprehensive characterisation of evolutionary history and potential, and can be applied to evaluate vulnerability, resilience and adaptive potential. As such, the ezRAD method was employed to obtain SNP data and examine both the neutral and putatively adaptive genomic variation and differentiation of 12 Z. capensis populations across its range. Anthropogenic drivers of genomic variation were investigated, and a spatial planning approach was utilised to evaluate regions that protect genomic diversity and evolutionary resilience. Results showed that every meadow had a high degree of clonality and low genomic diversity; this in combination with the lack of effective protection and negative feedback between environmental pressures and genomic diversity, increase the vulnerability of this species to further declines and even local extinctions. However, variation at putatively adaptive loci indicate local adaptation to temperature and precipitation regimes, which could confer some level of resilience to future environmental change. Although loci under selection are shared across sites, differences in their observed frequencies differentiate sites into a west coast and an east coast cluster. The formation of these clusters may have occurred as far back as the last glacial maximum where ensemble models project a loss of habitat between the two clusters, as well as a stable area of suitable habitat on the western-south coast, in terms of sea surface temperature, which may have served as a refugial area. In order to increase the representativeness of marine protected areas and the persistence of species therein, it is critical that conservation planning take measures of genomic variability into account. In this regard current and proposed MPAs based solely on habitat are far from sufficient, and their shortcomings are compounded by discordance with the distribution and intensity of environmental pressures. However, by including any one measure of genomic diversity, distinctness or adaptive potential, conservation managers may sufficiently represent the evolutionary processes behind the patterns of variation, while simplifying the conservation prioritisation procedure.AFRIKAANSE OPSOMMING: Geen opsommingDoctora