Conservation Implications of Strong Population Structure Despite Admixture in an Endangered African Seagrass

Zostera capensis is an African seagrass that is endangered throughout its range. In South Africa, it is solely confined to low wave energy estuarine habitats and characterised by two evolutionary lineages that diverge across a biogeographic transition. In this study, we sampled seagrass plants from five populations that span the region of lineage divergence and investigated the extent of lineage overlap. Using 2681 SNP loci, including 32 putative outlier loci, we calculated population structure, genomic diversity and levels of admixture. All populations were significantly different to each other, including those < 10 km apart and low levels of admixture indicate limited dispersal of Z. capensis. Every population was characterised by a high inbreeding coefficient (F_IS), suggesting a limited number of breeding individuals in each population. Given increasing anthropogenic stressors that are linked to declines in seagrass meadow cover in South Africa, our study provides strong support that populations of this endangered seagrass require targeted management and conservation actions of each individual population to avoid further loss of the unique evolutionary dynamics and to safeguard the ecosystem services seagrasses provide. Further, our evidence of significant population structure across geographically close populations highlights that conservation efforts relying on seagrass restoration would risk mixing unique evolutionary signatures of Z. capensis in the region when transplanting between estuaries. This represents a critical challenge to using transplants as a potential mechanism of restoring declining populations and highlights the crucial importance of preventing population extinction.