Informing marine biodiversity conservation with next generation sequencing tools : from genes to communities

Overview & Synopsis

Human activities and their resulting pressures on natural ecosystems are altering biodiversity and induce a loss of species, population and genetic diversity. Across the marine realm, networks of marine protected areas (MPAs) are increasingly established to alleviate pressures and restore biodiversity and ecosystem processes. Yet, the mechanisms by which MPAs can preserve biodiversity and sustain fisheries are still unclear, though they are essential to ensure the success and implementation of MPAS in order to reach the 30% protection target. My PhD uses Next-Generation Sequencing (NGS) tools to study biodiversity patterns of Mediterranean fishes at three levels – communities, populations and genes – and to better guide their conservation under increasing climate warming and fishing pressure.Understanding the effect of MPAs on fish communities requires the detection of a wide range of species. Yet, visual censuses only detect a fraction of biodiversity. I apply environmental DNA (eDNA) metabarcoding to study the diversity of fish communities in six Mediterranean MPAs. This approach allows the detection and identification of species from the thousands of sequences found in a single water sample. The results highlight a new conservation paradox: MPAs are less species-rich than their surroundings. However, they host different species assemblages compared to fished areas thus increasing regional diversity. This difference is mainly driven by species often overlooked by conventional visual methods but detected with eDNA: cryptobenthic, pelagic, and rare fishes.Biodiversity also depends on the connectivity between populations through the successful dispersal of propagules and individuals, leading to gene flow. I investigate the Mediterranean-wide connectivity of two fishes, the striped red mullet (Mullus surmuletus) and white seabream (Diplodus sargus). I develop a spatial graph approach that extends propagule dispersal networks over multiple generations to better match the spatio-temporal scale of genetic connectivity. Comparing these new estimates with the analysis of 1,153 neutral SNPs from 47 putative populations reveals how mullet populations achieve high levels of gene flow through multi-generational stepping-stone dispersal. Kinship estimations also reveal that seabream is capable of exceptional long-distance dispersal (about 2,000km) in only two or three generations.Such high levels of gene flow however can diminish population structure and impede local adaptation. To better understand these mechanisms, I analyse 823 individuals genotyped for 704 highly differentiated (i.e. outlier) SNPs potentially under selection. I can thus disentangle the relative influence of spatial distance, larval dispersal and environmental conditions - which are expected to change under climate change - on the genomic structure of both species. These analyses reveal that temperature plays a significant role in the genomic structure of mullet and seabream, allowing the detection of genes potentially involved in local adaptation.By combining powerful genomic and statistical tools, this thesis deciphers new patterns of biodiversity with novel implications for conservation. The results highlight how MPAs can preserve fish biodiversity and community structure in the face of fishing pressure. They also suggest how networks of well-connected MPAs could ensure the persistence and adaptive potential of populations facing climate change.