Fish biodiversity dynamics in impacted coastal ecosystems : integrating environmental DNA and genomic insights in groupers (genus: Epinephelus)

Abstract

Global marine biodiversity faces mounting pressures from anthropogenic activities, posing significant challenges to biodiversity assessments and conservation efforts. This thesis explores different aspects that shape contemporary marine biodiversity from past speciation events to current anthropogenic activities by means of various molecular approaches, with a focus on groupers from the subfamily Epinephelinae which are economically significant species vulnerable to overfishing. To develop efficient survey methods that maximize sampling efforts to address gaps in contemporary biodiversity, environmental DNA (eDNA) metabarcoding and underwater visual census (UVC) surveys were compared in performance to characterize marine fish diversity across environmental gradients. eDNA recorded 90 putative species never recorded in UVC, adding seven prospective new occurrence records for Hong Kong Special Administrative Region (HKSAR) waters. Importantly, each survey method featured a distinct species profile, with 32.3% and 39.6% species found exclusively by UVC and eDNA respectively, highlighting the importance of complementing both UVC and eDNA metabarcoding surveys for a more complete overview of local biodiversity. I then examined two major anthropogenic threats to the contemporary ecosystem, namely overexploitation and non-native species introduction. Here, I developed a novel species-specific quantitative PCR (qPCR) assay to detect the occurrence of Hong Kong Grouper, Epinephelus akaara, through environmental water samples. This endangered species suffers from overfishing, and monitoring will provide crucial insights for its conservation and management amidst dwindling populations. The designed qPCR assay offered high sensitivity and specificity to the target species, but only 6.81% of water samples collected spatially and temporally across Hong Kong detected the species at a concentration below the limit of detection, highlighting the present-day rarity of this species in Hong Kong. Overall, the designed assay is a promising tool to document endangered species for management and conservation. Gut content DNA metabarcoding was used to assess the dietary niche and prey composition of the Hybrid Grouper (TGGG) introduced from religious mercy releases. In comparison with four local grouper species, TGGG exhibited six unique prey taxa, and displayed a significantly lower mean number of prey taxa. TGGG also revealed a significantly different diet composition than native groupers, indicating diet transitioning and the acquisition of new feeding behaviours in this hybrid. Such high taxonomic resolution analysis of the diet of the released artificial hybrids demonstrates how local trophic dynamics could be impacted by their release by religious practices. Finally, I examined the role of interspecific genetic admixture in past speciation processes of Epinephelus spp. in the marine environment through whole genome resequencing. Rapid speciation rates were recorded, accompanied by multiple episodes of introgression events between ancestral lineages during speciation, with genetic admixture ranging from 1.67% to 6.78% between species pairs of a subclade lineage. The genetic admixture occurred between two lineages that preferred different habitats and water depths. This study provides novel insights into the genetic exchanges and evolutionary dynamics shaping the biodiversity of serranid fishes in the region. Collectively, these multidisciplinary investigations contribute to further understanding of anthropogenic impacts and evolutionary processes in South China coastal ecosystems, providing valuable insights for conservation and management strategies in rapidly changing marine environments.