Environmental DNA (eDNA)-based methods enable the detection of organisms from genetic material in environmental samples (e.g. water, soil, sediment) and are emerging as promising biomonitoring tools. In the research presented in this thesis, I explore the utility of eDNA-based analyses in elasmobranch conservation, in investigations of mesopelagic fish, and in fish population genetics, across three different aquatic ecosystems. In Chapter 1, I review the persistence and dispersal of aquatic eDNA, evaluate the advantages of eDNA compared to traditional aquatic survey methods, and discuss the potential of eDNA in marine conservation and population genetics. In Chapter 2, I present a study of eDNA metabarcoding of elasmobranch diversity in a temperate marine ecosystem. The study provides evidence of the ability of eDNA to reveal species richness, and spatial and temporal differences in community structure elasmobranch community, over a spatial scale of 30km. The eDNA-derived data are compared to historic trawl data, and demonstrate the ability of eDNA metabarcoding to serve as a semi-quantitative biomonitoring approach. In Chapter 3, I present an eDNA metabarcoding study of the mesopelagic fish composition of the Scotia Sea region of Southern Ocean, across a depth gradient from the surface to 1000m. The study showed a decoupling between eDNA read abundance and the abundance of fish in survey trawls. In addition, the distribution of marine mammal species encountered in eDNA “molecular bycatch” was used to investigate their diversity and distribution. In Chapter 4, I present a study using eDNA to quantify population genetic structure of the Eastern happy cichlid fish (
Astatotilapia calliptera) across a thermo-oxycline in crater Lake Masoko, Tanzania. This research demonstrated that eDNA could reveal differences in allele frequencies within aquatic environment across a small spatial scale (<30 m). In Chapter 5, I summarize these findings and discuss knowledge gaps. Overall, the research presented here shows that aquatic eDNA-based can be used to establish the patterns of biodiversity, both within and across species, and in freshwater and marine ecosystems.
Applications of eDNA-based methods: from marine conservation to population genetic structure
Liu, Z. (Author). 20 Jun 2023
Student thesis: Doctoral Thesis › Doctor of Philosophy (PhD)