Reconstructing the response of native fish in lakes to historical anthropogenic disturbances

Abstract

<p><strong>There is a well-documented decline in the native fish of Aotearoa New Zealand, with 74% of species currently categorised as at risk or threatened. There is an urgent need for more data on how fish communities respond to the complex and synergistic drivers that are causing their biodiversity loss in lakes. Paleolimnological studies overcome the limitation of short monitoring records and allow research which explores the impact of disturbances on fish and the wider ecosystem. Until recently the ability to detect changes in historical fish communities has been limited by the lack of fossil remains left behind by fish. This thesis explored the use of sedimentary DNA (sedDNA) to track fish communities in sediment cores. I began by reviewing available methods used to measure or infer how fish communities respond to disturbance. These included contemporary population surveys, manipulative experimental methods, paleolimnological approaches, Indigenous Knowledge and social histories. The benefits and limitations of these approaches were identified and discussed within the context of eutrophication, land use change and introduced fish. I highlighted the value of environmental DNA based approaches, and Indigenous Knowledge and social histories and how different methods can compensate for the limitations inherent in other methodologies. I demonstrated how the application of an integrative methodological approach could greatly advance knowledge on how native freshwater fish in lakes respond to anthropogenic disturbances. I identified fish sedDNA as an emerging tool in paleolimnology but highlighted the ongoing need for method development. Secondly, I tested five methods with various modifications to establish their ability to desorb extracellular fish DNA from aquatic sediments. I characterised the recovery of fish sedDNA from sediments using droplet digital PCR (ddPCR) assays targeting eel (Anguilla australis, Anguilla dieffenbachii) and perch (Perca fluviatilis). A range of sediment masses (0.25–20 g) were assessed to establish the optimal amount required to accurately assess fish sedDNA. An optimised extraction method was developed and used in my subsequent chapters. I assessed the effect of sediment core location (nearshore verses depocentre), fish or mussel species and molecular method (ddPCR versus metabarcoding) on sedDNA detection in sediment cores from a small eutrophic lake in the Wairarapa region (Aotearoa New Zealand). There were higher detections in the nearshore core compared to the depocenter core which was most likely related to the locality of the target species. Differential detection of target species was likely caused by their ecology and biomass. The ddPCR assays were more sensitive than the metabarcoding approach. Target species detection was negatively impacted by a reduction in total DNA concentration in older sediments. These results highlighted that current molecular techniques used to target fish sedDNA can result in inconsistent temporal and spatial detection of species, especially in older sediments.</strong></p><p>I reconstructed the abundance and diversity of a native fish community over 1390 years in a small eutrophic lake in the Gisborne region (Aotearoa New Zealand) using metabarcoding and a fish specific ddPCR approach. A suite of sedDNA and other traditional paleolimnological approaches, e.g., pollen analysis, X-ray fluorescence and hyperspectral scanning, and trace metal analysis were used to explore drivers of changes in the fish communities. Generalised additive mixed models identified distinct shifts in fish community composition, notably a decline in a Galaxias species concomitant with early land use changes starting around 1350 CE. A significant decline in fish abundance around 1950 CE aligned with agricultural intensification and shifts in both phytoplankton and zooplankton communities. The results suggested that the major changes in fish diversity and abundance in the lake were mostly related to external drivers (i.e., agricultural intensification) and correlated internal productivity (i.e., eutrophication) than to food web composition changes (i.e., dietary shifts). This study emphasised the potential of using fish sedDNA (with the appropriate methodological considerations) to investigate the impact of anthropogenic disturbance on lake fish communities. This knowledge will assist with the future management and conservation of native fish species in freshwater lakes.</p>