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Title: Testing the potential of enviromental DNA methods for surveying Lake Tanganyika's highly diverse fish communities
Author: Doble, Christopher James
ISNI:       0000 0004 9353 2013
Awarding Body: UCL (University College London)
Current Institution: University College London (University of London)
Date of Award: 2020
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Environmental DNA (eDNA) metabarcoding has become established as a highly sensitive and effective method of surveying fish communities across a broad range of freshwater ecosystems. To date this method has largely been restricted to temperate ecosystems, with few applications in the tropics where global freshwater fish diversity is at its richest. This thesis develops an environmental DNA metabarcoding methodology for surveying one of the planet’s most species rich tropical lakes - East Africa’s Lake Tanganyika (LT). This global aquatic hotspot contains exceptionally diverse fish communities, and therefore represents an excellent system to test the effectiveness of eDNA metabarcoding for surveying species rich tropical fish communities, as well as closely related species within adaptive radiations. Chapter one provides an introduction to the field, identifying key knowledge gaps. Chapter two develops a near comprehensive fish list and reference database for 358 species found within LT’s basin across three mitochondrial gene regions. These data are subsequently used to design two new primer sets including a novel cichlid-specific primer (Cichlid_CR), as well as undertake in silico testing of published primer sets. Chapter three investigates the relative effectiveness of eDNA metabarcoding and traditional underwater visual survey methods for surveying the species richness of LT’s littoral fish communities. Building on the results of this work Chapter four addresses if increased sequencing depth, reference database expansion and bioinformatic filtering stringencies can improve species richness estimates for LT’s highly diverse cichlid communities, with further comparisons made against the visual survey dataset. Overall, despite initial challenges detecting closely related species within LT’s cichlid radiations, this thesis demonstrates through the use of a family-specific primer set the capacity of eDNA metabarcoding methods for surveying LT’s littoral fish communities and therefore highly diverse tropical ecosystems, even those containing many closely related species comprising adaptive radiations. These findings support the capacity of eDNA metabarcoding methods for revolutionising our ability to survey freshwater fish communities globally.
Supervisor: Not available Sponsor: Not available
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
EThOS ID:  DOI: Not available