Testing the performance of environmental DNA metabarcoding for surveying highly diverse tropical fish communities: A case study from Lake Tanganyika
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Date
2019-10-02
Journal Title
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Publisher
John Wiley & Sons Ltd
Abstract
Background and Aims: Environmental DNA (eDNA) metabarcoding provides a highly
sensitive method of surveying freshwater fish communities, although studies to date
have largely been restricted to temperate ecosystems. Due to limited reference
sequence availability and challenges identifying closely related and rare species in
diverse tropical ecosystems, the effectiveness of metabarcoding methods for surveying
tropical fish communities from eDNA samples remains uncertain. To address
this, we applied an eDNA metabarcoding approach to survey Lake Tanganyika's (LT)
species‐rich littoral fish communities.
Materials and Methods: As this system contains many closely related species, particularly
cichlid fishes, we used four primer sets including a cichlid‐specific primer set
(Cichlid_CR). A reference database was built for the 12s, 16s, and control region for
358 fish species including over 93% of known cichlids.
Results and Discussion: In silico and in situ results demonstrated wide variability in the
taxonomic resolution of assignments by each primer with the cichlid‐specific marker
(Cichlid_CR) enabling greater species‐level assignments for this highly diverse family.
A greater number of non‐cichlid teleost species were detected at sites compared to
the visual survey data. For cichlid species however, sequencing depth substantially
influenced species richness estimates obtained from eDNA samples, with increased
depths producing estimates comparable to that obtained from the visual survey data.
Conclusions: Our study highlights the importance of sequencing depth and local
reference databases when undertaking metabarcoding studies within diverse ecosystems,
as well as demonstrating the potential of eDNA metabarcoding for surveying
diverse tropical fish communities, even those containing closely related species
within evolutionary radiations.
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Keywords
cichlids, environmental DNA, Lake Tanganyika, metabarcoding, reference database, tropical freshwaters