Barcoding and eDNA metabarcoding of a rapidly changing Neotropical freshwater fish community

Sales, NG 2019, Barcoding and eDNA metabarcoding of a rapidly changing Neotropical freshwater fish community , PhD thesis, University of Salford.

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Abstract

The Neotropical region comprises one of the greatest freshwater fish diversities in the world. Conservation and management actions in freshwater realms face great challenges in this region due to an insufficient knowledge base (e.g. shortage of taxonomic expertise, lack of robust, routine, standardised monitoring programmes), infrastructure limitations and logistic constraints (e.g. access to remote areas, insufficient funds to cover surveys). Biodiversity assessment depends on reliable detection and accurate identification of species; thus, additional methods (e.g. integrative taxonomy, DNA barcoding and other molecular diagnostic methods), associated with traditional taxonomic identification, are being increasingly implemented worldwide. Surprisingly, despite being a hugely biodiverse country, Brazil has not yet embraced these novel DNA-assisted approaches to biodiversity monitoring. Therefore, with this thesis, I aim to bolster the implementation of DNA barcoding and metabarcoding in Brazilian riverine ecosystems. With the cooperation of collaborators in both Brazilian and British institutions, I built a barcode library and provided a more robust biodiversity record for the ichthyofauna of the Doce river, reflecting communities as they were prior to a major chemical pollution disaster in that catchment. Furthermore, I evaluated the application of eDNA metabarcoding as a fish biodiversity assessment tool, along the course of the Jequitinhonha river. Results for the Doce suggested the occurrence of potentially cryptic species, species complex, or historical errors in morphological identification. Metabarcoding of the environmental samples in the Jequitinhonha allowed the detection of native and introduced species and provided data from localities often neglected due to the difficulties of traditional sampling. Collectively, my studies indicate that a range of powerful and cost-effective molecular approaches are now available to biologists and conservationists, which will empower and fast-track the process of characterising biodiversity, and ultimately ecosystem function, in Brazilian freshwater habitats.

Item Type: Thesis (PhD)
Contributors: Mariani, Stefano (Supervisor), McDevitt, Allan (Supervisor) and Carvalho, Daniel Cardoso (Supervisor)
Schools: Schools > School of Environment and Life Sciences > Ecosystems and Environment Research Centre
Funders: Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Science Without Borders Programme
Depositing User: NAIARA GUIMARAES Sales
Date Deposited: 07 May 2019 09:50
Last Modified: 07 May 2019 09:50
URI: http://usir.salford.ac.uk/id/eprint/50969

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