This is a repository copy of Testing the performance of environmental DNA metabarcoding for surveying highly diverse tropical fish communities: A case study from Lake Tanganyika.
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Article: Doble, C.J., Hipperson, H. orcid.org/0000-0001-7872-105X, Salzburger, W. et al. (4 more authors) (2020) Testing the performance of environmental DNA metabarcoding for surveying highly diverse tropical fish communities: A case study from Lake Tanganyika. Environmental DNA, 2 (1). pp. 24-41. ISSN 2637-4943 https://doi.org/10.1002/edn3.43
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Received Apri | Revised September | Accepted October DOI edn
ORIGINAL ARTICLE
Testing the performance of environmental DNA metabarcoding for surveying highly diverse tropical fish communities: A case study from Lake Tanganyika
Christopher J. Doble1,2,3 | Helen Hipperson3 | Walter Salzburger4 | Gavin J. Horsburgh3 | Chacha Mwita5 | David J. Murrell1,2 | Julia J. Day1,2
1Department of Genetics Evo ution and Environment University Co ege London Abstract London UK Background and Aims: Environmenta DNA eDNA metabarcoding provides a high y 2 Centre for Biodiversity and Environment sensitive method of surveying freshwater fish communitie s a though studies to date Research University Co ege London London UK have arge y been restricted to temperate ecosystems Due to imited reference 3Department of Anima and P ant sequence avai abi ity and cha enges identifying c ose y re ated and rare species in Sciences NERC Biomo ecu ar Ana ysis - Faci ity University of Sheffie d Sheffie d diverse tropica ecosystems the effectiveness of metaba rcoding methods for sur UK veying tropica fish communities from eDNA samp es remain s uncertain To address 4 Department of Environmenta this we app ied an eDNA metabarcoding approach to survey L ake Tanganyika s LT Sciences Zoo ogica Institute University of Base Base Switzer and species rich ittora fish communities 5Department of Aquatic Sciences and Materials and Methods: As this system contains many c ose y re ated species par- Fisheries University of Dar es Sa aam Dar ticu ar y cich id fishes we used four primer sets inc uding a cich id specific primer set es Sa aam Tanzania Cich id CR A reference database was bui t for the s s and contro region for Correspondence fish species inc uding over of known cich ids Christopher J Dob e Department of Genetics Evo ution and Environment Results and Discussion: In si ico and in situ resu ts demonstrated wide variabi it y in the University Co ege London Gower Street taxonomic reso ution of assignments by each primer with the cich id specific marker London WC E BT UK Emai christopher dob e uc ac uk Cich id CR enab ing greater species eve assignments for this high y diverse fami y Ju ia J Day Department of Genetics A greater number of non cich id te eost species were dete cted at sites compared to Evo ution and Environment University Co ege London Gower Street London the visua survey data For cich id species however seque ncing depth substantia y WC E BT UK inf uenced species richness estimates obtained from eDNA s amp es with increased Emai j day uc ac uk depths producing estimates comparab e to that obtained fr om the visua survey data Funding information Conclusions: Our study high ights the importance of sequencing depth and oca Natura Environment Research Counci Grant Award Number NE L reference databases when undertaking metabarcoding studies within diverse eco- Genetics Society Heredity Fie dwork Grant systems as we as demonstrating the potentia of eDNA met abarcoding for survey- Systematics Research Fund Fisheries Society of the British Is e Sma Research ing diverse tropica fish communities even those containing c ose y re ated species Grant Percy S aden Memoria Trust within evo utionary radiations Fund NERC Bimo ecu ar Ana ysis Faci ity Sheffie d European Research Counci Swiss Nationa Science Foundation KEYWORDS cich ids environmenta DNA Lake Tanganyika metabarcoding reference database tropica freshwaters
This is an open access artic e under the terms of the Creative Commons Attribution License which permits use distribution and reproduction in any medium provided the origina work is proper y cited The Authors Environmental DNA pub ished by John Wi ey Sons Ltd
24 | wileyonlinelibrary.com/journal/edn3 Environmental DNA. 2020;2:24–41. DOBLE ET AL. |