Westerduin, C., Suokas, M., Petäjä, T., Saarela, U., Vainio, S., & Mutanen, M. (2023). Exploring and validating observations of non-local species in eDNA samples. Ecology and Evolution, 13, e10612. https://doi.org/10.1002/ece3.10612
Exploring and validating observations of non-local species in eDNA samples
|Author:||Westerduin, Coen1; Suokas, Marko1; Petäjä, Tuukka2;|
1Ecology and Genetics Research Unit, Faculty of Science, University of Oulu, Oulu, Finland
2Department of Physics, Institute for Atmospheric and Earth System Research (INAR), University of Helsinki, Helsinki, Finland
3CRC, The Faculty of Medicine, University of Oulu, Oulu, Finland
4Laboratory of Developmental Biology, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
|Online Access:||PDF Full Text (PDF, 4.6 MB)|
|Persistent link:|| http://urn.fi/urn:nbn:fi-fe20231018140599
John Wiley & Sons,
|Publish Date:|| 2023-10-18
The development of DNA-based methods in recent decades has opened the door to numerous new lines of research in the biological sciences. While the speed and accuracy of DNA methodologies are clearly beneficial, the sensitivity of these methods has the adverse effect of increased susceptibility to false positives resulting from contamination in field or lab. Here, we present findings from a metabarcoding study on the diet of and food availability for five insectivorous birds, in which multiple lepidopteran species not known to occur locally were discovered. After describing the pattern of occurrences of these non-local species in the samples, we discuss various potential origins of these sequences. First, we assessed that the taxonomic assignments appeared reliable, and local occurrences of many of the species could be plausibly ruled out. Then, we looked into the possibilities of natural environmental contamination, judging it to be unlikely, albeit impossible to fully falsify. Finally, while dissimilar combinations of non-local species’ occurrences across the samples did not initially suggest lab contamination, we found overlap with taxa and sequences handled in the same lab, which was undoubtedly not coincidental. Even so, not all exact sequences were accounted for in these locally conducted studies, nor was it clear if these and other sequences could remain detectable years later. Although the full explanation for the observations of non-local species remains inconclusive, these findings highlight the importance of critical examination of metabarcoding results, and showcase how species-level taxonomic assignments utilizing comprehensive reference libraries may be a tool in detecting potential contamination events, and false positives in general.
Ecology and evolution
|Type of Publication:||
A1 Journal article – refereed
|Field of Science:||
1181 Ecology, evolutionary biology
We are thankful to the Finnish Cultural Foundation, the Technology and Natural Sciences Doctoral Programme at the University of Oulu and the Academy of Finland for funding the metabarcoding costs and the Kvantum Institute at the University of Oulu as well as the Kone Foundation for funding supporting CW. Support via Academy of Finland via Flagship ‘The Atmosphere and Climate Competence Center (ACCC)’, project number 337549, via NANOBIOMASS (307537) and via ACRoBEAR (334792) are gratefully acknowledged.
Detailed information on the relevant samples, sequences and assigned identities is provided in the Appendices S1–S6. Complete reads for the focal samples are furthermore uploaded to NCBI's Sequence Read Archive (SRA), accession numbers SAMN31544596–SAMN31544690.
© 2023 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.