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Consistent findings from ddPCR and metabarcoding analyses of piscivorous bird diets
Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.ORCID iD: 0000-0003-2001-5077
Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.ORCID iD: 0000-0001-5634-8602
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(English)Manuscript (preprint) (Other academic)
Abstract [en]

The diet of apex predators is crucial for addressing fundamental ecological questions. The diets ofpiscivorous birds have traditionally been studied using invasive methods that may be harmful.Consequently, researchers have been compelled to explore alternative options. Molecular toolshave proven effective in discerning dietary preferences of piscivorous birds. In this study, a totalof 151 faecal samples were collected from 6 bird species of lacustrine piscivorous birds occupying36 lakes from 2018 to 2022. Faecal samples were analysed using two molecular methods todetermine the proportion of fish DNA using 1) high-throughput sequencing metabarcoding withthe teleo-2 universal fish primer and 2) a digital droplet PCR array with 7 species-specific newlydesigned primers targeting the most common prey fish species in Scandinavian freshwaterecosystems. The dominant prey species identified by both methods were: whitefish (Coregonuslavaretus), Eurasian perch (Perca fluviatilis) and Eurasian minnow (Phoxinus phoxinus). The twomethods showed a high degree of agreement, suggesting that they both provide accurateassessments of the dietary compositions of bird diets.

National Category
Ecology
Research subject
biology; biology
Identifiers
URN: urn:nbn:se:umu:diva-224500OAI: oai:DiVA.org:umu-224500DiVA, id: diva2:1858847
Available from: 2024-05-20 Created: 2024-05-20 Last updated: 2024-05-20
In thesis
1. Using environmental DNA to unravel aquatic ecosystem dynamics
Open this publication in new window or tab >>Using environmental DNA to unravel aquatic ecosystem dynamics
2024 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Human-induced climate change has led to unprecedented declines in Earth's biodiversity and significant habitat loss. Aquatic ecosystems areespecially at risk, facing pollution, overexploitation, and destruction. Consequently, monitoring biodiversity is critical. Traditional monitoring methods are often low in detection rates, time-consuming, invasive, and harmful to species, which hampers comprehensive biodiversity assessments. Environmental DNA (eDNA) offers a rapid alternative fortaxonomic identification, extracting genetic material from soil, sediments, or water without capturing living organisms, proving useful where traditional methods fall short. However, its integration into aquatic ecology is hampered by unresolved methodological issues.

This thesis demonstrates how eDNA can help reconstruct fish colonization histories in lakes post-glacial retreat. I employed species-specific primers with digital droplet PCR and metagenomic shotgun sequencing on ancient DNA from Holocene lake sediments. My findings show the detectability of DNA from ancient fish populations. However, each method exhibited technical limitations that led to varying degrees offalse negatives and false positive results. Additionally, I examined how Northern pike (Esox Lucius) affects ecological speciation in Europeanwhitefish (Coregonus lavaretus), promoting a shift from insectivorous to piscivorous states, enhancing predator biodiversity and biomass. Dietan alyses of piscivorous birds through digital droplet PCR revealed that smaller whitefish support a larger, more diverse bird community. Finally, I compared two molecular techniques for quantifying bird diets from fecal DNA, finding that metabarcoding with a universal fish primer and digital droplet PCR yielded similar results. This research enhances ourunderstanding of the potential and limitations of molecular tools forspecies identification and aids the integration of eDNA into aquatic ecology.

Place, publisher, year, edition, pages
Umeå: Umeå University, 2024. p. 24
Keywords
Environmental DNA, ancient DNA, colonization, apex predator, pike, whitefish, piscivorous birds, aquatic ecosystems, metabarcoding, digital droplet PCR
National Category
Ecology
Research subject
biology
Identifiers
urn:nbn:se:umu:diva-224501 (URN)978-91-8070-412-0 (ISBN)978-91-8070-413-7 (ISBN)
Public defence
2024-06-14, KBE303, Stora Hörsalen, KBC-huset, Umeå, 13:00 (English)
Opponent
Supervisors
Available from: 2024-05-24 Created: 2024-05-20 Last updated: 2024-05-21Bibliographically approved

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Olajos, FredrikEnglund, Göran

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CiteExportLink to record
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Citation style
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