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Fish colonization patterns in central Sweden from dropletdigital PCR and shotgun sequencing of sedimentary DNA
Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.ORCID iD: 0000-0003-2001-5077
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(English)Manuscript (preprint) (Other academic)
Abstract [en]

The natural establishment of Scandinavian fish populations took place following the lastdeglaciation 9,000 to 12,000 years ago when the retreating ice exposed new habitats. Accessibilityof lakes from the Proto-Baltic sea and the southern freshwater habitats was influenced by theirelevation relative to the post-glacial coastline, with some lakes being unreachable due to migrationbarriers. Long standing hypotheses regarding colonization routes have been formulated based onmodern distribution patterns, knowledge of historic climate variations, and species’ tolerances toenvironmental conditions. These hypotheses have not been tested with other forms of evidencebecause long-term data on past fish histories are limited. In this study, the colonization history ofseveral fish species was investigated using historical data combined with analyses of sedimentaryDNA from Lake Hotagen in central Sweden which is located above the post-glacial coastline.DNA was analyzed with droplet digital PCR (ddPCR) and metagenomic shotgun sequencingapproaches. The ddPCR array used specific primers of seven species known to have beenhistorically present at the lake, and successfully detected 5/7 species in the top 80 cm (~3000 years)of the sediment core where DNA was best preserved. Metagenomics however detected 6/8expected genera in all sediment samples dating back 7000 years. Based on our findings, we inferthat 1) (dd)PCR based methods had too low sensitivity to allow consistent detection of fish inancient samples and 2) metagenomics, while sufficiently sensitive, require expanded databases toincrease granularity across species, especially those who are currently underrepresented. 3) Mostfish species likely colonized lake Hotagen soon after the last deglaciation despite the presence ofmigration barriers.

National Category
Ecology
Research subject
biology
Identifiers
URN: urn:nbn:se:umu:diva-224498OAI: oai:DiVA.org:umu-224498DiVA, id: diva2:1858840
Available from: 2024-05-20 Created: 2024-05-20 Last updated: 2024-05-21
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, Fredrik

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