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dc.contributor.advisorAlsos, Inger Greve
dc.contributor.authorElliott, Lucas Dane
dc.date.accessioned2024-10-25T10:29:30Z
dc.date.available2024-10-25T10:29:30Z
dc.date.issued2024-11-15
dc.description.abstractPast ecosystem dynamics provide valuable information to inform current and future management. Ancient DNA has rapidly become a powerful tool in uncovering these lost environments. We demonstrate the ecological inferences made possible by metabarcoding analysis on sedimentary ancient DNA by investigating the role climate and glacial activity have had on a catchment’s vegetation community. We identified four plant assemblages spanning the Holocene at Jøkelvatnet, a lake in northern Norway, that shifted concurrently with glacial activity and mean summer temperatures. The taxonomic resolution of metabarcoding allowed for traits of the assemblages, such as soil disturbance dependence and temperature optimum, to be reconstructed through time. However, metabarcoding and standard shotgun sequencing analysis methods are targeting only a small fraction of the total DNA preserved in sediment archives. We present two workflows that expand the genomic breadth of information able to be retrieved from these repositories. Multiplex PCR allows for the reliable recovery of intraspecific variable sites for an organism of interest. We demonstrate this ability by identifying four populations of Vaccinium uliginosum in five sediment cores spanning the Holocene. In shotgun sequencing analysis, reference databases are currently limited to assembled genomic regions which comprise only a small fraction of total biodiversity. Here we present wholeskim, a pipeline that allows for unassembled genome skims to be used as a reference for annotating ancient metagenomes, unlocking previously inaccessible nuclear genomic regions for study. These tools show promise for obtaining larger amounts and more varied information from sedimentary ancient DNA.en_US
dc.description.abstractEndringer i fortidens økosystemer gir verdifull innsikt for å veilede nåværende og fremtidige miljøtiltak. Urgammelt DNA (aDNA) har raskt etablert seg som et effektivt verktøy for å utforske disse tapte økosystemene. Vi demonstrerer økologiske innsikter muliggjort av metabarcoding-analyse på urgammelt DNA fra innsjøsedimenter (sedaDNA), ved å utforske hvordan klimaendringer og bre-aktivitet har påvirket vegetasjonsutviklingen. Ved Jøkelvannet, en innsjø i Nord-Norge, identifiserte vi fire vegetasjonsperioder i Holocen som endret seg i takt med bre-aktivitet og gjennomsnittlige sommertemperaturer. Metabarcodingens taksonomiske oppløsningen muliggjorde rekonstruksjon av plantenes egenskaper over tid, inkludert deres tilpasning til forstyrrelser og temperaturforhold.  Metabarcoding og standard shotgun sequencing metoder fokuserer imidlertid kun på en liten brøkdel av det totale DNA som er bevart i sedimentene. Vi presenterer to teknikker som utvider den genomiske bredden av informasjon som kan ekstraheres fra disse kildene. Multiplex PCR muliggjør pålitelig utvinning av intraspesifikke variable DNA koder for fokusorganismer. Vi demonstrerer denne metoden ved å identifisere fire populasjoner av blokkebær i fem sedimentkjerner gjennom Holocen. I shotgun sequencing er referansedatabaser for tiden begrenset til sammensatte genomiske regioner som bare omfatter en liten brøkdel av det totale biologiske mangfoldet. Vi introduserer wholeskim, en bioinformatisk prosess som gjør det mulig å bruke primære DNA fragmenter som referanse for å identifisere urgammle metagenomer, og derved åpne opp tidligere utilgjengelige nukleære genomiske områder for forskning. Disse verktøyene viser stort potensiale for å utvide mengder og variasjon av informasjon fra urgammelt DNA.en_US
dc.description.doctoraltypeph.d.en_US
dc.description.popularabstractPast ecosystem dynamics provide valuable information to inform current and future management. Ancient DNA has rapidly become a powerful tool in uncovering these lost environments. We demonstrate the ecological inferences made possible by metabarcoding analysis on sedimentary ancient DNA by investigating the role climate and glacial activity have had on a catchment’s vegetation community. We identified four plant assemblages spanning the Holocene at Jøkelvatnet, a lake in northern Norway, that shifted concurrently with glacial activity and mean summer temperatures. The taxonomic resolution of metabarcoding allowed for traits of the assemblages, such as soil disturbance dependence and temperature optimum, to be reconstructed through time. However, metabarcoding and standard shotgun sequencing analysis methods are targeting only a small fraction of the total DNA preserved in sediment archives. We present two workflows that expand the genomic breadth of information able to be retrieved from these repositories. Multiplex PCR allows for the reliable recovery of intraspecific variable sites for an organism of interest. We demonstrate this ability by identifying four populations of Vaccinium uliginosum in five sediment cores spanning the Holocene. In shotgun sequencing analysis, reference databases are currently limited to assembled genomic regions which comprise only a small fraction of total biodiversity. Here we present wholeskim, a pipeline that allows for unassembled genome skims to be used as a reference for annotating ancient metagenomes, unlocking previously inaccessible nuclear genomic regions for study. These tools show promise for obtaining larger amounts and more varied information from sedimentary ancient DNA.en_US
dc.identifier.isbn978-82-8266-268-0
dc.identifier.urihttps://hdl.handle.net/10037/35339
dc.language.isoengen_US
dc.publisherUiT The Arctic University of Norwayen_US
dc.publisherUiT Norges arktiske universiteten_US
dc.relation.haspart<p>Paper I: Elliott, L.D., Rijal, D.P., Brown, A.G., Bakke, J., Topstad, L., Heintzman, PD., & Alsos, I.G. (2023). Sedimentary ancient DNA reveals local vegetation changes driven by glacial activity and climate. <i>Quaternary, 6</i>(1), 7. Also available in Munin at <a href=https://hdl.handle.net/10037/28744>https://hdl.handle.net/10037/28744</a>. <p>Paper II: Lammers, Y., Taberlet, P., Coissac, E., Elliott, L.D., Merkel, M.F., Pitelkova, I., PhyloAlps Consortium, PhyloNorway Consortium & Alsos, I.G. (2024). Multiplexing PCR allows the identification of within‐species genetic diversity in ancient eDNA. <i>Molecular Ecology Resources, 24</i>(3), e13926. Also available in Munin at <a href=https://hdl.handle.net/10037/34467> https://hdl.handle.net/10037/34467</a>. <p>Paper III: Elliott, L.D., Boyer, F., Lemane, T. PhyloNorway Consortium, Alsos, I.G. & Coissac, E. Wholeskim: utilizing genome skims for taxonomically annotating ancient DNA metagenomes. (Manuscript). <p>Paper IV: Elliott, L.D., Murchie, T., Stoof-Leichsenring, K., Strandberg, N., Merkel, M.F., Pitelkova, I. & Alsos, I.G. Comparison of target enrichment and shotgun sequencing of lake sedaDNA metagenomes. (Manuscript).en_US
dc.rights.accessRightsopenAccessen_US
dc.rights.holderCopyright 2024 The Author(s)
dc.rights.urihttps://creativecommons.org/licenses/by-nc-sa/4.0en_US
dc.rightsAttribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)en_US
dc.titleUnlocking the potential of sedimentary ancient DNAen_US
dc.typeDoctoral thesisen_US
dc.typeDoktorgradsavhandlingen_US


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