Logo: to the web site of Uppsala University

uu.sePublications from Uppsala University
Change search
Link to record
Permanent link

Direct link
Alternative names
Publications (10 of 41) Show all publications
Johnson, M. D., Freeland, J. R., Parducci, L., Evans, D. M., Meyer, R. S., Molano-Flores, B. & Davis, M. A. (2023). Environmental DNA as an emerging tool in botanical research. American Journal of Botany, 110(2), Article ID e16120.
Open this publication in new window or tab >>Environmental DNA as an emerging tool in botanical research
Show others...
2023 (English)In: American Journal of Botany, ISSN 0002-9122, E-ISSN 1537-2197, Vol. 110, no 2, article id e16120Article, review/survey (Refereed) Published
Abstract [en]

Over the past quarter century, environmental DNA (eDNA) has been ascendant as a tool to detect, measure, and monitor biodiversity (species and communities), as a means of elucidating biological interaction networks, and as a window into understanding past patterns of biodiversity. However, only recently has the potential of eDNA been realized in the botanical world. Here we synthesize the state of eDNA applications in botanical systems with emphases on aquatic, ancient, contemporary sediment, and airborne systems, and focusing on both single-species approaches and multispecies community metabarcoding. Further, we describe how abiotic and biotic factors, taxonomic resolution, primer choice, spatiotemporal scales, and relative abundance influence the utilization and interpretation of airborne eDNA results. Lastly, we explore several areas and opportunities for further development of eDNA tools for plants, advancing our knowledge and understanding of the efficacy, utility, and cost-effectiveness, and ultimately facilitating increased adoption of eDNA analyses in botanical systems.

Place, publisher, year, edition, pages
John Wiley & Sons, 2023
Keywords
ancient botanical eDNA, aquatic botanical eDNA, botanical eDNA, eDNA, organism derived botanical eDNA, review
National Category
Biological Systematics Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-502445 (URN)10.1002/ajb2.16120 (DOI)000928386300001 ()36632660 (PubMedID)
Available from: 2023-05-25 Created: 2023-05-25 Last updated: 2023-05-25Bibliographically approved
Bell, K. L., Turo, K. J., Lowe, A., Nota, K., Keller, A., Encinas-Viso, F., . . . de Vere, N. (2023). Plants, pollinators and their interactions under global ecological change: The role of pollen DNA metabarcoding. Molecular Ecology, 32(23), 6345-6362
Open this publication in new window or tab >>Plants, pollinators and their interactions under global ecological change: The role of pollen DNA metabarcoding
Show others...
2023 (English)In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 32, no 23, p. 6345-6362Article in journal (Refereed) Published
Abstract [en]

Anthropogenic activities are triggering global changes in the environment, causing entire communities of plants, pollinators and their interactions to restructure, and ultimately leading to species declines. To understand the mechanisms behind community shifts and declines, as well as monitoring and managing impacts, a global effort must be made to characterize plant-pollinator communities in detail, across different habitat types, latitudes, elevations, and levels and types of disturbances. Generating data of this scale will only be feasible with rapid, high-throughput methods. Pollen DNA metabarcoding provides advantages in throughput, efficiency and taxonomic resolution over traditional methods, such as microscopic pollen identification and visual observation of plant-pollinator interactions. This makes it ideal for understanding complex ecological networks and their responses to change. Pollen DNA metabarcoding is currently being applied to assess plant-pollinator interactions, survey ecosystem change and model the spatiotemporal distribution of allergenic pollen. Where samples are available from past collections, pollen DNA metabarcoding has been used to compare contemporary and past ecosystems. New avenues of research are possible with the expansion of pollen DNA metabarcoding to intraspecific identification, analysis of DNA in ancient pollen samples, and increased use of museum and herbarium specimens. Ongoing developments in sequencing technologies can accelerate progress towards these goals. Global ecological change is happening rapidly, and we anticipate that high-throughput methods such as pollen DNA metabarcoding are critical for understanding the evolutionary and ecological processes that support biodiversity, and predicting and responding to the impacts of change.

Place, publisher, year, edition, pages
John Wiley & Sons, 2023
Keywords
DNA metabarcoding, ecosystem change, environmental DNA, global change ecology, metagenomics, pollen, pollination
National Category
Ecology
Identifiers
urn:nbn:se:uu:diva-531648 (URN)10.1111/mec.16689 (DOI)000859506700001 ()36086900 (PubMedID)
Available from: 2024-06-17 Created: 2024-06-17 Last updated: 2024-06-17Bibliographically approved
Williams, J. W., Spanbauer, T. L., Heintzman, P. D., Blois, J., Capo, E., Goring, S. J., . . . Wood, J. (2023). Strengthening global-change science by integrating aeDNA with paleoecoinformatics. Trends in Ecology & Evolution, 38(10), 946-960
Open this publication in new window or tab >>Strengthening global-change science by integrating aeDNA with paleoecoinformatics
Show others...
2023 (English)In: Trends in Ecology & Evolution, ISSN 0169-5347, E-ISSN 1872-8383, Vol. 38, no 10, p. 946-960Article in journal (Refereed) Published
Abstract [en]

Ancient environmental DNA (aeDNA) data are close to enabling insights into past global-scale biodiversity dynamics at unprecedented taxonomic extent and resolution. However, achieving this potential requires solutions that bridge bioinformatics and paleoecoinformatics. Essential needs include support for dynamic taxonomic inferences, dynamic age inferences, and precise stratigraphic depth. Moreover, aeDNA data are complex and heterogeneous, generated by dispersed researcher networks, with methods advancing rapidly. Hence, expert community governance and curation are essential to building high-value data resources. Immediate recommendations include uploading metabarcoding-based taxonomic inventories into paleoecoinformatic resources, building linkages among open bioinformatic and paleoecoinformatic data resources, harmonizing aeDNA processing workflows, and expanding community data governance. These advances will enable transformative insights into global-scale biodiversity dynamics during large environmental and anthropogenic changes.

Place, publisher, year, edition, pages
Elsevier, 2023
National Category
Ecology
Identifiers
urn:nbn:se:uu:diva-519968 (URN)10.1016/j.tree.2023.04.016 (DOI)001079251100001 ()37230884 (PubMedID)
Available from: 2024-01-10 Created: 2024-01-10 Last updated: 2024-01-12Bibliographically approved
Nota, K., Klaminder, J., Milesi, P., Bindler, R., Nobile, A., van Steijn, T., . . . Parducci, L. (2022). Norway spruce postglacial recolonization of Fennoscandia. Nature Communications, 13, Article ID 1333.
Open this publication in new window or tab >>Norway spruce postglacial recolonization of Fennoscandia
Show others...
2022 (English)In: Nature Communications, E-ISSN 2041-1723, Vol. 13, article id 1333Article in journal (Refereed) Published
Abstract [en]

Contrasting theories exist regarding how Norway spruce (Picea abies) recolonized Fennoscandia after the last glaciation and both early Holocene establishments from western microrefugia and late Holocene colonization from the east have been postulated. Here, we show that Norway spruce was present in southern Fennoscandia as early as 14.7 ± 0.1 cal. kyr BP and that the millennia-old clonal spruce trees present today in central Sweden likely arrived with an early Holocene migration from the east. Our findings are based on ancient sedimentary DNA from multiple European sites (N = 15) combined with nuclear and mitochondrial DNA analysis of ancient clonal (N = 135) and contemporary spruce forest trees (N = 129) from central Sweden. Our other findings imply that Norway spruce was present shortly after deglaciation at the margins of the Scandinavian Ice Sheet, and support previously disputed finds of pollen in southern Sweden claiming spruce establishment during the Lateglacial.

Place, publisher, year, edition, pages
Springer NatureSpringer Nature, 2022
National Category
Ecology
Identifiers
urn:nbn:se:uu:diva-467857 (URN)10.1038/s41467-022-28976-4 (DOI)000769063600023 ()35288569 (PubMedID)
Funder
Swedish Research Council, 2017-04548Swedish Research Council, 2018-05973Knut and Alice Wallenberg Foundation
Available from: 2022-02-17 Created: 2022-02-17 Last updated: 2024-01-15Bibliographically approved
Capo, E., Giguet-Covex, C., Rouillard, A., Nota, K., Heintzman, P. D., Vuillemin, A., . . . Parducci, L. (2021). Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations. Quaternary, 4(1), Article ID 6.
Open this publication in new window or tab >>Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations
Show others...
2021 (English)In: Quaternary, E-ISSN 2571-550X, Vol. 4, no 1, article id 6Article, review/survey (Refereed) Published
Abstract [en]

The use of lake sedimentary DNA to track the long-term changes in both terrestrial and aquatic biota is a rapidly advancing field in paleoecological research. Although largely applied nowadays, knowledge gaps remain in this field and there is therefore still research to be conducted to ensure the reliability of the sedimentary DNA signal. Building on the most recent literature and seven original case studies, we synthesize the state-of-the-art analytical procedures for effective sampling, extraction, amplification, quantification and/or generation of DNA inventories from sedimentary ancient DNA (sedaDNA) via high-throughput sequencing technologies. We provide recommendations based on current knowledge and best practises.

Place, publisher, year, edition, pages
MDPIMDPI AG, 2021
Keywords
sedimentary ancient DNA, sedimentary DNA, lake sediments, paleolimnology, paleoecology, paleogenetics, paleogenomics, metabarcoding, metagenomics, biodiversity
National Category
Oceanography, Hydrology and Water Resources
Identifiers
urn:nbn:se:uu:diva-440931 (URN)10.3390/quat4010006 (DOI)000633093700001 ()
Funder
Knut and Alice Wallenberg Foundation, 2016.0083Swedish Research Council Formas, FR-2016/0005Swedish Research Council, 2018-05973
Available from: 2021-04-22 Created: 2021-04-22 Last updated: 2024-01-15Bibliographically approved
Parducci, L. (2020). Environmental DNA: For Biodiversity Research and Monitoring [Review]. The Holocene, 30(1), 197-198
Open this publication in new window or tab >>Environmental DNA: For Biodiversity Research and Monitoring
2020 (English)In: The Holocene, ISSN 0959-6836, E-ISSN 1477-0911, Vol. 30, no 1, p. 197-198Article, book review (Other academic) Published
Place, publisher, year, edition, pages
SAGE PUBLICATIONS LTD, 2020
National Category
Physical Geography
Identifiers
urn:nbn:se:uu:diva-403531 (URN)10.1177/0959683619877297 (DOI)000506460700017 ()
Available from: 2020-01-31 Created: 2020-01-31 Last updated: 2020-01-31Bibliographically approved
Shamsabad, M. M., Assadi, M. & Parducci, L. (2019). Phylogeography and population genetics of Acanthophyllum squarrosum complex (Caryophyllaceae) in the Irano-Turanian region. Systematics and Biodiversity, 17(4), 412-421
Open this publication in new window or tab >>Phylogeography and population genetics of Acanthophyllum squarrosum complex (Caryophyllaceae) in the Irano-Turanian region
2019 (English)In: Systematics and Biodiversity, ISSN 1477-2000, E-ISSN 1478-0933, Vol. 17, no 4, p. 412-421Article in journal (Refereed) Published
Abstract [en]

Acanthophyllum squarrosum and two closely related species, A. heratense and A. laxiusculum (Caryophyllaceae), form a complex that covers parts of subalpine steppes of the Irano-Turanian (IT) region. In this study, we explored the genetic structure and phylogeography of this complex based on partial sequences of two chloroplasts (psbA-trnH and rpl32-trnL (UAG)) and two nuclear (EST24 and nrITS) DNA regions. We analysed 80 individuals from eight populations and detected 12 chloroplast haplotypes, 16 and eight nuclear alleles in EST24 and nrITS sequences, respectively. Phylogenetic trees and haplotype networks did not show distinct genetic groups in the complex and this could be explained by incomplete lineage sorting or introgression between species. Divergence time analysis revealed a Quaternary origin for A. squarrosum complex at approximately 1.8 million years ago (Mya) and the neutrality test results indicated that this complex experienced a recent population expansion. AMOVA analysis of the chloroplast regions showed a significant genetic differentiation among populations and low genetic differentiation within populations, but opposite results were found with nuclear markers, implying introgression between A. squarrosum complex populations.

Place, publisher, year, edition, pages
Taylor & Francis, 2019
Keywords
Acanthophyllum, Irano-Turanian region, phylogeny, phylogeography, population genetics, species complex
National Category
Genetics
Identifiers
urn:nbn:se:uu:diva-390684 (URN)10.1080/14772000.2019.1590476 (DOI)000475183500001 ()
Available from: 2019-08-14 Created: 2019-08-14 Last updated: 2019-08-14Bibliographically approved
Parducci, L. (2019). Quaternary DNA: A Multidisciplinary Research Field. Quaternary, 2(4), Article ID 37.
Open this publication in new window or tab >>Quaternary DNA: A Multidisciplinary Research Field
2019 (English)In: Quaternary, E-ISSN 2571-550X, Vol. 2, no 4, article id 37Article, review/survey (Refereed) Published
Abstract [en]

The purpose of this Milankovitch review is to explain the significance of Quaternary DNA studies and the importance of the recent methodological advances that have enabled the study of late Quaternary remains in more detail, and the testing of new assumptions in evolutionary biology and phylogeography to reconstruct the past. The topic is wide, and this review is not intended to be an exhaustive account of all the aDNA work performed in the last three decades on late-Quaternary remains. Instead, it is a selection of relevant studies aimed at illustrating how aDNA has been used to reconstruct not only environments of the past, but also the history of many species including our own.

National Category
Ecology
Identifiers
urn:nbn:se:uu:diva-402211 (URN)10.3390/quat2040037 (DOI)000505539900004 ()
Available from: 2020-01-13 Created: 2020-01-13 Last updated: 2020-12-16Bibliographically approved
Parducci, L., Alsos, I. G., Unneberg, P., Pedersen, M. W., Han, L., Lammers, Y., . . . Wohlfarth, B. (2019). Shotgun Environmental DNA, Pollen, and Macrofossil Analysis of Lateglacial Lake Sediments From Southern Sweden. Frontiers in Ecology and Evolution, 7, Article ID 189.
Open this publication in new window or tab >>Shotgun Environmental DNA, Pollen, and Macrofossil Analysis of Lateglacial Lake Sediments From Southern Sweden
Show others...
2019 (English)In: Frontiers in Ecology and Evolution, E-ISSN 2296-701X, Vol. 7, article id 189Article in journal (Refereed) Published
Abstract [en]

The lake sediments of Hasseldala Port in south-east Sweden provide an archive of local and regional environmental conditions similar to 14.5-9.5 ka BP (thousand years before present) and allow testing DNA sequencing techniques to reconstruct past vegetation changes. We combined shotgun sequencing with plant micro- and macrofossil analyses to investigate sediments dating to the Allerod (14.1-12.7 ka BP), Younger Dryas (12.7-11.7 ka BP), and Preboreal (<11.7 ka BP). Number of reads and taxa were not associated with sample age or organic content. This suggests that, beyond the initial rapid degradation, DNA is still present. The proportion of recovered plant DNA was low, but allowed identifying an important number of plant taxa, thus adding valid information on the composition of the local vegetation. Importantly, DNA provides a stronger signal of plant community changes than plant micro- and plant macrofossil analyses alone, since a larger number of new taxa were recorded in Younger Dryas samples. A comparison between the three proxies highlights differences and similarities and supports earlier findings that plants growing close to or within a lake are recorded by DNA. Plant macrofossil remains moreover show that tree birch was present close to the ancient lake since the Allerod; together with the DNA results, this indicates that boreal to subarctic climatic conditions also prevailed during the cold Younger Dryas interval. Increasing DNA reference libraries and enrichment strategies prior to sequencing are necessary to improve the potential and accuracy of plant identification using the shotgun metagenomic approach.

Place, publisher, year, edition, pages
Frontiers Media S.A., 2019
Keywords
environmental DNA, ancient DNA, shotgun sequencing (metagenomics), pollen, macrofossils remains, lake sediments
National Category
Geosciences, Multidisciplinary
Identifiers
urn:nbn:se:uu:diva-390682 (URN)10.3389/fevo.2019.00189 (DOI)000472627800001 ()
Funder
Swedish Research Council, 2013-D0568401Swedish Research Council Formas, Dnr 2016-01236Knut and Alice Wallenberg FoundationCarl Tryggers foundation , 14:371The Research Council of Norway, 226134/F50Academy of Finland, 1278692Academy of Finland, 1310649
Available from: 2019-08-15 Created: 2019-08-15 Last updated: 2019-08-15Bibliographically approved
Ahmed, E., Parducci, L., Unneberg, P., Ågren, R., Schenk, F., Rattray, J. E., . . . Wohlfarth, B. (2018). Archaeal community changes in Lateglacial lake sediments: Evidence from ancient DNA. Quaternary Science Reviews, 181, 19-29
Open this publication in new window or tab >>Archaeal community changes in Lateglacial lake sediments: Evidence from ancient DNA
Show others...
2018 (English)In: Quaternary Science Reviews, ISSN 0277-3791, E-ISSN 1873-457X, Vol. 181, p. 19-29Article in journal (Refereed) Published
Abstract [en]

The Lateglacial/early Holocene sediments from the ancient lake at Hasseldala Port, southern Sweden provide an important archive for the environmental and climatic shifts at the end of the last ice age and the transition into the present Interglacial. The existing multi-proxy data set highlights the complex interplay of physical and ecological changes in response to climatic shifts and lake status changes. Yet, it remains unclear how microorganisms, such as Archaea, which do not leave microscopic features in the sedimentary record, were affected by these climatic shifts. Here we present the metagenomic data set of Hasseldala Port with a special focus on the abundance and biodiversity of Archaea. This allows reconstructing for the first time the temporal succession of major Archaea groups between 13.9 and 10.8 ka BP by using ancient environmental DNA metagenomics and fossil archaeal cell membrane lipids. We then evaluate to which extent these findings reflect physical changes of the lake system, due to changes in lake-water summer temperature and seasonal lake-ice cover. We show that variations in archaeal composition and diversity were related to a variety of factors (e.g., changes in lake water temperature, duration of lake ice cover, rapid sediment infilling), which influenced bottom water conditions and the sediment-water interface. Methanogenic Archaea dominated during the Allerod and Younger Dryas pollen zones, when the ancient lake was likely stratified and anoxic for large parts of the year. The increase in archaeal diversity at the Younger Dryas/Holocene transition is explained by sediment infilling and formation of a mire/peatbog. (C) 2017 Elsevier Ltd. All rights reserved.

Place, publisher, year, edition, pages
Elsevier, 2018
Keywords
Ancient DNA, Shotgun sequencing, Archaea, Metagenomics, Lipid biomarkers, Last deglaciation, Paleoclimate, Paleoenvironment, Lake sediments, Southern Sweden
National Category
Geology Climate Research
Identifiers
urn:nbn:se:uu:diva-346889 (URN)10.1016/j.quascirev.2017.11.037 (DOI)000424178200002 ()
Funder
Swedish Nuclear Fuel and Waste Management Company, SKBKnut and Alice Wallenberg Foundation
Available from: 2018-04-04 Created: 2018-04-04 Last updated: 2018-04-04Bibliographically approved
Projects
Ancient DNA of Nordic environments reveals tree response to climate change [2013-05684_VR]; Uppsala University
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0003-1956-4757

Search in DiVA

Show all publications