| 1. |
- Capo, Eric, et al.
(författare)
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Lake sedimentary dna research on past terrestrial and aquatic biodiversity: Overview and recommendations
- 2021
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Ingår i: Quaternary. - : MDPI. - 2571-550X. ; 4:1
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Forskningsöversikt (refereegranskat)abstract
- 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.
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| 2. |
- Williams, John W., et al.
(författare)
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Strengthening global-change science by integrating aeDNA with paleoecoinformatics
- 2023
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Ingår i: Trends in Ecology & Evolution. - : Elsevier. - 0169-5347 .- 1872-8383. ; 38:10, s. 946-960
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 3. |
- Bell, Karen L., et al.
(författare)
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Plants, pollinators and their interactions under global ecological change : The role of pollen DNA metabarcoding
- 2023
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Ingår i: Molecular Ecology. - : John Wiley & Sons. - 0962-1083 .- 1365-294X. ; 32:23, s. 6345-6362
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 4. |
- Johnson, Mark D., et al.
(författare)
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Environmental DNA as an emerging tool in botanical research
- 2023
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Ingår i: American Journal of Botany. - : John Wiley & Sons. - 0002-9122 .- 1537-2197. ; 110:2
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Forskningsöversikt (refereegranskat)abstract
- 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.
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| 5. |
- Michel, Alice, et al.
(författare)
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Isolated Grauer's gorilla populations differ in diet and gut microbiome
- 2023
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Ingår i: Molecular Ecology. - : John Wiley & Sons. - 0962-1083 .- 1365-294X. ; 32:23, s. 6523-6542
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Tidskriftsartikel (refereegranskat)abstract
- The animal gut microbiome has been implicated in a number of key biological processes, ranging from digestion to behaviour, and has also been suggested to facilitate local adaptation. Yet studies in wild animals rarely compare multiple populations that differ ecologically, which is the level at which local adaptation may occur. Further, few studies simultaneously characterize diet and gut microbiome from the same sample, despite their probable interdependence. Here, we investigate the interplay between diet and gut microbiome in three geographically isolated populations of the critically endangered Grauer's gorilla (Gorilla beringei graueri), which we show to be genetically differentiated. We find population- and social group-specific dietary and gut microbial profiles and covariation between diet and gut microbiome, despite the presence of core microbial taxa. There was no detectable effect of age, and only marginal effects of sex and genetic relatedness on the microbiome. Diet differed considerably across populations, with the high-altitude population consuming a lower diversity of plants compared to low-altitude populations, consistent with plant availability constraining dietary choices. The observed pattern of covariation between diet and gut microbiome is probably a result of long-term social and environmental factors. Our study suggests that the gut microbiome is sufficiently plastic to support flexible food selection and hence contribute to local adaptation.
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| 6. |
- Nota, Kevin, 1993-, et al.
(författare)
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Norway spruce postglacial recolonization of Fennoscandia
- 2022
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Ingår i: Nature Communications. - : Nature Publishing Group. - 2041-1723. ; 13:1
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 7. |
- Nota, Kevin, 1993-
(författare)
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Palaeoenvironmental reconstructions from modern and ancient plant DNA
- 2022
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Palaeoecological studies on lake sediments and peat archives have provided fundamental knowledge about past environments, nevertheless, a lot remains to be learned. In this thesis, I focussed on plant ancient DNA extracted from sedimentary archives (sedaDNA), in combination with DNA from living trees with the aims of: (1) investigating different extraction methods and levels of inhibition in sediments, (2) investigating postglacial recolonisation history of Norway spruce in Fennoscandia, (3) comparing different sequencing and bioinformatic approaches to investigate past flora changes using sedaDNA and investigating past flora change in contrasting environments (southern Italy versus southern Sweden), and (4) communicating my work more broadly using art.Based on seven original methodological case studies investigating enzyme inhibition, the effect of freeze-thaw and oxygen exposure on microbial composition, and the effects of DNA extraction methods on biological diversity, we formulated guidelines and recommendations for future sedaDNA analyses. We analysed DNA traces of spruce in multiple sediments from northern Europe and confirmed that the species was present in central Sweden already at the beginning of the Holocene and, more controversially, at the end of the last glaciation in southern Sweden. Moreover, genetic ancestry of spruce trees still growing today in central Sweden suggested eastern origin of early spruce colonisers. We further demonstrated that, when sedaDNA reads are mapped to a large and high-quality nuclear plant DNA database, shotgun metagenomic analysis outperforms metabarcoding for reconstructing flora in degraded samples. However, metabarcoding remains a powerful tool to investigate past flora, because our metabarcoding analysis on southern Italian lake sediment, showed woody taxa replacement in the Holocene in good agreement with previous pollen analysis. Despite several methodological issues which complicated our floristic interpretations, at this site we also recovered a rich herbaceous flora and many aquatics. Similar methodological issues and complications, however, were also observed at higher latitudes in southern Sweden during the transition from full Glacial to the Holocene, indicating that sedaDNA from temperate environments is a comparable source of information for floral reconstruction as from high-latitude lakes. Finally, during the work of my thesis, we produced five original paintings through a long collaboration with the scientist and artist Jill Pelto, which I used in this thesis and on many other occasions to illustrate and communicate our work to a broader audience.
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