| 1. |
- Kjær, Kurt H., et al.
(författare)
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A 2-million-year-old ecosystem in Greenland uncovered by environmental DNA
- 2022
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Ingår i: Nature. - : Springer Nature. - 0028-0836 .- 1476-4687. ; 612:7939, s. 283-291
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Tidskriftsartikel (refereegranskat)abstract
- Late Pliocene and Early Pleistocene epochs 3.6 to 0.8 million years ago1 had climates resembling those forecasted under future warming2. Palaeoclimatic records show strong polar amplification with mean annual temperatures of 11–19 °C above contemporary values3,4. The biological communities inhabiting the Arctic during this time remain poorly known because fossils are rare5. Here we report an ancient environmental DNA6 (eDNA) record describing the rich plant and animal assemblages of the Kap København Formation in North Greenland, dated to around two million years ago. The record shows an open boreal forest ecosystem with mixed vegetation of poplar, birch and thuja trees, as well as a variety of Arctic and boreal shrubs and herbs, many of which had not previously been detected at the site from macrofossil and pollen records. The DNA record confirms the presence of hare and mitochondrial DNA from animals including mastodons, reindeer, rodents and geese, all ancestral to their present-day and late Pleistocene relatives. The presence of marine species including horseshoe crab and green algae support a warmer climate than today. The reconstructed ecosystem has no modern analogue. The survival of such ancient eDNA probably relates to its binding to mineral surfaces. Our findings open new areas of genetic research, demonstrating that it is possible to track the ecology and evolution of biological communities from two million years ago using ancient eDNA.
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| 2. |
- Olajos, Fredrik, et al.
(författare)
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Fish colonization patterns in central Sweden from dropletdigital PCR and shotgun sequencing of sedimentary DNA
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- 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.
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| 3. |
- Parducci, Laura, 1965-, et al.
(författare)
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Ancient plant DNA in lake sediments
- 2017
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Ingår i: New Phytologist. - : Wiley. - 0028-646X .- 1469-8137. ; 214:3, s. 924-942
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Forskningsöversikt (refereegranskat)abstract
- Recent advances in sequencing technologies now permit the analyses of plant DNA from fossil samples (ancient plant DNA, plant aDNA), and thus enable the molecular reconstruction of palaeofloras. Hitherto, ancient frozen soils have proved excellent in preserving DNA molecules, and have thus been the most commonly used source of plant aDNA. However, DNA from soil mainly represents taxa growing a few metres from the sampling point. Lakes have larger catchment areas and recent studies have suggested that plant a DNA from lake sediments is a more powerful tool for palaeofloristic reconstruction. Furthermore, lakes can be found globally in nearly all environments, and are therefore not limited to perennially frozen areas. Here, we review the latest approaches and methods for the study of plant aDNA from lake sediments and discuss the progress made up to the present. We argue that a DNA analyses add new and additional perspectives for the study of ancient plant populations and, in time, will provide higher taxonomic resolution and more precise estimation of abundance. Despite this, key questions and challenges remain for such plant aDNA studies. Finally, we provide guidelines on technical issues, including lake selection, and we suggest directions for future research on plant aDNA studies in lake sediments.
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| 4. |
- Wang, Yucheng, et al.
(författare)
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Late Quaternary Dynamics of Arctic Biota from Ancient Environmental Genomics
- 2021
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 600:7887, s. 86-92
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Tidskriftsartikel (refereegranskat)abstract
- During the last glacial–interglacial cycle, Arctic biotas experienced substantial climatic changes, yet the nature, extent and rate of their responses are not fully understood1–8. Here we report a large-scale environmental DNA metagenomic study of ancient plant and mammal communities, analysing 535 permafrost and lake sediment samples from across the Arctic spanning the past 50,000 years. Furthermore, we present 1,541 contemporary plant genome assemblies that were generated as reference sequences. Our study provides several insights into the long-term dynamics of the Arctic biota at the circumpolar and regional scales. Our key fndings include: (1) a relatively homogeneous steppe–tundra fora dominated the Arctic during the Last Glacial Maximum, followed by regional divergence of vegetation during the Holocene epoch; (2) certain grazing animals consistently co-occurred in space and time; (3) humans appear to have been a minor factor in driving animal distributions; (4) higher efective precipitation, as well as an increase in the proportion of wetland plants, show negative efects on animal diversity; (5) the persistence of the steppe–tundra vegetation in northern Siberia enabled the late survival of several now-extinct megafauna species, including the woolly mammoth until 3.9 ± 0.2 thousand years ago (ka) and the woolly rhinoceros until 9.8 ± 0.2 ka; and (6) phylogenetic analysis of mammoth environmental DNA reveals a previously unsampled mitochondrial lineage. Our fndings highlight the power of ancient environmental metagenomics analyses to advance understanding of population histories and long-term ecological dynamics
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| 5. |
- Wang, Yucheng, et al.
(författare)
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Reply to: When did mammoths go extinct?
- 2022
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 612:7938, s. 4-6
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Tidskriftsartikel (refereegranskat)
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| 6. |
- 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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