| 1. |
- Kjær, Kurt H., et al.
(author)
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A 2-million-year-old ecosystem in Greenland uncovered by environmental DNA
- 2022
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In: Nature. - : Springer Nature. - 0028-0836 .- 1476-4687. ; 612:7939, s. 283-291
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Journal article (peer-reviewed)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. |
- Rijal, Dilli P., et al.
(author)
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Sedimentary ancient DNA shows terrestrial plant richness continuously increased over the Holocene in northern Fennoscandia
- 2021
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In: Science Advances. - : American Association for the Advancement of Science (AAAS). - 2375-2548. ; 7:31
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Journal article (peer-reviewed)abstract
- The effects of climate change on species richness are debated but can be informed by the past. Here, we generated a sedimentary ancient DNA dataset covering 10 lakes and applied novel methods for data harmonization. We assessed the impact of Holocene climate changes and nutrients on terrestrial plant richness in northern Fennoscandia. We find that richness increased steeply during the rapidly warming Early Holocene. In contrast to findings from most pollen studies, we show that richness continued to increase thereafter, although the climate was stable, with richness and the regional species pool only stabilizing during the past three millennia. Furthermore, overall increases in richness were greater in catchments with higher soil nutrient availability. We suggest that richness will increase with ongoing warming, especially at localities with high nutrient availability and assuming that human activity remains low in the region, although lags of millennia may be expected.
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| 3. |
- Capo, Eric, et al.
(author)
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Lake sedimentary dna research on past terrestrial and aquatic biodiversity: Overview and recommendations
- 2021
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In: Quaternary. - : MDPI. - 2571-550X. ; 4:1
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Research review (peer-reviewed)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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| 4. |
- Elliott, Lucas D., et al.
(author)
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Sedimentary Ancient DNA Reveals Local Vegetation Changes Driven by Glacial Activity and Climate
- 2023
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In: Quaternary. - : MDPI AG. - 2571-550X. ; 6:1
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Journal article (peer-reviewed)abstract
- Disentangling the effects of glaciers and climate on vegetation is complicated by the confounding role that climate plays in both systems. We reconstructed changes in vegetation occurring over the Holocene at Jøkelvatnet, a lake located directly downstream from the Langfjordjøkel glacier in northern Norway. We used a sedimentary ancient DNA (sedaDNA) metabarcoding dataset of 38 samples from a lake sediment core spanning 10,400 years using primers targeting the P6 loop of the trnL (UAA) intron. A total of 193 plant taxa were identified revealing a pattern of continually increasing richness over the time period. Vegetation surveys conducted around Jøkelvatnet show a high concordance with the taxa identified through sedaDNA metabarcoding. We identified four distinct vegetation assemblage zones with transitions at ca. 9.7, 8.4 and 4.3 ka with the first and last mirroring climatic shifts recorded by the Langfjordjøkel glacier. Soil disturbance trait values of the vegetation increased with glacial activity, suggesting that the glacier had a direct impact on plants growing in the catchment. Temperature optimum and moisture trait values correlated with both glacial activity and reconstructed climatic variables showing direct and indirect effects of climate change on the vegetation. In contrast to other catchments without an active glacier, the vegetation at Jøkelvatnet has displayed an increased sensitivity to climate change throughout the Middle and Late Holocene. Beyond the direct impact of climate change on arctic and alpine vegetation, our results suggest the ongoing disappearance of glaciers will have an additional effect on plant communities.
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| 5. |
- Reveret, Alois, et al.
(author)
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Environmental DNA of aquatic macrophytes : The potential for reconstructing past and present vegetation and environments
- 2023
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In: Freshwater Biology. - 0046-5070 .- 1365-2427. ; 68:10, s. 1929-1950
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Journal article (peer-reviewed)abstract
- Environmental DNA is increasingly being used to reconstruct past and present biodiversity including from freshwater ecosystems. Macrophytes are especially good environmental indicators, thus their environmental DNA palaeorecord might shed light on past postglacial environments. Here, we first review and compare studies that use metagenomics, targeted capture, and various barcoding and metabarcoding markers, in order to explore how each of these methods can be used to capture aquatic vegetation diversity and change. We then investigate the extent to which such a record can be leveraged for reconstructing local environmental conditions, using a case study based on macrophyte ecological niches. We find that, with state-of-the-art DNA barcode reference libraries, using metabarcoding to target the P6 loop region of the chloroplast trnL (UAA) intron is optimal to maximise taxonomic resolution and the diversity of past macrophyte communities. Shotgun sequencing also retrieves a high proportion of aquatic macrophyte diversity, but has the lowest taxonomic resolution, and targeted capture needs to be more widely applied before comparisons can be made. From our case study, we infer past aquatic habitats from sedimentary ancient DNA records of macrophyte taxa. We reconstructed Holocene thermal range, continentality, water pH, trophic status, and light conditions in northern Fennoscandia. We show an overall stability since 9,000 years ago, even though individual lakes display different trends and variation in local climatic and physico-chemical conditions. Combined with the availability of near-exhaustive barcode and traits databases, metabarcoding data can support wider ecological reconstructions that are not limited to aquatic plant taxonomic inventories but can also be used to infer past changes in water conditions and their environmental drivers. Sedimentary DNA is also a powerful tool to measure present diversity, as well as to reconstruct past lacustrine and fluvial communities of aquatic macrophytes.
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| 6. |
- Graae, Bente J., et al.
(author)
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Stay or go - how topographic complexity influences alpine plant population and community responses to climate change
- 2018
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In: Perspectives in plant ecology, evolution and systematics. - : Elsevier BV. - 1433-8319 .- 1618-0437. ; 30, s. 41-50
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Journal article (peer-reviewed)abstract
- In the face of climate change, populations have two survival options - they can remain in situ and tolerate the new climatic conditions (stay), or they can move to track their climatic niches (go). For sessile and small-stature organisms like alpine plants, staying requires broad climatic tolerances, realized niche shifts due to changing biotic interactions, acclimation through plasticity, or rapid genetic adaptation. Going, in contrast, requires good dispersal and colonization capacities. Neither the magnitude of climate change experienced locally nor the capacities required for staying/going in response to climate change are constant across landscapes, and both aspects may be strongly affected by local microclimatic variation associated with topographic complexity. We combine ideas from population and community ecology to discuss the effects of topographic complexity in the landscape on the immediate stay or go opportunities of local populations and communities, and on the selective pressures that may have shaped the stay or go capacities of the species occupying contrasting landscapes. We demonstrate, using example landscapes of different topographical complexity, how species' thermal niches could be distributed across these landscapes, and how these, in turn, may affect many population and community ecological processes that are related to adaptation or dispersal. Focusing on treeless alpine or Arctic landscapes, where temperature is expected to be a strong determinant, our theorethical framework leads to the hypothesis that populations and communities of topographically complex (rough and patchy) landscapes should be both more resistant and more resilient to climate change than those of topographically simple (flat and homogeneous) landscapes. Our theorethical framework further points to how meta-community dynamics such as mass effects in topographically complex landscapes and extinction lags in simple landscapes, may mask and delay the long-term outcomes of these landscape differences under rapidly changing climates.
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| 7. |
- Salonen, J. Sakari, et al.
(author)
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Uncovering Holocene climate fluctuations and ancient conifer populations : Insights from a high-resolution multi-proxy record from Northern Finland
- 2024
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In: Global and Planetary Change. - 0921-8181 .- 1872-6364. ; 237
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Journal article (peer-reviewed)abstract
- A series of abrupt climate events linked to circum-North Atlantic meltwater forcing have been recognised in Holocene paleoclimate data. To address the paucity of proxy records able to characterise robustly the regional impacts of these events, we retrieved a sub-centennial resolution, well-dated core sequence from Lake Kuutsjarvi, northeast Finland. By analysing a range of paleo-environmental proxies (pollen, plant sedimentary ancient DNA, plant macrofossils, conifer stomata, and non-pollen palynomorphs), and supported with proxy-based paleotemperature and moisture reconstructions, we unravel a well-defined sequence of vegetation and climate dynamics over the early-to-middle Holocene. The birch-dominated pioneer vegetation stage was intersected by two transient tree-cover decrease events at 10.4 and 10.1 thousand years ago (ka), likely representing a two-pronged signal of the 10.3 ka climate event. Our data also show a clear signal of the 8.2 ka climate event, previously not well recorded in the European Arctic, with a collapse of the pine-birch forest and replacement by juniper developing in tight synchrony with Greenland isotopic proxies over 8.4-8.0 ka. Supported by climate modelling, severe winter cooling rather than summer might have been driving vegetation disruptions in the early Holocene. The Kuutsjarvi data indicate an early arrival of Norway spruce (Picea abies) by 9.2 ka (pollen, DNA, and stoma finds), as well as the first evidence for Holocene presence of larch (Larix) in Finland, with pollen finds dating to 9.6-5.9 ka.
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| 8. |
- Voldstad, Linn H., et al.
(author)
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A complete Holocene lake sediment ancient DNA record reveals long-standing high Arctic plant diversity hotspot in northern Svalbard
- 2020
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In: Quaternary Science Reviews. - : Elsevier. - 0277-3791 .- 1873-457X. ; 234
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Journal article (peer-reviewed)abstract
- Arctic hotspots, local areas of high biodiversity, are potential key sites for conservation of Arctic biodiversity. However, there is a need for improved understanding of their long-term resilience. The Arctic hotspot of Ringhorndalen has the highest registered diversity of vascular plants in the Svalbard archipelago, including several remarkable and isolated plant populations located far north of their normal distribution range. Here we analyze a lake sediment core from Ringhorndalen for sedimentary ancient DNA (sedaDNA) and geochemical proxies to detect changes in local vegetation and climate. Half of the plant taxa appeared already before 10,600 cal. yr BP, indicating rapid colonization as the ice retreated. Thermophilous species had a reoccurring presence throughout the Holocene record, but stronger signal in the early than Late Holocene period. Thus, thermophilous Arctic plant species had broader distribution ranges during the Early Holocene thermal maximum c. 10,000 cal. yr BP than today. Most of these thermophilous species are currently not recorded in the catchment area of the studied lake, but occur locally in favourable areas further into the valley. For example, Empetrum nigrum was found in >40% of the sedaDNA samples, whereas its current distribution in Ringhorndalen is highly restricted and outside the catchment area of the lake. Our findings support the hypothesis of isolated relict populations in Ringhorndalen. The findings are also consistent with main Holocene climatic shifts in Svalbard identified by previous studies and indicate an early warm and species-rich postglacial period until c. 6500 cal. yr BP, followed by fluctuating cool and warm periods throughout the later Holocene.
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| 9. |
- Wang, Yucheng, et al.
(author)
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Late Quaternary Dynamics of Arctic Biota from Ancient Environmental Genomics
- 2021
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 600:7887, s. 86-92
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Journal article (peer-reviewed)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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| 10. |
- Wang, Yucheng, et al.
(author)
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Reply to: When did mammoths go extinct?
- 2022
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 612:7938, s. 4-6
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Journal article (peer-reviewed)
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