92 results on '"Inger Greve Alsos"'
Search Results
2. LocoGSE, a sequence-based genome size estimator for plants
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Pierre Guenzi-Tiberi, Benjamin Istace, Inger Greve Alsos, The PhyloNorway Consortium, Eric Coissac, Sébastien Lavergne, The PhyloAlps Consortium, Jean-Marc Aury, France Denoeud, L.G. Alsos, M.K. Føreid Merkel, Y. Lammers, E. Coissac, C. Pouchon, A. Alberti, F. Denoeud, and P. Wincker
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genome size estimation ,genome size ,ploidy ,genome-skimming ,environmental DNA ,plant genomics ,Plant culture ,SB1-1110 - Abstract
Extensive research has focused on exploring the range of genome sizes in eukaryotes, with a particular emphasis on land plants, where significant variability has been observed. Accurate estimation of genome size is essential for various research purposes, but existing sequence-based methods have limitations, particularly for low-coverage datasets. In this study, we introduce LocoGSE, a novel genome size estimator designed specifically for low-coverage datasets generated by genome skimming approaches. LocoGSE relies on mapping the reads on single copy consensus proteins without the need for a reference genome assembly. We calibrated LocoGSE using 430 low-coverage Angiosperm genome skimming datasets and compared its performance against other estimators. Our results demonstrate that LocoGSE accurately predicts monoploid genome size even at very low depth of coverage (
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- 2024
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3. The drivers of plant community composition have shifted from external to internal processes over the past 20,000 years
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C. Patrick Doncaster, Mary E. Edwards, Charlotte L. Clarke, and Inger Greve Alsos
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Geology ,QE1-996.5 ,Environmental sciences ,GE1-350 - Abstract
Abstract Internal and external factors regulating the past composition of plant communities are difficult to identify in palaeo-vegetation records. Here, we develop an index of relative entropy of community assembly, which applies to changes in the composition of a community over time, measuring disorder in its assembly relative to disassembly. Historical periods of relatively ordered assembly (negative index values) are characteristic of a community undergoing endogenous self-organisation, in contrast to relatively disordered assembly (positive values) characterising periods of exogenous abiotic forcing. We quantified the relative entropy index for a 22,000-year time-series of tundra vegetation obtained in the Polar Urals, based on sedimentary DNA. We find it most positive during the Late Pleistocene characterized by persistent taxa, and most negative during the post-glacial Holocene characterized by more ephemeral floras. Changes in relative entropy coincide with changes in regional temperature as reconstructed from stable oxygen composition of an Arctic ice-core. Our results suggest that temperature strongly influenced community assembly in the Polar Urals until about 9000 years before present, after which endogenous community self-organization prevailed through to the present. We conclude that time-series of community composition can reveal changes in the balance between internal and external influences on taxonomic turnover and resulting diversity.
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- 2023
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4. Plant biodiversity assessment through soil eDNA reflects temporal and local diversity
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María Ariza, Bertrand Fouks, Quentin Mauvisseau, Rune Halvorsen, Inger Greve Alsos, and Hugo J. deBoer
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metabarcoding ,plant identification ,soil eDNA ,spatial scale ,temporal change ,vegetation assessments ,Ecology ,QH540-549.5 ,Evolution ,QH359-425 - Abstract
Abstract Several studies have shown the potential of eDNA‐based proxies for plant identification, but little is known about their spatial and temporal resolution. This limits its use for plant biodiversity assessments and monitoring of vegetation responses to environmental changes. Here we calibrate the temporal and spatial plant signals detected with soil eDNA surveys by comparing with a standard visual above‐ground vegetation survey. Our approach compares vegetation in an old‐growth boreal forest in southern Norway, surveyed in 100 permanent 1‐m2 plots seven times over a 30‐year period, with a single soil eDNA metabarcoding‐based survey from soil samples collected at the same 100 plots in the year of the last vegetation survey. On average, 60% and 10% of the vascular plants and bryophytes recorded across all vegetation surveys were detected by soil eDNA. Taxa detected by soil eDNA were more representative for the local taxa pool than for the specific plot, and corresponded to those surveyed over the 30‐year period although most closely matched the current taxa composition. Soil eDNA detected abundant taxa better than rare ones although both rare taxa and taxa unrecorded by the visual survey were detected. Our study highlights the potential of soil eDNA assessments for monitoring of vegetation responses over broad spatial and temporal scales. The method's ability to detect abundant taxa makes it suitable for assessment of vegetation composition in a specific area and for broad‐scale plant diversity assessments.
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- 2023
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5. High resolution ancient sedimentary DNA shows that alpine plant diversity is associated with human land use and climate change
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Sandra Garcés-Pastor, Eric Coissac, Sébastien Lavergne, Christoph Schwörer, Jean-Paul Theurillat, Peter D. Heintzman, Owen S. Wangensteen, Willy Tinner, Fabian Rey, Martina Heer, Astrid Rutzer, Kevin Walsh, Youri Lammers, Antony G. Brown, Tomasz Goslar, Dilli P. Rijal, Dirk N. Karger, Loïc Pellissier, The PhyloAlps Consortium, Oliver Heiri, and Inger Greve Alsos
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Science - Abstract
Here, the authors use sedimentary DNA, pollen, fungal spores, chironomids, and microcharcoal from an alpine lake core to reconstruct vegetation across 12,000 years. They find that vegetation responded to climate in the early Holocene, followed by a shift to human activity from 6000 years onward corresponding with an increase in deforestation and agropastoralism.
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- 2022
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6. Molecular dietary analyses of western capercaillies (Tetrao urogallus) reveal a diverse diet
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Physilia Ying Shi Chua, Youri Lammers, Emmanuel Menoni, Torbjørn Ekrem, Kristine Bohmann, Sanne Boessenkool, and Inger Greve Alsos
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ecology ,environmental DNA ,grouse ,herbivory ,high‐throughput sequencing ,Environmental sciences ,GE1-350 ,Microbial ecology ,QR100-130 - Abstract
Abstract Conservation strategies centered around species habitat protection rely on species’ dietary information. One species at the focal point of conservation efforts is the herbivorous grouse, the western capercaillie (Tetrao urogallus), which is an indicator species for forest biodiversity conservation. Non‐molecular means used to study their diet are time‐consuming and at low taxonomic resolution. This delays the implementation of conservation strategies including resource protection due to uncertainty about its diet. Thus, limited knowledge on diet is hampering conservation efforts. Here, we use non‐invasive environmental DNA (eDNA) metabarcoding on DNA extracted from faces to present the first large‐scale molecular dietary analysis of capercaillies. Facal samples were collected from seven populations located in Norway (Finnmark, Troms, Trøndelag, Innlandet) and France (Vosges, Jura, Pyrenees) (n = 172). We detected 122 plant taxa belonging to 46 plant families of which 37.7% of the detected taxa could be identified at species level. The average dietary richness of each sample was 7 ± 5 SD taxa. The most frequently occurring plant groups with the highest relative read abundance (RRA) were trees and dwarf shrubs, in particular, Pinus and Vaccinium myrtillus, respectively. There was a difference in dietary composition (RRA) between samples collected from the different locations (adonis pseudo F5,86 = 11.01, r2 = 0.17, p = 0.001) and seasons (adonis pseudo F2,03 = 0.64, r2 = 0.01, p = 0.036). Dietary composition also differed between sexes at each location (adonis pseudo F1,47 = 2.77, r2 = 0.04, p = 0.024), although not significant for all data combined. In total, 35 taxa (36.8% of taxa recorded) were new capercaillie food items compared with existing knowledge from non‐molecular means. The non‐invasive molecular dietary analysis applied in this study provides new ecological information of capercaillies’ diet, improving our understanding of adequate habitat required for their conservation.
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- 2021
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7. Environmental palaeogenomic reconstruction of an Ice Age algal population
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Youri Lammers, Peter D. Heintzman, and Inger Greve Alsos
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Biology (General) ,QH301-705.5 - Abstract
Lammers et al. use sedimentary ancient DNA to reconstruct palaeogenomes of Nannochloropsis. This study demonstrates the value of sedaDNA for palaeogenomic reconstructions and population genomic analysis.
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- 2021
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8. Prevention of microbial species introductions to the Arctic: The efficacy of footwear disinfection measures on cruise ships
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Sabine B. Rumpf, Inger Greve Alsos, and Chris Ware
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Biology (General) ,QH301-705.5 - Abstract
Biosecurity measures are commonly used to prevent the introduction of non-native species to natural environments globally, yet the efficacy of practices is rarely tested under operational conditions. A voluntary biosecurity measure was trialled in the Norwegian high Arctic following concern that non-native species might be transferred to the region on the footwear of travellers. Passengers aboard an expedition cruise ship disinfected their footwear with the broad spectrum disinfectant Virkon S prior to and in-between landing at sites around the remote Svalbard archipelago. The authors evaluated the efficacy of simply stepping through a disinfectant foot bath, which is the most common practice of footwear disinfection aboard expedition cruise ships in the Arctic. This was compared to a more time consuming and little-used method involving drying disinfected footwear, as proposed by other studies. The two practices were evaluated by measuring microbial growth on paired footwear samples before and after disinfection under both conditions. Step-through disinfection did not substantially reduce microbial growth on the footwear. Allowing disinfected footwear to dry, however, reduced the microbial burden significantly to lower levels. Thus, the currently adopted procedures used aboard ships are ineffective at removing microbial burden and are only effective when footwear is given more time to dry than currently granted under operational conditions. These findings underscore results from empirical research performed elsewhere and suggest the need to better relay this information to practitioners. It is suggested that footwear should minimally be wiped dry after step-through disinfection as a reasonable compromise between biosecurity and practicability.
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- 2018
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9. Shotgun Environmental DNA, Pollen, and Macrofossil Analysis of Lateglacial Lake Sediments From Southern Sweden
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Laura Parducci, Inger Greve Alsos, Per Unneberg, Mikkel W. Pedersen, Lu Han, Youri Lammers, J. Sakari Salonen, Minna M. Väliranta, Tanja Slotte, and Barbara Wohlfarth
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environmental DNA ,ancient DNA ,shotgun sequencing (metagenomics) ,pollen ,macrofossils remains ,lake sediments ,Evolution ,QH359-425 ,Ecology ,QH540-549.5 - Abstract
The lake sediments of Hässeldala Port in south-east Sweden provide an archive of local and regional environmental conditions ~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 Allerød (14.1–12.7 ka BP), Younger Dryas (12.7–11.7 ka BP), and Preboreal (
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- 2019
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10. The Treasure Vault Can be Opened: Large-Scale Genome Skimming Works Well Using Herbarium and Silica Gel Dried Material
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Inger Greve Alsos, Sebastien Lavergne, Marie Kristine Føreid Merkel, Marti Boleda, Youri Lammers, Adriana Alberti, Charles Pouchon, France Denoeud, Iva Pitelkova, Mihai Pușcaș, Cristina Roquet, Bogdan-Iuliu Hurdu, Wilfried Thuiller, Niklaus E. Zimmermann, Peter M. Hollingsworth, and Eric Coissac
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alpine ,chloroplast DNA ,environmental DNA ,ITS ,matK ,nuclear ribosomal DNA ,Botany ,QK1-989 - Abstract
Genome skimming has the potential for generating large data sets for DNA barcoding and wider biodiversity genomic studies, particularly via the assembly and annotation of full chloroplast (cpDNA) and nuclear ribosomal DNA (nrDNA) sequences. We compare the success of genome skims of 2051 herbarium specimens from Norway/Polar regions with 4604 freshly collected, silica gel dried specimens mainly from the European Alps and the Carpathians. Overall, we were able to assemble the full chloroplast genome for 67% of the samples and the full nrDNA cluster for 86%. Average insert length, cover and full cpDNA and rDNA assembly were considerably higher for silica gel dried than herbarium-preserved material. However, complete plastid genomes were still assembled for 54% of herbarium samples compared to 70% of silica dried samples. Moreover, there was comparable recovery of coding genes from both tissue sources (121 for silica gel dried and 118 for herbarium material) and only minor differences in assembly success of standard barcodes between silica dried (89% ITS2, 96% matK and rbcL) and herbarium material (87% ITS2, 98% matK and rbcL). The success rate was > 90% for all three markers in 1034 of 1036 genera in 160 families, and only Boraginaceae worked poorly, with 7 genera failing. Our study shows that large-scale genome skims are feasible and work well across most of the land plant families and genera we tested, independently of material type. It is therefore an efficient method for increasing the availability of plant biodiversity genomic data to support a multitude of downstream applications.
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- 2020
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11. Plant DNA metabarcoding of lake sediments: How does it represent the contemporary vegetation.
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Inger Greve Alsos, Youri Lammers, Nigel Giles Yoccoz, Tina Jørgensen, Per Sjögren, Ludovic Gielly, and Mary E Edwards
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Medicine ,Science - Abstract
Metabarcoding of lake sediments have been shown to reveal current and past biodiversity, but little is known about the degree to which taxa growing in the vegetation are represented in environmental DNA (eDNA) records. We analysed composition of lake and catchment vegetation and vascular plant eDNA at 11 lakes in northern Norway. Out of 489 records of taxa growing within 2 m from the lake shore, 17-49% (mean 31%) of the identifiable taxa recorded were detected with eDNA. Of the 217 eDNA records of 47 plant taxa in the 11 lakes, 73% and 12% matched taxa recorded in vegetation surveys within 2 m and up to about 50 m away from the lakeshore, respectively, whereas 16% were not recorded in the vegetation surveys of the same lake. The latter include taxa likely overlooked in the vegetation surveys or growing outside the survey area. The percentages detected were 61, 47, 25, and 15 for dominant, common, scattered, and rare taxa, respectively. Similar numbers for aquatic plants were 88, 88, 33 and 62%, respectively. Detection rate and taxonomic resolution varied among plant families and functional groups with good detection of e.g. Ericaceae, Roseaceae, deciduous trees, ferns, club mosses and aquatics. The representation of terrestrial taxa in eDNA depends on both their distance from the sampling site and their abundance and is sufficient for recording vegetation types. For aquatic vegetation, eDNA may be comparable with, or even superior to, in-lake vegetation surveys and may therefore be used as an tool for biomonitoring. For reconstruction of terrestrial vegetation, technical improvements and more intensive sampling is needed to detect a higher proportion of rare taxa although DNA of some taxa may never reach the lake sediments due to taphonomical constrains. Nevertheless, eDNA performs similar to conventional methods of pollen and macrofossil analyses and may therefore be an important tool for reconstruction of past vegetation.
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- 2018
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12. Tetraploids do not form cushions: association of ploidy level, growth form and ecology in the High Arctic Saxifraga oppositifolia L. s. lat. (Saxifragaceae) in Svalbard
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Pernille Bronken Eidesen, Eike Müller, Christian Lettner, Inger Greve Alsos, Morgan Bender, Martin Kristiansen, Bart Peeters, Froukje Postma, and Koen Frans Verweij
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Autopolyploidy ,flow cytometry ,morphotypes ,habitat segregation ,purple saxifrage ,Environmental sciences ,GE1-350 ,Oceanography ,GC1-1581 - Abstract
Saxifraga oppositifolia L. is a common circumpolar plant species that displays considerable morphological and genetic variation throughout its range. It is mainly diploid, but tetraploids are reported from several regions. The growth form varies from prostate to cushion-shaped, and the plant thrives in wet snow beds as well as on dry ridges. This variation has triggered the curiosity of many researchers, but as yet, no one has explained the observed morphological variation using ecological and/or genetic factors. However, the ploidy level has rarely been taken into account. This is the first study that demonstrates a significant correlation between ploidy level, ecology and growth form in S. oppositifolia. We successfully analysed 193 individuals of S. oppositifolia from 15 locations in Svalbard to investigate possible relationships among growth forms (prostrate, intermediate and cushion), ecological factors (vegetation and soil characteristics) and ploidy level. Results from flow cytometry reported 106 diploids, eight triploids and 79 tetraploids. Tetraploids almost exclusively showed prostrate growth, while the diploids displayed all three growth forms, evidence that growth form is at least partly genetically determined. Our analyses of environmental and vegetation data in relation to ploidy level indicated overlapping niches, but the tetraploids showed a narrower niche, and one shifted towards more benign habitats characterized by higher pH, higher soil temperatures and higher cover of vascular plants. The latter may suggest that tetraploids are slightly better competitors, but less hardy. Thus, autopolyploidy in S. oppositifolia has expanded the ecological amplitude of this species complex.
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- 2013
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13. Colonization of the arctic archipelago Svalbard
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Inger Greve Alsos
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Ecology ,QH540-549.5 ,Microbial ecology ,QR100-130 - Published
- 2009
14. Lateglacial and Early Holocene palaeoenvironmental change and human activity at Killerby Quarry, North Yorkshire, UK
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Samuel M Hudson, Clive Waddington, Ben Pears, Natalie Ellis, Luke Parker, Derek Hamilton, Inger Greve Alsos, Paul Hughes, and Antony Brown
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Arts and Humanities (miscellaneous) ,Earth and Planetary Sciences (miscellaneous) ,Paleontology - Abstract
The hunter-gatherers that entered the British peninsula after ice-retreat were exploiting a dynamic, rapidly changing environment. Records of vegetation change and human occupation during the Lateglacial to Early Holocene in northern Britain are more commonly found at upland and cave sites. However, recent research highlights many areas of the Swale–Ure Washlands that preserve extensive environmental sequences in low-lying ice-wastage basins, channels and depressions. The Lateglacial–Early Holocene environment of Killerby Quarry, North Yorkshire, is investigated here using a multi-proxy approach of sedimentary ancient DNA (sedaDNA), pollen, sedimentological (geochemistry and portable optically stimulated luminescence), and rare and well-preserved archaeology (Lavvu structures and lithics). Results show that the wetland basins and kettleholes were small lakes or ponds in the Lateglacial surrounded by sedge-fen and birch woodland. A gradual (centennial scale) succession to reed-swamp and then marsh is seen by the Early Holocene. This environment formed the resource-scape for hunter-gatherer transitory settlement in both the Lateglacial (Late Upper Palaeolithic) and Holocene (Early Mesolithic), attracted by the rich communities of pond-related flora and fauna as well as easy strategic landscape access by way of the River Swale, an arterial route through the landscape connecting the North Sea Basin with the Pennine uplands via the palaeolakes around Killerby.
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- 2022
15. Plant biodiversity assessment through soil eDNA reflects temporal and local diversity
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María Ariza, Bertrand Fouks, Quentin Mauvisseau, Rune Halvorsen, Inger Greve Alsos, and Hugo J. de Boer
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Ecological Modeling ,Ecology, Evolution, Behavior and Systematics - Abstract
1. Several studies have shown the potential of eDNA-based proxies for plant identification, but little is known about their spatial and temporal resolution. This limits its use for plant biodiversity assessments and monitoring of vegetation responses to environmental changes. Here we calibrate the temporal and spatial plant signals detected with soil eDNA surveys by comparing with a standard visual above-ground vegetation survey. 2. Our approach compares vegetation in an old-growth boreal forest in southern Norway, surveyed in 100 permanent 1-m2 plots seven times over a 30-year period, with a single soil eDNA metabarcoding-based survey from soil samples collected at the same 100 plots in the year of the last vegetation survey. 3. On average, 60% and 10% of the vascular plants and bryophytes recorded across all vegetation surveys were detected by soil eDNA. Taxa detected by soil eDNA were more representative for the local taxa pool than for the specific plot, and corresponded to those surveyed over the 30-year period although most closely matched the current taxa composition. Soil eDNA detected abundant taxa better than rare ones although both rare taxa and taxa unrecorded by the visual survey were detected. 4. Our study highlights the potential of soil eDNA assessments for monitoring of vegetation responses over broad spatial and temporal scales. The method's ability to detect abundant taxa makes it suitable for assessment of vegetation composition in a specific area and for broad-scale plant diversity assessments.
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- 2022
16. Reply to: When did mammoths go extinct?
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Yucheng Wang, Ana Prohaska, Haoran Dong, Adriana Alberti, Inger Greve Alsos, David W. Beilman, Anders A. Bjørk, Jialu Cao, Anna A. Cherezova, Eric Coissac, Bianca De Sanctis, France Denoeud, Christoph Dockter, Richard Durbin, Mary E. Edwards, Neil R. Edwards, Julie Esdale, Grigory B. Fedorov, Antonio Fernandez-Guerra, Duane G. Froese, Galina Gusarova, James Haile, Philip B. Holden, Kristian K. Kjeldsen, Kurt H. Kjær, Thorfinn Sand Korneliussen, Youri Lammers, Nicolaj Krog Larsen, Ruairidh Macleod, Jan Mangerud, Hugh McColl, Marie Kristine Føreid Merkel, Daniel Money, Per Möller, David Nogués-Bravo, Ludovic Orlando, Hannah Lois Owens, Mikkel Winther Pedersen, Fernando Racimo, Carsten Rahbek, Jeffrey T. Rasic, Alexandra Rouillard, Anthony H. Ruter, Birgitte Skadhauge, John Inge Svendsen, Alexei Tikhonov, Lasse Vinner, Patrick Wincker, Yingchun Xing, Yubin Zhang, David J. Meltzer, and Eske Willerslev
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Mammoths ,Multidisciplinary ,Animals - Published
- 2022
17. Pollen, macrofossils and sedaDNA reveal climate and land use impacts on Holocene mountain vegetation of the Lepontine Alps, Italy
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Lieveke van Vugt, Sandra Garcés-Pastor, Erika Gobet, Sarah Brechbühl, Antonietta Knetge, Youri Lammers, Katja Stengele, Inger Greve Alsos, Willy Tinner, and Christoph Schwörer
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Archeology ,Global and Planetary Change ,Geology ,580 Plants (Botany) ,Ecology, Evolution, Behavior and Systematics - Abstract
Both climate change and anthropogenic disturbance affect vegetation composition, but it is difficult to separate these drivers of vegetation change from one another. A better understanding of past vegetation dynamics is necessary to disentangle the influence of different forcing factors and assess future vegetation change. Here we present the first multi-proxy palaeoecological study combining sedimentary ancient DNA (sedaDNA), pollen, spores, stomata, charcoal and plant macrofossils from the Alps. We reconstructed the Holocene vegetation dynamics and fire history at Lago Inferiore del Sangiatto (1980 m asl), a small lake in the subalpine belt of the Ossola region, Italian Lepontine Alps. Afforestation in response to climate warming started at 10,700 cal yr BP with Larix decidua and tree Betula, which formed open forests together with Pinus cembra from 10,500 cal yr BP onwards. Human impact on the regional vegetation started at 5100 cal yr BP, resulting in expansions of Picea abies and Alnus viridis and the collapse of Abies alba. Species response models and ordination analysis show that livestock grazing and fire were major drivers of vegetation change at Lago Inferiore del Sangiatto during the late Holocene. Finally, increasing human impact during the Bronze (ca. 4200e2900 cal yr BP) and Iron Age (ca. 2900 e2000 cal yr BP) led to the formation of species-rich larch meadows and alpine pastures that are still dominant today. The palaeoecological data suggest that under projected climate change and land abandonment, the treeline ecotone will likely shift to higher altitudes, leading to important changes in species composition and increasing the risk of biodiversity loss.
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- 2022
18. Metagenomics: A viable tool for reconstructing herbivore diet
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Physilia Ying Shi Chua, Inger Greve Alsos, Kristine Bohmann, Youri Lammers, Sanne Boessenkool, and Alex Crampton-Platt
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0106 biological sciences ,0301 basic medicine ,In silico ,Computational biology ,Biology ,shotgun sequencing ,010603 evolutionary biology ,01 natural sciences ,Plant identification ,03 medical and health sciences ,VDP::Mathematics and natural science: 400::Zoology and botany: 480 ,Genetics ,DNA Barcoding, Taxonomic ,Environmental DNA ,Resource Article ,Herbivory ,Ecology, Evolution, Behavior and Systematics ,2. Zero hunger ,Herbivore ,plants ,Shotgun sequencing ,Environmental DNA, Faeces, Grouse, Plants, Shotgun sequencing ,RESOURCE ARTICLES ,Significant difference ,Molecular and Statistical Advance ,environmental DNA ,Diet ,030104 developmental biology ,Metagenomics ,Metagenome ,grouse ,Identification (biology) ,faeces ,VDP::Matematikk og Naturvitenskap: 400::Zoologiske og botaniske fag: 480 ,Biotechnology - Abstract
Metagenomics can generate data on the diet of herbivores, without the need for primer selection and PCR enrichment steps as is necessary in metabarcoding. Metagenomic approaches to diet analysis have remained relatively unexplored, requiring validation of bioinformatic steps. Currently, no metagenomic herbivore diet studies have utilized both chloroplast and nuclear markers as reference sequences for plant identification, which would increase the number of reads that could be taxonomically informative. Here, we explore how in silico simulation of metagenomic data sets resembling sequences obtained from faecal samples can be used to validate taxonomic assignment. Using a known list of sequences to create simulated data sets, we derived reliable identification parameters for taxonomic assignments of sequences. We applied these parameters to characterize the diet of western capercaillies (Tetrao urogallus) located in Norway, and compared the results with metabarcoding trnL P6 loop data generated from the same samples. Both methods performed similarly in the number of plant taxa identified (metagenomics 42 taxa, metabarcoding 43 taxa), with no significant difference in species resolution (metagenomics 24%, metabarcoding 23%). We further observed that while metagenomics was strongly affected by the age of faecal samples, with fresh samples outperforming old samples, metabarcoding was not affected by sample age. On the other hand, metagenomics allowed us to simultaneously obtain the mitochondrial genome of the western capercaillies, thereby providing additional ecological information. Our study demonstrates the potential of utilizing metagenomics for diet reconstruction but also highlights key considerations as compared to metabarcoding for future utilization of this technique.
- Published
- 2021
19. sPlotOpen – An environmentally balanced, open‐access, global dataset of vegetation plots
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Ben Sparrow, V. B. Martynenko, Jonathan Lenoir, Eszter Ruprecht, Idoia Biurrun, Luzmila Arroyo, Borja Jiménez-Alfaro, Aníbal Pauchard, Roberto Venanzoni, Stephan M. Hennekens, Mohamed Z. Hatim, Cyrus Samimi, Arkadiusz Nowak, Gerhard E. Overbeck, Petr Sklenář, Renata Ćušterevska, Valentin Golub, Eduardo Vélez-Martin, Gwendolyn Peyre, Inger Greve Alsos, Ioannis Tsiripidis, Tarek Hattab, Andrey Yu. Korolyuk, Jutta Kapfer, Jörg Ewald, Donald M. Waller, Ute Jandt, Tetiana Dziuba, Marco Schmidt, Alvaro G. Gutiérrez, Thomas Wohlgemuth, Adrian Indreica, Zygmunt Kącki, Jürgen Dengler, Željko Škvorc, Dirk Nikolaus Karger, Panayotis Dimopoulos, Viktor Onyshchenko, Hanhuai Shan, John Janssen, Hua Feng Wang, Holger Kreft, Jérôme Munzinger, Brian J. Enquist, Frederic Lens, Wannes Hubau, Birgit Jedrzejek, Alexander Christian Vibrans, Miguel D. Mahecha, Emmanuel Garbolino, Sophie Gachet, Abel Monteagudo Mendoza, Josep Peñuelas, Melisa A. Giorgis, Svetlana Aćić, Débora Vanessa Lingner, Victor V. Chepinoga, Richard Field, Ladislav Mucina, Michele De Sanctis, Mohamed A. El-Sheikh, Isabelle Aubin, Hamid Gholizadeh, Fahmida Sultana, Fabio Attorre, Valerijus Rašomavičius, Cindy Q. Tang, Tomáš Černý, Gonzalo Rivas-Torres, Donald A. Walker, Alicia Teresa Rosario Acosta, Timothy J. Killeen, Francesco Maria Sabatini, Susan K. Wiser, Urban Šilc, Andraž Čarni, Florian Jansen, Valério D. Pillar, Jonas V. Müller, Aaron Pérez-Haase, Els De Bie, Antonio Galán-de-Mera, Zhiyao Tang, Anne D. Bjorkman, Sylvia Haider, Kiril Vassilev, Risto Virtanen, Henrik von Wehrden, Hjalmar S. Kühl, Manfred Finckh, Zvjezdana Stančić, Pavel Shirokikh, Elizabeth Kearsley, Petr Petřík, Yves Bergeron, Iva Apostolova, Emiliano Agrillo, Jozef Šibík, Norbert Jürgens, Marta Gaia Sperandii, Anna Kuzemko, Jens-Christian Svenning, Timothy J. S. Whitfeld, Michael Kessler, Bruno Hérault, John-Arvid Grytnes, Laura Casella, Tomáš Peterka, Miguel Alvarez, Tsipe Aavik, Gregory Richard Guerin, André Luis de Gasper, Corrado Marcenò, Luis Cayuela, Brody Sandel, Cyrille Violle, Jens Kattge, Guillermo Hinojos Mendoza, Anke Jentsch, Arindam Banerjee, Jesper Erenskjold Moeslund, Mohammed Abu Sayed Arfin Khan, Patrice de Ruffray, Milan Chytrý, S. M. Yamalov, Tatiana Lysenko, Meelis Pärtel, Viktoria Bondareva, Helge Bruelheide, John S. Rodwell, Jiri Dolezal, Oliver L. Phillips, Rasmus Revermann, Larisa Khanina, Erwin Bergmeier, Robert K. Peet, Jörg Brunet, Solvita Rūsiņa, Oliver Purschke, Gianmaria Bonari, Jürgen Homeier, Martin Zobel, János Csiky, Marijn Bauters, Jalil Noroozi, Karsten Wesche, Kim André Vanselow, Norbert Hölzel, Flavia Landucci, Farideh Fazayeli, Wolfgang Willner, Viktoria Wagner, Alireza Naqinezhad, Aurora Levesley, Vadim Prokhorov, Hongyan Liu, Ali Kavgaci, Rodolfo Vásquez Martínez, Franziska Schrodt, Attila Lengyel, Elise A. Arnst, Sabatini F.M., Lenoir J., Hattab T., Arnst E.A., Chytry M., Dengler J., De Ruffray P., Hennekens S.M., Jandt U., Jansen F., Jimenez-Alfaro B., Kattge J., Levesley A., Pillar V.D., Purschke O., Sandel B., Sultana F., Aavik T., Acic S., Acosta A.T.R., Agrillo E., Alvarez M., Apostolova I., Arfin Khan M.A.S., Arroyo L., Attorre F., Aubin I., Banerjee A., Bauters M., Bergeron Y., Bergmeier E., Biurrun I., Bjorkman A.D., Bonari G., Bondareva V., Brunet J., Carni A., Casella L., Cayuela L., Cerny T., Chepinoga V., Csiky J., Custerevska R., De Bie E., de Gasper A.L., De Sanctis M., Dimopoulos P., Dolezal J., Dziuba T., El-Sheikh M.A.E.-R.M., Enquist B., Ewald J., Fazayeli F., Field R., Finckh M., Gachet S., Galan-de-Mera A., Garbolino E., Gholizadeh H., Giorgis M., Golub V., Alsos I.G., Grytnes J.-A., Guerin G.R., Gutierrez A.G., Haider S., Hatim M.Z., Herault B., Hinojos Mendoza G., Holzel N., Homeier J., Hubau W., Indreica A., Janssen J.A.M., Jedrzejek B., Jentsch A., Jurgens N., Kacki Z., Kapfer J., Karger D.N., Kavgaci A., Kearsley E., Kessler M., Khanina L., Killeen T., Korolyuk A., Kreft H., Kuhl H.S., Kuzemko A., Landucci F., Lengyel A., Lens F., Lingner D.V., Liu H., Lysenko T., Mahecha M.D., Marceno C., Martynenko V., Moeslund J.E., Monteagudo Mendoza A., Mucina L., Muller J.V., Munzinger J., Naqinezhad A., Noroozi J., Nowak A., Onyshchenko V., Overbeck G.E., Partel M., Pauchard A., Peet R.K., Penuelas J., Perez-Haase A., Peterka T., Petrik P., Peyre G., Phillips O.L., Prokhorov V., Rasomavicius V., Revermann R., Rivas-Torres G., Rodwell J.S., Ruprecht E., Rusina S., Samimi C., Schmidt M., Schrodt F., Shan H., Shirokikh P., Sibik J., Silc U., Sklenar P., Skvorc Z., Sparrow B., Sperandii M.G., Stancic Z., Svenning J.-C., Tang Z., Tang C.Q., Tsiripidis I., Vanselow K.A., Vasquez Martinez R., Vassilev K., Velez-Martin E., Venanzoni R., Vibrans A.C., Violle C., Virtanen R., von Wehrden H., Wagner V., Walker D.A., Waller D.M., Wang H.-F., Wesche K., Whitfeld T.J.S., Willner W., Wiser S.K., Wohlgemuth T., Yamalov S., Zobel M., Bruelheide H., Sabatini, Fm, Lenoir, J, Hattab, T, Arnst, Ea, Chytry, M, Dengler, J, De Ruffray, P, Hennekens, Sm, Jandt, U, Jansen, F, Jimenez-Alfaro, B, Kattge, J, Levesley, A, Pillar, Vd, Purschke, O, Sandel, B, Sultana, F, Aavik, T, Acic, S, Acosta, Atr, Agrillo, E, Alvarez, M, Apostolova, I, Khan, Masa, Arroyo, L, Attorre, F, Aubin, I, Banerjee, A, Bauters, M, Bergeron, Y, Bergmeier, E, Biurrun, I, Bjorkman, Ad, Bonari, G, Bondareva, V, Brunet, J, Carni, A, Casella, L, Cayuela, L, Cerny, T, Chepinoga, V, Csiky, J, Custerevska, R, De Bie, E, de Gasper, Al, De Sanctis, M, Dimopoulos, P, Dolezal, J, Dziuba, T, El-Sheikh, Mam, Enquist, B, Ewald, J, Fazayeli, F, Field, R, Finckh, M, Gachet, S, Galan-de-Mera, A, Garbolino, E, Gholizadeh, H, Giorgis, M, Golub, V, Alsos, Ig, Grytnes, Ja, Guerin, Gr, Gutierrez, Ag, Haider, S, Hatim, Mz, Herault, B, Mendoza, Gh, Holzel, N, Homeier, J, Hubau, W, Indreica, A, Janssen, Jam, Jedrzejek, B, Jentsch, A, Jurgens, N, Kacki, Z, Kapfer, J, Karger, Dn, Kavgaci, A, Kearsley, E, Kessler, M, Khanina, L, Killeen, T, Korolyuk, A, Kreft, H, Kuhl, H, Kuzemko, A, Landucci, F, Lengyel, A, Lens, F, Lingner, Dv, Liu, Hy, Lysenko, T, Mahecha, Md, Marceno, C, Martynenko, V, Moeslund, Je, Mendoza, Am, Mucina, L, Muller, Jv, Munzinger, Jm, Naqinezhad, A, Noroozi, J, Nowak, A, Onyshchenko, V, Overbeck, Ge, Partel, M, Pauchard, A, Peet, Rk, Penuelas, J, Perez-Haase, A, Peterka, T, Petrik, P, Peyre, G, Phillips, Ol, Prokhorov, V, Rasomavicius, V, Revermann, R, Rivas-Torres, G, Rodwell, J, Ruprecht, E, Rusina, S, Samimi, C, Schmidt, M, Schrodt, F, Shan, Hh, Shirokikh, P, Sibik, J, Silc, U, Sklenar, P, Skvorc, Z, Sparrow, B, Sperandii, Mg, Stancic, Z, Svenning, Jc, Tang, Zy, Tang, Cq, Tsiripidis, I, Vanselow, Ka, Martinez, Rv, Vassilev, K, Velez-Martin, E, Venanzoni, R, Vibrans, Ac, Violle, C, Virtanen, R, von Wehrden, H, Wagner, V, Walker, Da, Waller, Dm, Wang, Hf, Wesche, K, Whitfeld, Tj, Willner, W, Wiser, Sk, Wohlgemuth, T, Yamalov, S, Zobel, M, Bruelheide, H, Ecologie et Dynamique des Systèmes Anthropisés - UMR CNRS 7058 (EDYSAN), Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS), MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), Centre de recherche sur les Risques et les Crises (CRC), Mines Paris - PSL (École nationale supérieure des mines de Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), ANR-07-BDIV-0006,BIONEOCAL,L'endémisme en Nouvelle-Calédonie : étude phylogénétique et populationnelle des son émergence.(2007), ANR-07-BDIV-0008,INC,Incendies et biodiversité de écosystèmes en Nouvelle-Calédonie.(2007), ANR-07-BDIV-0010,ULTRABIO,Biodiversité et stratégies adaptatives végétales et microbiennes des écosystèmes ultramafiques en Nouvelle-Calédonie.(2007), European Project: 610028,EC:FP7:ERC,ERC-2013-SyG,IMBALANCE-P(2014), European Project: 291585,EC:FP7:ERC,ERC-2011-ADG_20110209,T-FORCES(2012), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut de Recherche pour le Développement (IRD), MINES ParisTech - École nationale supérieure des mines de Paris, Université Paul-Valéry - Montpellier 3 (UPVM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
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0106 biological sciences ,Biome ,Bos- en Landschapsecologie ,Biodiversity ,DIVERSITY ,FOREST VEGETATION ,01 natural sciences ,purl.org/becyt/ford/1 [https] ,Abundance (ecology) ,big data ,Vegetation type ,PHYTOSOCIOLOGICAL DATABASE ,parcelle ,Forest and Landscape Ecology ,functional traits ,vascular plants ,biodiversity ,biogeography ,database ,macroecology ,vegetation plots ,Macroecology ,[SDV.EE]Life Sciences [q-bio]/Ecology, environment ,Global and Planetary Change ,Ecology ,vascular plant ,Vegetation ,F70 - Taxonomie végétale et phytogéographie ,PE&RC ,Vegetation plot ,Geography ,580: Pflanzen (Botanik) ,Ecosystems Research ,Diffusion de l'information ,Plantenecologie en Natuurbeheer ,Vegetatie, Bos- en Landschapsecologie ,Biodiversité ,ARCHIVE ,Communauté végétale ,Evolution ,[SDE.MCG]Environmental Sciences/Global Changes ,Biogéographie ,GRASSLAND VEGETATION ,Plant Ecology and Nature Conservation ,[SDV.BID]Life Sciences [q-bio]/Biodiversity ,010603 evolutionary biology ,Behavior and Systematics ,Couverture végétale ,577: Ökologie ,PLANT ,purl.org/becyt/ford/1.6 [https] ,functional trait ,Biology ,Ecology, Evolution, Behavior and Systematics ,Vegetatie ,010604 marine biology & hydrobiology ,Impact sur l'environnement ,DRY GRASSLANDS ,Plant community ,15. Life on land ,Végétation ,WETLAND VEGETATION ,Earth and Environmental Sciences ,UNIVERSITY ,Physical geography ,Vegetation, Forest and Landscape Ecology ,[SDE.BE]Environmental Sciences/Biodiversity and Ecology ,données ouvertes - Abstract
Datos disponibles en https://github.com/fmsabatini/sPlotOpen_Code, EU H2020 project BACI, Grant No. 640176 (...), Sabatini, F.M., Lenoir, J., Hattab, T., Arnst, E.A., Chytrý, M., Dengler, J., De Ruffray, P., Hennekens, S.M., Jandt, U., Jansen, F., Jiménez-Alfaro, B., Kattge, J., Levesley, A., Pillar, V.D., Purschke, O., Sandel, B., Sultana, F., Aavik, T., Aćić, S., Acosta, A.T.R., Agrillo, E., Alvarez, M., Apostolova, I., Arfin Khan, M.A.S., Arroyo, L., Attorre, F., Aubin, I., Banerjee, A., Bauters, M., Bergeron, Y., Bergmeier, E., Biurrun, I., Bjorkman, A.D., Bonari, G., Bondareva, V., Brunet, J., Čarni, A., Casella, L., Cayuela, L., Černý, T., Chepinoga, V., Csiky, J., Ćušterevska, R., De Bie, E., de Gasper, A.L., De Sanctis, M., Dimopoulos, P., Dolezal, J., Dziuba, T., El-Sheikh, M.A.E.-R.M., Enquist, B., Ewald, J., Fazayeli, F., Field, R., Finckh, M., Gachet, S., Galán-de-Mera, A., Garbolino, E., Gholizadeh, H., Giorgis, M., Golub, V., Alsos, I.G., Grytnes, J.-A., Guerin, G.R., Gutiérrez, A.G., Haider, S., Hatim, M.Z., Hérault, B., Hinojos Mendoza, G., Hölzel, N., Homeier, J., Hubau, W., Indreica, A., Janssen, J.A.M., Jedrzejek, B., Jentsch, A., Jürgens, N., Kącki, Z., Kapfer, J., Karger, D.N., Kavgacı, A., Kearsley, E., Kessler, M., Khanina, L., Killeen, T., Korolyuk, A., Kreft, H., Kühl, H.S., Kuzemko, A., Landucci, F., Lengyel, A., Lens, F., Lingner, D.V., Liu, H., Lysenko, T., Mahecha, M.D., Marcenò, C., Martynenko, V., Moeslund, J.E., Monteagudo Mendoza, A., Mucina, L., Müller, J.V., Munzinger, J., Naqinezhad, A., Noroozi, J., Nowak, A., Onyshchenko, V., Overbeck, G.E., Pärtel, M., Pauchard, A., Peet, R.K., Peñuelas, J., Pérez-Haase, A., Peterka, T., Petřík, P., Peyre, G., Phillips, O.L., Prokhorov, V., Rašomavičius, V., Revermann, R., Rivas-Torres, G., Rodwell, J.S., Ruprecht, E., Rūsiņa, S., Samimi, C., Schmidt, M., Schrodt, F., Shan, H., Shirokikh, P., Šibík, J., Šilc, U., Sklenář, P., Škvorc, Ž., Sparrow, B., Sperandii, M.G., Stančić, Z., Svenning, J.-C., Tang, Z., Tang, C.Q., Tsiripidis, I., Vanselow, K.A., Vásquez Martínez, R., Vassilev, K., Vélez-Martin, E., Venanzoni, R., Vibrans, A.C., Violle, C., Virtanen, R., von Wehrden, H., Wagner, V., Walker, D.A., Waller, D.M., Wang, H.-F., Wesche, K., Whitfeld, T.J.S., Willner, W., Wiser, S.K., Wohlgemuth, T., Yamalov, S., Zobel, M., Bruelheide, H.
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- 2021
20. Towards the extended barcode concept: Generating DNA reference data through genome skimming of danish plants
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Ida Hartvig, Inger Greve Alsos, Ashot Margaryan, Marlene Elise Møller Restrup, Kristine Bohmann, Stine Raith Richter, Frederik Leerhøi, Hans Henrik Bruun, Eric Coissac, Physilia Ying Shi Chua, Sanne Boessenkool, Emilia Marie Rolander Langkjær, and Christina Lehmkuhl Noer
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Reference data ,Metagenomics ,law ,GenBank ,Environmental DNA ,Computational biology ,Biology ,Barcode ,Ribosomal DNA ,Genome ,GC-content ,law.invention - Abstract
BackgroundRecently, there has been a push towards the extended barcode concept of utilising chloroplast genomes (cpGenome) and nuclear ribosomal DNA (nrDNA) sequences for molecular identification of plants instead of the standard barcode regions. These extended barcodes has a wide range of applications, including biodiversity monitoring and assessment, primer design, and evolutionary studies. However, these extended barcodes are not well represented in global reference databases. To fill this gap, we generated cpGenomes and nrDNA reference data from genome skims of 184 plant species collected in Denmark. We further explored the application of our generated reference data for molecular identifications of plants in an environmental DNA metagenomics study.ResultsWe assembled partial cpGenomes for 82.1% of sequenced species and full or partial nrDNA sequences for 83.7% of species. We added all assemblies to GenBank, of which chloroplast reference data from 101 species and nuclear reference data from 6 species were not previously represented. On average, we recovered 45 genes per species. The rate of recovery of standard barcodes was higher for nuclear barcodes (>89%) than chloroplast barcodes (< 60%). Extracted DNA yield did not affect assembly outcome, whereas high GC content did so negatively. For thein silicosimulation of metagenomic reads, taxonomic assignments using the reference data generated had better species resolution (94.9%) as compared to GenBank (18.1%) without any identification errors.ConclusionsGenome skimming generates reference data of both standard barcodes and other loci, contributing to the global DNA reference database for plants.
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- 2021
21. Sedimentary ancient DNA shows terrestrial plant richness continuously increased over the Holocene in northern Fennoscandia
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Iva Pitelkova, Dilli Prasad Rijal, Tomasz Goslar, Youri Lammers, Nigel G. Yoccoz, Karin F. Helmens, Inger Greve Alsos, Francisco Javier Ancin Murguzur, Torbjørn Alm, Kari Anne Bråthen, Mary E. Edwards, Peter D. Heintzman, Antony G. Brown, Kelsey Lorberau, Jostein Bakke, J. Sakari Salonen, and Department of Geosciences and Geography
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0106 biological sciences ,1171 Geosciences ,010506 paleontology ,010504 meteorology & atmospheric sciences ,Climate Change ,ved/biology.organism_classification_rank.species ,Annan geovetenskap och miljövetenskap ,Climate change ,medicine.disease_cause ,010603 evolutionary biology ,01 natural sciences ,Nutrient ,Effects of global warming ,Pollen ,Terrestrial plant ,medicine ,Humans ,DNA, Ancient ,Research Articles ,Ecosystem ,Holocene ,1172 Environmental sciences ,VDP::Mathematics and natural science: 400 ,0105 earth and related environmental sciences ,Multidisciplinary ,Ecology ,ved/biology ,Plant Sciences ,SciAdv r-articles ,VDP::Matematikk og Naturvitenskap: 400 ,Plants ,15. Life on land ,Lakes ,Geography ,Ancient DNA ,13. Climate action ,Species richness ,Other Earth and Related Environmental Sciences ,Research Article - Abstract
SedaDNA reveals regional climate and bedrock nutrients as major drivers of terrestrial plant diversity in northern Fennoscandia., 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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- 2021
22. Clitellate worms (Annelida) in lateglacial and Holocene sedimentary<scp>DNA</scp>records from the Polar Urals and northern Norway
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Emilia Rota, Haflidi Haflidason, Youri Lammers, Charlotte Clarke, Inger Greve Alsos, Antony G. Brown, Ludovic Gielly, Mary E. Edwards, Jan Mangerud, Christer Erséus, and John Inge Svendsen
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010506 paleontology ,Archeology ,010504 meteorology & atmospheric sciences ,biology ,Ecology ,Range (biology) ,Geology ,VDP::Matematikk og Naturvitenskap: 400 ,Enchytraeidae ,biology.organism_classification ,01 natural sciences ,DNA barcoding ,Ancient DNA ,Arctic ,Environmental DNA ,Quaternary ,Ecology, Evolution, Behavior and Systematics ,Holocene ,VDP::Mathematics and natural science: 400 ,0105 earth and related environmental sciences - Abstract
While there are extensive macro- and microfossil records of a range of plants and animals from Quaternary records, earthworms and their close relatives among annelids are not preserved as fossils, and therefore we have limited knowledge of their Quaternary distributions. This lack of fossils means that clitellate worms (Annelida) are currently underused in palaeoecological research, even though they can provide valuable information about terrestrial and aquatic environmental conditions. Their DNA might be preserved in sediments, which offers an alternative method for detection. Here we analyse lacustrine sediments from lakes in the Polar Urals, Arctic Russia, covering the period 24,000-1,300 cal. years BP, and NE Norway (10,700-3,300 cal. years BP) using a universal mammal 16S rDNA marker. While mammals were recorded using the marker (reindeer was detected twice in the Polar Urals core at 23,000 and 14,000 cal. years BP, and four times in the Norwegian core at 11,000 cal. years BP and between 3,600-3,300 cal. years BP), worm extracellular DNA “bycatch” was rather high. In this paper we present the first reported worm detection from ancient DNA. Our results demonstrate that both aquatic and terrestrial clitellates can be identified in late-Quaternary lacustrine sediments, and the ecological information retrievable from this group warrants further research with a more targeted approach.
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- 2018
23. Environmental palaeogenomic reconstruction of an Ice Age algal population
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Peter D. Heintzman, Inger Greve Alsos, and Youri Lammers
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0106 biological sciences ,Geologic Sediments ,Chloroplasts ,Population genetics ,QH301-705.5 ,Population ,Medicine (miscellaneous) ,Biology ,Polymorphism, Single Nucleotide ,010603 evolutionary biology ,01 natural sciences ,Genome ,Article ,General Biochemistry, Genetics and Molecular Biology ,Haplogroup ,03 medical and health sciences ,DNA, Algal ,Algae ,Microalgae ,Ice age ,DNA, Ancient ,Biology (General) ,education ,Phylogeny ,030304 developmental biology ,VDP::Mathematics and natural science: 400 ,0303 health sciences ,education.field_of_study ,Fossils ,Haplotype ,Paleontology ,Palaeoecology ,Last Glacial Maximum ,VDP::Matematikk og Naturvitenskap: 400 ,biology.organism_classification ,Computational biology and bioinformatics ,Taxon ,Ancient DNA ,Haplotypes ,Evolutionary biology ,Genome, Mitochondrial ,Metagenomics ,General Agricultural and Biological Sciences - Abstract
Palaeogenomics has greatly increased our knowledge of past evolutionary and ecological change, but has been restricted to the study of species that preserve either as or within fossils. Here we show the potential of shotgun metagenomics to reveal population genomic information for a taxon that does not preserve in the body fossil record, the algae Nannochloropsis. We shotgun sequenced two lake sediment samples dated to the Last Glacial Maximum and reconstructed full chloroplast and mitochondrial genomes to explore within-lake population genomic variation. This revealed two major haplogroups for each organellar genome, which could be assigned to known varieties of N. limnetica, although we show that at least three haplotypes were present using our minimum haplotype diversity estimation method. These approaches demonstrate the utility of lake sedimentary ancient DNA (sedaDNA) for population genomic analysis, thereby opening the door to environmental palaeogenomics, which will unlock the full potential of sedaDNA., Lammers et al. use sedimentary ancient DNA to reconstruct palaeogenomes of Nannochloropsis. This study demonstrates the value of sedaDNA for palaeogenomic reconstructions and population genomic analysis.
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- 2021
24. Ancient sedimentary DNA shows rapid post-glacial colonisation of Iceland followed by relatively stable vegetation until Landnám
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Emma M. Bender, Wesley R. Farnsworth, Inger Greve Alsos, Alexandra Rouillard, Ívar Örn Benediktsson, Skafti Brynjólfsson, Guthrun Gisladottir, Anders Schomacker, Sigrún Dögg Eddudóttir, Esther Ruth Guthmundsdottir, Sofia E. Kjellman, Youri Lammers, Marie Kf Merkel, and Egill Erlendsson
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Colonisation ,Geography ,Arctic ,Ecology ,Biological dispersal ,Forb ,Climate change ,Glacial period ,Vegetation ,Holocene - Abstract
Understanding patterns of colonisation is important for explaining both the distribution of single species and anticipating how ecosystems may respond to global warming. Insular flora may be especially vulnerable because oceans represent severe dispersal barriers. Here we analyse two lake sediment cores from Iceland for ancient sedimentary DNA to infer patterns of colonisation and Holocene vegetation development. Our cores from lakes Torfdalsvatn and Nykurvatn span the last c. 12,000 cal. yr BP and c. 8600 cal. yr BP, respectively. With near-centennial resolution, we identified a total of 191 plant taxa, with 152 taxa identified in the sedimentary record of Torfdalsvatn and 172 plant taxa in the sedimentary record of Nykurvatn. The terrestrial vegetation at Torfdalsvatn was first dominated by bryophytes, arctic herbs such as Saxifraga spp. and grasses. Around 10,100 cal. yr BP, a massive immigration of new taxa was observed, and shrubs and dwarf shrubs became common whereas aquatic macrophytes became dominant. At Nykurvatn, all dominant taxa occurred already in the earliest samples; shrubs and dwarf shrubs were more abundant at this site than at Torfdalsvatn. There was an overall steep increase both in the local and regional species pool until 8000 cal. yr BP, by which time ¾ of all taxa identified had arrived. In the period 4500-1000 cal. yr BP, a few new taxa of bryophytes, graminoids and forbs are identified. The last millennium, after human settlement of the island (Landnám), is characterised by a sudden disappearance of Juniperus communis, but also reappearance of some high arctic forbs and dwarf shrubs. Notable immigration during the Holocene coincides with periods of dense sea-ice cover, and we hypothesise that this may have acted as a dispersal vector. Thus, although ongoing climate change might provide a suitable habitat in Iceland for a large range of species only found in the neighbouring regions today, the reduction of sea ice may in fact limit the natural colonisation of new plant species.
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- 2021
25. Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations
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Ulrike Herzschuh, Inger Greve Alsos, Marco J. L. Coolen, Marie-Eve Monchamp, Stefan Bertilsson, Daniel Ariztegui, Antony G. Brown, Laura S. Epp, Sarah E. Crump, Aurèle Vuillemin, Mikkel Winther Pedersen, Rebecca E. Garner, Irene Gregory-Eaves, David A. Walsh, Simon Belle, Kevin Nota, Youri Lammers, Kurt H. Kjær, Liv Heinecke, Camille Thomas, Fredrik Olajos, Joanna Gauthier, Göran Englund, Liisi Talas, Isabelle Domaizon, Joanne E. Littlefair, Charlotte Clarke, Eric Capo, Anan Ibrahim, Eske Willerslev, Didier Debroas, Johan Rydberg, Y. L. Wang, Fabien Arnaud, Trisha L. Spanbauer, Peter D. Heintzman, Pierre Taberlet, Gentile Francesco Ficetola, Dilli Prasad Rijal, Charline Giguet-Covex, Richard Bindler, Laura Parducci, Alexandra Rouillard, Kathleen R. Stoof-Leichsenring, Veljo Kisand, Heike Zimmermann, Christian Bigler, Anne van Woerkom, William D. Orsi, Erwan Messager, Umeå University, Environnements, Dynamiques et Territoires de Montagne (EDYTEM), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS), The Arctic University of Norway [Tromsø, Norway] (UiT), University of Copenhagen = Københavns Universitet (UCPH), Uppsala University, Department of Earth & Environmental Sciences, Ludwig-Maximilians-Universität München, 80331 Munich, GeoBio-CenterLMU, Université de Genève = University of Geneva (UNIGE), Swedish University of Agricultural Sciences (SLU), School of Geography and Environmental Science, University of Southampton, Southampton SO17 1BJ, Institute of Arctic Alpine Research [University of Colorado Boulder] (INSTAAR), University of Colorado [Boulder], Laboratoire Microorganismes : Génome et Environnement (LMGE), Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne (UCA), Department of Environmental Science and Policy [Milano], Università degli Studi di Milano = University of Milan (UNIMI), Laboratoire d'Ecologie Alpine (LECA ), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Department of Biology [Concordia], Concordia University [Montreal], Groupe de recherche interuniversitaire en limnologie et en environnement aquatique - GRIL (Montréal, Canada), Université de Montréal (UdeM), Department of Biology [McGill University], McGill University = Université McGill [Montréal, Canada], ALFRED WEGENER INSTITUTE HELMHOLTZ CENTRE FOR POLAR AND MARINE RESEARCH POTSDAM DEU, Partenaires IRSTEA, Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), Institute of Mathematics, University of Potsdam = Universität Potsdam, Institute for Environmental Sciences and Geography, University of Potsdam, Department of Biology, University of Konstanz, Konstanz, Germany, University of Tartu, School of Biological and Chemical Sciences, Queen Mary University of London, London, UK., Department of Environmental Sciences and Lake Erie Center, University of Toledo, Toledo, OH 43606, University of Cambridge [UK] (CAM), Western Australia Organic and Isotope Geochemistry Centre, School of Earth and Planetary Sciences, the Institute for Geoscience Research (TIGeR), Curtin University, Bentley 6102, Limnological Institute, Department of Biology, University of Konstanz, 78464 Konstanz, Centre Alpin de Recherche sur les Réseaux Trophiques et Ecosystèmes Limniques (CARRTEL), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Environmental Biology, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Roma, Italy, Knut & Alice Wallenberg Foundation2016.0083Swedish Research Council for Sustainable Development FormasFR-2016/0005Research Council of NorwayEuropean Commission250963/F20German Research Foundation (DFG)OR 417/1-1VU 94/1-1E, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Ecology and Environmental Science, Umeå University, Environnements, Dynamiques et Territoires de la Montagne (EDYTEM), Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), Department of Geosciences, UiT the Arctic University of Norway, 9019 Tromsø, Section for Geogenetics, GLOBE Institute, University of Copenhagen, 1350 Copenhagen, Department of Ecology and Genetics, the Evolutionary Biology Centre, Uppsala University, 752 36 Uppsala, The Arctic University Museum of Norway, UiT the Arctic University of Norway, 9010 Tromsø, Department of Earth Sciences, University of Geneva, University of Geneva [Switzerland], Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, 75007 Uppsala, Institute of Arctic and Alpine Research (INSTAAR), Università degli Studi di Milano [Milano] (UNIMI), Department of Biology, Concordia University, Montréal, Department of Biology, McGill University, Montreal, Canada, University of Potsdam, Institute of Technology, University of Tartu, 50090 Tartu, Department of Zoology, University of Cambridge, Cambridge, United Kingdom, Willerslev, Eske [0000-0002-7081-6748], and Apollo - University of Cambridge Repository
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0106 biological sciences ,Earth science ,[SDV]Life Sciences [q-bio] ,Biodiversity ,lake sediments ,Sedimentary DNA ,lcsh:GN281-289 ,Oceanografi, hydrologi och vattenresurser ,Aquatic biota ,01 natural sciences ,Paleolimnology ,paleoecology ,Oceanography, Hydrology and Water Resources ,sedimentary ancient DNA ,Earth and Planetary Sciences (miscellaneous) ,ddc:550 ,lcsh:QE640-699 ,biodiversity ,0303 health sciences ,paleolimnology ,Paleogenetics ,Lake sediments ,VDP::Mathematics and natural science: 400::Geosciences: 450::Stratigraphy and paleontology: 461 ,[SDE]Environmental Sciences ,lcsh:Human evolution ,ancient DNA ,VDP::Matematikk og Naturvitenskap: 400::Geofag: 450::Sedimentologi: 456 ,sedimentary DNA ,paleogenetics ,paleogenomics ,metabarcoding ,metagenomics ,010603 evolutionary biology ,03 medical and health sciences ,lcsh:Stratigraphy ,VDP::Mathematics and natural science: 400::Geosciences: 450::Sedimentology: 456 ,ddc:570 ,030304 developmental biology ,Earth-Surface Processes ,Sedimentary ancient DNA ,VDP::Matematikk og Naturvitenskap: 400::Geofag: 450::Stratigrafi og paleontologi: 461 ,Geokemi ,Ancient DNA ,Geochemistry ,Paleogenomics ,Metagenomics ,Paleoecology ,Metabarcoding ,Environmental science ,Sedimentary rock - Abstract
International audience; 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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- 2021
26. Late Quaternary dynamics of Arctic biota from ancient environmental genomics
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Inger Greve Alsos, David Bravo Nogues, Adriana Alberti, Jialu Cao, Youri Lammers, Thorfinn Sand Korneliussen, Yubin Zhang, Alexandra Rouillard, Eske Willerslev, Antonio Fernandez-Guerra, John Inge Svendsen, Jeffrey T. Rasic, David W. Beilman, Patrick Wincker, Per Möller, Fernando Racimo, Christoph Dockter, Alexei Tikhonov, Marie Kristine Føreid Merkel, Anna Cherezova, Julie Esdale, Lasse Vinner, Daniel Money, Duane G. Froese, Bianca De Sanctis, Anthony Ruter, Hannah L. Owens, Hugh McColl, Richard Durbin, Galina Gusarova, David J. Meltzer, Neil R. Edwards, James Haile, Nicolaj K. Larsen, Yingchun Xing, Kurt H. Kjær, Jan Mangerud, Mary E. Edwards, Kristian K. Kjeldsen, Mikkel Winther Pedersen, Birgitte Skadhauge, Carsten Rahbek, Grigory Fedorov, Eric Coissac, Ludovic Orlando, Anders A. Bjørk, Y. L. Wang, Philip B. Holden, Ana Prohaska, Wang, Yucheng [0000-0002-7838-226X], Pedersen, Mikkel Winther [0000-0002-7291-8887], Alsos, Inger Greve [0000-0002-8610-1085], Prohaska, Ana [0000-0001-5459-6186], Rouillard, Alexandra [0000-0001-5778-6620], Alberti, Adriana [0000-0003-3372-9423], Denoeud, France [0000-0001-8819-7634], Money, Daniel [0000-0001-5151-3648], McColl, Hugh [0000-0002-7568-4270], Cherezova, Anna A. [0000-0002-6199-8164], Haile, James [0000-0002-8521-8337], Orlando, Ludovic [0000-0003-3936-1850], Beilman, David W. [0000-0002-2625-6747], Dockter, Christoph [0000-0001-5923-3667], Kjeldsen, Kristian K. [0000-0002-8557-5131], Mangerud, Jan [0000-0003-4793-7557], Rasic, Jeffrey T. [0000-0002-3549-6590], Skadhauge, Birgitte [0000-0001-7317-4376], Wincker, Patrick [0000-0001-7562-3454], Zhang, Yubin [0000-0003-4920-3100], Froese, Duane G. [0000-0003-1032-5944], Holden, Philip B. [0000-0002-2369-0062], Edwards, Neil R. [0000-0001-6045-8804], Durbin, Richard [0000-0002-9130-1006], Meltzer, David J. [0000-0001-8084-9802], Willerslev, Eske [0000-0002-7081-6748], Apollo - University of Cambridge Repository, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Cherezova, Anna A [0000-0002-6199-8164], Beilman, David W [0000-0002-2625-6747], Kjeldsen, Kristian K [0000-0002-8557-5131], Rasic, Jeffrey T [0000-0002-3549-6590], Froese, Duane G [0000-0003-1032-5944], Holden, Philip B [0000-0002-2369-0062], Edwards, Neil R [0000-0001-6045-8804], Meltzer, David J [0000-0001-8084-9802], Apollo-University Of Cambridge Repository, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)
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Geologic Sediments ,010504 meteorology & atmospheric sciences ,Woolly mammoth ,Rain ,[SDV]Life Sciences [q-bio] ,Greenland ,Population Dynamics ,Datasets as Topic ,Permafrost ,01 natural sciences ,631/158/2463 ,631/158/2462 ,Mammoths ,631/208/212/2142 ,Woolly rhinoceros ,Megafauna ,Databases, Genetic ,38/23 ,History, Ancient ,Phylogeny ,0303 health sciences ,education.field_of_study ,Multidisciplinary ,biology ,Arctic Regions ,Ecology ,Climate-change ecology ,631/208/514/2254 ,704/158/2165 ,article ,Palaeoecology ,Biota ,Vegetation ,Plants ,Grassland ,Mitochondria ,Geography ,[SDE]Environmental Sciences ,Climate Change ,Population ,45/22 ,Extinction, Biological ,03 medical and health sciences ,Spatio-Temporal Analysis ,VDP::Mathematics and natural science: 400::Zoology and botany: 480 ,Animals ,Humans ,Herbivory ,14. Life underwater ,DNA, Ancient ,education ,Perissodactyla ,030304 developmental biology ,0105 earth and related environmental sciences ,Mammoth ,15. Life on land ,biology.organism_classification ,DNA, Environmental ,Siberia ,Lakes ,Haplotypes ,Arctic ,13. Climate action ,Wetlands ,Ecological networks ,Next-generation sequencing ,Metagenomics ,VDP::Matematikk og Naturvitenskap: 400::Zoologiske og botaniske fag: 480 - Abstract
Acknowledgements: Acknowledgements: We thank D. H. Mann for his detailed and constructive comments; and T. Ager, J. Austin, T. B. Brand, A. Cooper, S. Funder, M. T. P. Gilbert, T. Jørgensen, N. J. Korsgaard, S. Liu, M. Meldgaard, P. V. S. Olsen, M. L. Siggaard-Andersen, J. Stenderup, S. A. Woodroffe and staff at the GeoGenetics Sequencing Core and National Park Service-Western Arctic National Parklands for help and support. E.W. and D.J.M. thank the staff at St. John’s College, Cambridge, for providing a stimulating environment for scientific discussion of the project. E.W. thanks Illumina for collaboration. The Lundbeck Foundation GeoGenetics Centre is supported by the Carlsberg Foundation (CF18-0024), the Lundbeck Foundation (R302-2018-2155), the Novo Nordisk Foundation (NNF18SA0035006), the Wellcome Trust (UNS69906) and GRF EXC CRS Chair (44113220)—Cluster of Excellence. The PhyloNorway plant genome database is part of the Norwegian Barcode of Life Network (https://www.norbol.org) funded by the Research Council of Norway (226134/F50), the Norwegian Biodiversity Information Centre (14-14, 70184209) and The Arctic University Museum of Norway. Metabarcoding sequencing was funded by the Central Public-Interest Scientific Institution Basal Research Fund, CAFS (2017B001 and 2020A001). B.D.S. is supported by the Wellcome Trust programme in Mathematical Genomics and Medicine (WT220023); F.R. by a Villum Fonden Young Investigator award (no. 00025300); D.J.M. by the Quest Archaeological Research Fund; P.M. by the Swedish Research Council (VR); R.D. by the Wellcome Trust (WT207492); and A.R. by a Marie Skłodowska-Curie Actions Individual Fellowship (MSCA-IF, 703542) and the Research Council of Norway (KLIMAFORSK, 294929). L.O. has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (no. 681605); I.G.A. and Y.L. from the ERC under the European Union’s Horizon 2020 research and innovation programme (no. 819192). J.I.S. and J.M. are supported by the Research Council of Norway. P.B.H. and N.R.E. acknowledge NERC funding (grant NE/P015093/1). D.W.B. was supported by a Marie Skłodowska-Curie Actions Incoming International Fellowship (MCIIF-40974). T.S.K. is funded by a Carlsberg Foundation Young Researcher Fellowship (CF19-0712)., 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 findings include: (1) a relatively homogeneous steppe-tundra flora 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 effective precipitation, as well as an increase in the proportion of wetland plants, show negative effects 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 findings highlight the power of ancient environmental metagenomics analyses to advance understanding of population histories and long-term ecological dynamics.
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- 2021
27. Rapid climate changes during the Lateglacial and the early Holocene as seen from plant community dynamics in the Polar Urals, Russia
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Charlotte Clarke, Aage Paus, Haflidi Haflidason, Maren S. Johansen, Jo Brendryen, Anne E. Bjune, Inger Greve Alsos, Jan Mangerud, Mary E. Edwards, John Inge Svendsen, and Carl Regnéll
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Paleontology ,Climate change ,Plant community ,medicine.disease_cause ,Arts and Humanities (miscellaneous) ,Pollen ,Earth and Planetary Sciences (miscellaneous) ,medicine ,VDP::Mathematics and natural science: 400::Zoology and botany: 480 ,Polar ,Physical geography ,Holocene ,Geology ,VDP::Matematikk og Naturvitenskap: 400::Zoologiske og botaniske fag: 480 - Abstract
A detailed, well-dated record of pollen and sedimentary ancient DNA (sedaDNA) for the period 15 000–9500 cal a bp describes changes at Lake Bolshoye Shchuchye in the Polar Ural Mountains, located far east of the classical Lateglacial sites in western Europe. Arctic tundra rapidly changed to lusher vegetation, possibly including both dwarf (Betula nana) and tree birch (B. pubescens), dated in our record to take place 14 565 cal a bp, coincident with the onset of the Bølling in western Europe; this was paralleled by increased summer temperatures. A striking feature is an early decline in Betula pollen and sedaDNA reads 300 years before the onset of the Younger Dryas (YD) in western Europe. Given the solid site chronology, this could indicate that the YD cooling started in Siberia and propagated westwards, or that the vegetation reacted to the inter-Allerød cooling at 13 100 cal a bp and did not recover during the late Allerød. During the YD, increases in steppe taxa such as Artemisia and Chenopodiaceae suggest drier conditions. At the onset of the Holocene, the vegetation around the lake reacted fast to the warmer conditions, as seen in the increase of arboreal taxa, especially Betula, and a decrease in herbs such as Artemisia and Cyperaceae. publishedVersion
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- 2021
28. Ancient DNA, Lipid Biomarkers and Palaeoecological Evidence Reveals Construction and Life on early Medieval Lake Settlements
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Ludovic Gielly, Nicki J. Whitehouse, Gentile Francesco Ficetola, Andrew C. G. Henderson, Peter G. Langdon, K. Head, Antony G. Brown, Phil Barratt, Finbar McCormick, Inger Greve Alsos, Graeme Cavers, Kimberley Davies, E. Murray, Thierry Fonville, Duncan Pirrie, M. van Hardenbroek, Helen Mackay, and Anne Crone
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0301 basic medicine ,010506 paleontology ,Celtic languages ,Science ,Wetland ,01 natural sciences ,Article ,03 medical and health sciences ,Human settlement ,Limnology ,Animals ,Humans ,DNA, Ancient ,0105 earth and related environmental sciences ,geography ,Minerals ,Multidisciplinary ,geography.geographical_feature_category ,Ecology ,Biological techniques ,Radiometric Dating ,food and beverages ,Excavation ,Archaeology ,Lipids ,History, Medieval ,United Kingdom ,Food resources ,Environmental social sciences ,Lakes ,030104 developmental biology ,Ancient DNA ,Medicine ,Lipid biomarkers ,Ireland ,Biomarkers ,Chronology - Abstract
Direct evidence of ancient human occupation is typically established through archaeological excavation. Excavations are costly and destructive, and practically impossible in some lake and wetland environments. We present here an alternative approach, providing direct evidence from lake sediments using DNA metabarcoding, steroid lipid biomarkers (bile acids) and from traditional environmental analyses. Applied to an early Medieval Celtic settlement in Ireland (a crannog) this approach provides a site chronology and direct evidence of human occupation, crops, animal farming and on-site slaughtering. This is the first independently-dated, continuous molecular archive of human activity from an archeological site, demonstrating a link between animal husbandry, food resources, island use. These sites are under threat but are impossible to preserve in-situ so this approach can be used, with or without excavation, to produce a robust and full site chronology and provide direct evidence of occupation, the use of plants and animals, and activities such as butchery.
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- 2021
29. Ancient sedimentary DNA shows rapid post-glacial colonisation of Iceland followed by relatively stable vegetation until the Norse settlement (Landnám) AD 870
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Skafti Brynjólfsson, Anders Schomacker, Wesley R. Farnsworth, Emma M. Bender, Sigrún Dögg Eddudóttir, Sofia E. Kjellman, Inger Greve Alsos, Youri Lammers, Egill Erlendsson, Guðrún Gísladóttir, Esther Ruth Guðmundsdóttir, Alexandra Rouillard, Ívar Örn Benediktsson, and Marie Kristine Føreid Merkel
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010506 paleontology ,Archeology ,010504 meteorology & atmospheric sciences ,VDP::Mathematics and natural science: 400::Zoology and botany: 480::Vegetation history: 495 ,01 natural sciences ,Island ,VDP::Mathematics and natural science: 400::Geosciences: 450::Sedimentology: 456 ,14. Life underwater ,Glacial period ,Ecology, Evolution, Behavior and Systematics ,Holocene ,0105 earth and related environmental sciences ,Ekologi ,Global and Planetary Change ,Ancient DNA ,Ecology ,Geology ,Colonisation ,Vegetation ,15. Life on land ,Miljövetenskap ,Lake sediments ,VDP::Matematikk og Naturvitenskap: 400::Zoologiske og botaniske fag: 480::Vegetasjonshistorie: 495 ,Geography ,Arctic ,Vegetation history ,13. Climate action ,Metabarcoding ,Biological dispersal ,Species richness ,VDP::Matematikk og Naturvitenskap: 400::Geofag: 450::Sedimentologi: 456 ,Environmental Sciences - Abstract
Understanding patterns of colonisation is important for explaining both the distribution of single species and anticipating how ecosystems may respond to global warming. Insular flora may be especially vulnerable because oceans represent severe dispersal barriers. Here we analyse two lake sediment cores from Iceland for ancient sedimentary DNA to infer patterns of colonisation and Holocene vegetation development. Our cores from lakes Torfdalsvatn and Nykurvatn span the last c. 12,000 cal yr BP and c. 8600 cal yr BP, respectively. With near-centennial resolution, we identified a total of 191 plant taxa, with 152 taxa identified in the sedimentary record of Torfdalsvatn and 172 plant taxa in the sedimentary record of Nykurvatn. The terrestrial vegetation at Torfdalsvatn was initially dominated by bryophytes, arctic herbs such as Saxifraga spp. and grasses. Around 10,100 cal yr BP, a massive immigration of new taxa was observed, and shrubs and dwarf shrubs became common whereas aquatic macrophytes became dominant. At Nykurvatn, the dominant taxa were all present in the earliest samples; shrubs and dwarf shrubs were more abundant at this site than at Torfdalsvatn. There was an overall steep increase both in the local accumulated richness and regional species pool until 8000 cal yr BP, by which time ¾ of all taxa identified had arrived. The period 4500-1000 cal yr BP witnessed the appearance of a a small number of bryophytes, graminoids and forbs that were not recorded in earlier samples. The last millennium, after human settlement of the island (Landnám), is characterised by a sudden disappearance of Juniperus communis, but also reappearance of some high arctic forbs and dwarf shrubs. Notable immigration during the Holocene coincides with periods of increased incidence of sea ice, and we hypothesise that this may have acted as a dispersal vector. Thus, although ongoing climate change might provide a suitable habitat in Iceland for a large range of species only found in the neighbouring regions today, the reduction of sea ice may in fact limit the natural colonisation of new plant species.
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- 2021
30. Molecular dietary analyses of western capercaillies (Tetrao urogallus) reveal a diverse diet
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Youri Lammers, Emmanuel Menoni, Inger Greve Alsos, Kristine Bohmann, Sanne Boessenkool, Physilia Ying Shi Chua, and Torbjørn Ekrem
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0106 biological sciences ,Adonis ,Zoology ,Grouse ,010603 evolutionary biology ,01 natural sciences ,Microbial ecology ,03 medical and health sciences ,Abundance (ecology) ,Genetics ,GE1-350 ,Ecology, Evolution, Behavior and Systematics ,030304 developmental biology ,VDP::Mathematics and natural science: 400 ,2. Zero hunger ,0303 health sciences ,Herbivore ,Ecology ,biology ,herbivory ,QR100-130 ,high‐throughput sequencing ,high-throughput sequencing ,Vegetation ,VDP::Matematikk og Naturvitenskap: 400 ,15. Life on land ,biology.organism_classification ,environmental DNA ,Environmental sciences ,Habitat ,grouse ,Species richness ,Tetrao urogallus ,ecology - Abstract
Conservation strategies centred around species habitat protection rely on species’ dietary information. One species at the focal point of conservation efforts is the herbivorous grouse, the western capercaillie (Tetrao urogallus). Traditional microhistological analysis of crop contents or faeces and/or direct observations are time-consuming and at low taxonomic resolution. Thus, limited knowledge on diet is hampering conservation efforts. Here we use non-invasive environmental DNA (eDNA) metabarcoding on DNA extracted from faeces to present the first large-scale molecular dietary analysis of capercaillies. Faecal samples were collected from seven populations located in Norway (Finnmark, Troms, Trøndelag, Innlandet) and France (Vosges, Jura, Pyrenees) (n=172). We detected 122 plant taxa belonging to 46 plant families of which 37.7% of the detected taxa could be identified at species level. The average dietary richness of each sample was 7 ± 5 SD taxa. The most frequently occurring plant groups with the highest relative read abundance (RRA) were trees and dwarf shrubs, in particular, Pinus and Vaccinium myrtillus, respectively. There was a difference in dietary composition (RRA) between samples collected from the different locations (adonis F5,86= 11.01, p 2,03= 0.64, p 1,47 = 2.77, p
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- 2021
31. Author Correction: Late Quaternary dynamics of Arctic biota from ancient environmental genomics
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Yucheng Wang, Mikkel Winther Pedersen, Inger Greve Alsos, Bianca De Sanctis, Fernando Racimo, Ana Prohaska, Eric Coissac, Hannah Lois Owens, Marie Kristine Føreid Merkel, Antonio Fernandez-Guerra, Alexandra Rouillard, Youri Lammers, Adriana Alberti, France Denoeud, Daniel Money, Anthony H. Ruter, Hugh McColl, Nicolaj Krog Larsen, Anna A. Cherezova, Mary E. Edwards, Grigory B. Fedorov, James Haile, Ludovic Orlando, Lasse Vinner, Thorfinn Sand Korneliussen, David W. Beilman, Anders A. Bjørk, Jialu Cao, Christoph Dockter, Julie Esdale, Galina Gusarova, Kristian K. Kjeldsen, Jan Mangerud, Jeffrey T. Rasic, Birgitte Skadhauge, John Inge Svendsen, Alexei Tikhonov, Patrick Wincker, Yingchun Xing, Yubin Zhang, Duane G. Froese, Carsten Rahbek, David Nogues Bravo, Philip B. Holden, Neil R. Edwards, Richard Durbin, David J. Meltzer, Kurt H. Kjær, Per Möller, and Eske Willerslev
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Multidisciplinary - Published
- 2022
32. A 24,000-year ancient DNA and pollen record from the Polar Urals reveals temporal dynamics of arctic and boreal plant communities
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Ludovic Gielly, Aage Paus, Charlotte Clarke, John Inge Svendsen, Anne E. Bjune, Carl Regnéll, Paul D.M. Hughes, Inger Greve Alsos, Mary E. Edwards, Jan Mangerud, and Haflidi Haflidason
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010506 paleontology ,Archeology ,Global and Planetary Change ,Carex ,VDP::Matematikk og Naturvitenskap: 400::Basale biofag: 470::Molekylærbiologi: 473 ,010504 meteorology & atmospheric sciences ,biology ,Ecology ,VDP::Mathematics and natural science: 400::Basic biosciences: 470::Molecular biology: 473 ,Geology ,Plant community ,biology.organism_classification ,medicine.disease_cause ,01 natural sciences ,VDP::Humanities: 000 ,Tundra ,VDP::Humaniora: 000 ,Boreal ,Pollen ,medicine ,Dominance (ecology) ,Bryophyte ,Younger Dryas ,Ecology, Evolution, Behavior and Systematics ,0105 earth and related environmental sciences - Abstract
A 24,000-year record of plant community dynamics, based on pollen and ancient DNA from the sediments (sedaDNA) of Lake Bolshoye Shchuchye in the Polar Ural Mountains, provides detailed information on the flora of the Last Glacial Maximum (LGM) and also changes in plant community composition and dominance. It greatly improves on incomplete records from short and fragmented stratigraphic sequences found in exposed sedimentary sections in the western Russian Arctic. In total, 162 plant taxa were detected by sedaDNA and 115 by pollen analysis. Several shifts in dominance between and within plant functional groups occurred over the studied period, but most taxa appear to have survived in situ. A diverse arctic-alpine herb flora characterised the interval ca. 24,000–17,000 cal years BP and persisted into the Holocene. Around 17,000 cal years BP, sedges (e.g. Carex) and bryophytes (e.g. Bryum, Aulacomnium) increased. The establishment of shrub-tundra communities of Dryas and Vaccinium sp., with potentially some Betula pubescens trees (influx ∼290 grains cm2 year−1), followed at ca. 15,000 cal years BP. Forest taxa such as Picea and ferns (e.g. Dryopteris fragrans, Gymnocarpium dryopteris) established near the lake from ca. 10,000 cal years BP, followed by the establishment of Larix trees from ca. 9000 cal years BP. Picea began to decline from ca. 7000 cal years BP. A complete withdrawal of forest tree taxa occurred by ca. 4000 cal years BP, presumably due to decreasing growing-season temperatures, allowing the expansion of dwarf-shrub tundra and a diverse herb community similar to the present-day vegetation mosaic. Contrary to some earlier comparative studies, sedaDNA and pollen from Lake Bolshoye Shchuchye showed high similarity in the timing of compositional changes and the occurrence of key plant taxa. The sedaDNA record revealed several features that the pollen stratigraphy and earlier palaeorecords in the region failed to detect; a sustained, long-term increase in floristic richness since the LGM until the early Holocene, turnover in grass and forb genera over the Pleistocene-Holocene transition, persistence of a diverse arctic-alpine flora over the late Quaternary, and a variable bryophyte flora through time. As pollen records are often limited by taxonomic resolution, differential productivity and dispersal, sedaDNA can provide improved estimates of floristic richness and is better able to distinguish between different plant assemblages. However, pollen remains superior at providing quantitative estimates of plant abundance changes and detecting several diverse groups (e.g. Poaceae, Cyperaceae, Asteraceae) which may be underreported in the sedaDNA. Joint use of the two proxies provided unprecedented floristic detail of past plant communities and helped to distinguish between long-distance transport of pollen and local presence, particularly for woody plant taxa.
- Published
- 2020
33. Ancient plant DNA, macro- and microfossil studies of the lake sediments from the High Arctic lake Tenndammen, Svalbard
- Author
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Sandra Garces Pastor, Inger Greve Alsos, Anastasia Poliakova, Anders Schomacker, and Lena Håkansson
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Oceanography ,VDP::Mathematics and natural science: 400::Geosciences: 450 ,Arctic ,VDP::Matematikk og Naturvitenskap: 400::Geofag: 450 ,Macro ,Geology - Abstract
Ancient DNA metabarcoding applied together with the investigations of the plant macro-remains, pollen, spores and non-pollen palynomorphs (NPP), open new perspectives and give better taxonomical resolution, allowing to obtain more precise and specific data on the local environment conditions and their changes. So far, only three multiproxy studies that involve both molecular and palaeobotanical/palynological methods are available for the high Arctic archipelago Svalbard. We intend to contribute filling this gap. Therefore, a field trip to Svalbard was undertaken in September, 2019, and three sediment cores were retrieved from the Tenndammen lake (N 78°06.118; E 15°02.024, 7 m asl) which is a small and shallow water body (ca 2.5 m depth). The lake is located in the valley of Colesdalen, a well-known Svalbard’s biodiversity hot spots and a home for about seven to ten thermophilic plant species.To investigate the Holocene to modern vegetation history of this place, the 85cm core Te2019 was chosen, it was described for lithology, X-rayed, µXRF-scanned, line-scan photographed with high resolution and sampled for sedaDNA, pollen, spores and NPP studies as well as for studies on plant macrofossils. Ten 14C AMS dates were taken in order to establish an age-depth model. The DNA record contains around 100 taxa, most findings of those are supported by pollen studies (Asteraceae, Betula, Brassicaceae, Salix, Saxifraga, Vaccinium/Ericaceae) and by spores (Equisetum and Bryophyta). In addition, various fungi spores were identified. Investigations of plant macro-remains well support findings of the aquatic (i.e. Warnstorfia fluitans) and terrestrial mosses (e.g. Aulacomnium conf. turgidum, Bryum spp., Distichium capillaceum, Calliergon richardsonii, Scorpidium cossonii, Sphagnum spp., Rhizomnium spp.). Besides, fragments of Salix and Betula leaves and fruit parts, various leaf, stem tissues and flower fragments of Saxifraga species were found within the samples from the same depths with the correspondence to DNA records. Three DNA zones (SvDNA 1 – SvDNA3) and one subzone within the earliest zone (SvDNA-1a – SvDNA-1b) were established. Relations between DNA, pollen and macrofossil zones were studied. This study is performed within the “Future ArcTic Ecosystems” (FATE) research program: Initiative for investigation on drivers of diversity and future scenarios from ethnoecology, contemporary ecology and ancient DNA.
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- 2020
34. Survival and spread of arctic plants in response to climate change: DNA-based evidence
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Inger Greve Alsos, Mary E. Edwards, and Charlotte Clarke
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chemistry.chemical_compound ,Geography ,Ancient DNA ,chemistry ,Ecology ,Species distribution ,Biodiversity ,Climate change ,Arctic vegetation ,DNA - Abstract
Preserving biodiversity requires knowledge of the processes that underlie geographical patterns of species distribution and sustain diverse communities over long periods of time. Studies of modern and ancient DNA may provide new insight into these processes.
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- 2020
35. The Treasure Vault Can be Opened : Large-Scale Genome Skimming Works Well Using Herbarium and Silica Gel Dried Material
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Mihai Pușcaș, Sébastien Lavergne, Bogdan-Iuliu Hurdu, Martí Boleda, Niklaus E. Zimmermann, Inger Greve Alsos, Iva Pitelkova, Adriana Alberti, Peter M. Hollingsworth, Charles Pouchon, Cristina Roquet, Youri Lammers, Marie Kristine Føreid Merkel, Wilfried Thuiller, Eric Coissac, National Centre for Biosystematics [Oslo], Natural History Museum [Oslo], University of Oslo (UiO)-University of Oslo (UiO), Laboratoire d'Ecologie Alpine (LECA ), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Génomique métabolique (UMR 8030), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Institut Fédéral de Recherches sur la Forêt, la Neige et le Paysage (WSL), Institut Fédéral de Recherches [Suisse], Royal Botanic Garden [Edinburgh], UMR, Lab Ecol Alpine, Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), and Royal Botanic Garden Edinburgh
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0106 biological sciences ,0301 basic medicine ,[SDV]Life Sciences [q-bio] ,Plant Science ,rbcL ,01 natural sciences ,Genome ,DNA barcoding ,chemistry.chemical_compound ,chloroplast DNA ,lcsh:Botany ,Environmental DNA ,VDP::Mathematics and natural science: 400 ,Ecology ,biology ,Silica gel ,Nuclear ribosomal DNA ,Boraginaceae ,[SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM] ,lcsh:QK1-989 ,Chloroplast DNA ,Rbcl ,Polar ,[SDV.BID]Life Sciences [q-bio]/Biodiversity ,Plant DNA barcode ,010603 evolutionary biology ,Article ,03 medical and health sciences ,matK ,Botany ,[SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology ,polar ,Phylogenomic ,Ribosomal DNA ,Ecology, Evolution, Behavior and Systematics ,MatK ,phylogenomic ,alpine ,plant DNA barcode ,VDP::Matematikk og Naturvitenskap: 400 ,nuclear ribosomal DNA ,biology.organism_classification ,environmental DNA ,Alpine ,030104 developmental biology ,Herbarium ,chemistry ,ITS - Abstract
Genome skimming has the potential for generating large data sets for DNA barcoding and wider biodiversity genomic studies, particularly via the assembly and annotation of full chloroplast (cpDNA) and nuclear ribosomal DNA (nrDNA) sequences. We compare the success of genome skims of 2051 herbarium specimens from Norway/Polar regions with 4604 freshly collected, silica gel dried specimens mainly from the European Alps and the Carpathians. Overall, we were able to assemble the full chloroplast genome for 67% of the samples and the full nrDNA cluster for 86%. Average insert length, cover and full cpDNA and rDNA assembly were considerably higher for silica gel dried than herbarium-preserved material. However, complete plastid genomes were still assembled for 54% of herbarium samples compared to 70% of silica dried samples. Moreover, there was comparable recovery of coding genes from both tissue sources (121 for silica gel dried and 118 for herbarium material) and only minor differences in assembly success of standard barcodes between silica dried (89% ITS2, 96% matK and rbcL) and herbarium material (87% ITS2, 98% matK and rbcL). The success rate was >, 90% for all three markers in 1034 of 1036 genera in 160 families, and only Boraginaceae worked poorly, with 7 genera failing. Our study shows that large-scale genome skims are feasible and work well across most of the land plant families and genera we tested, independently of material type. It is therefore an efficient method for increasing the availability of plant biodiversity genomic data to support a multitude of downstream applications.
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- 2020
36. A complete Holocene lake sediment ancient DNA record reveals long-standing high Arctic plant diversity hotspot in northern Svalbard
- Author
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Inger Greve Alsos, Peter D. Heintzman, Alexandra Rouillard, Anders Schomacker, Wesley R. Farnsworth, Linn H. Voldstad, Sofia E. Kjellman, Lena Håkansson, Pernille Bronken Eidesen, Jarðvísindastofnun (HÍ), Institute of Earth Sciences (UI), Verkfræði- og náttúruvísindasvið (HÍ), School of Engineering and Natural Sciences (UI), Háskóli Íslands, and University of Iceland
- Subjects
SedaDNA ,ATLANTIC ,010506 paleontology ,Archeology ,LAND ,010504 meteorology & atmospheric sciences ,CONSERVATION ,Biodiversity ,01 natural sciences ,COLONIZATION ,Svalbard ,Vegetation dynamics ,Nýlífsöld ,Hotspot (geology) ,Eldvirkni ,Ecology, Evolution, Behavior and Systematics ,Holocene ,0105 earth and related environmental sciences ,VDP::Mathematics and natural science: 400 ,Global and Planetary Change ,biology ,Ancient DNA ,EDGEOYA ,Jarðlög ,AREA ,Biodiversity hotspot ,Geology ,VDP::Matematikk og Naturvitenskap: 400 ,biology.organism_classification ,Lake sediments ,SPITSBERGEN ,Geography ,Arctic ,NORWAY ,Metabarcoding ,Sedimentary rock ,Physical geography ,VEGETATION ,Empetrum nigrum ,GLACIAL HISTORY - Abstract
Publisher's version (útgefin grein), 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., The core-samplingfield campaign, subsequent sub-sampling ofsediments and macrofossils, ITRAX-scans, and radiocarbon datingwere funded by the Svalbard Environmental Protection Fund(project 16/35 to WRF). Financial support for molecular analysisandfield work was provided by the Svalbard Environmental Pro-tection Fund (project 14/118 to PBE) and Jan Christensen’sendowment (to LHV). IGA and PDH acknowledge support from theResearch Council of Norway (Grant 250963:“ECOGEN”). We thankJohannes Sand Bolstad forfield assistance, Kari Klanderud forproject administration, the wider ECOGEN research group inTromsø, including Dilli Rijal for pooling and cleaning of the PCRproducts and Youri Lammers for helping with bioinformatic ana-lyses and reference libraries. Bioinformatic analyses were per-formed on the Abel Cluster, owned by the University of Oslo andUninett/Sigma2, and operated by the Department for ResearchComputing at USIT, the University of Oslo IT-department.http://www.hpc.uio.no/. We thank Marie-Louise Siggaard-Andersen forassistance with the ITRAX-scanning of the sediment core as well asDr. Skafti Brynj olfsson and Dr. Marc Macias-Fauria for collaborationin the field.
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- 2020
37. Ending the Cinderella Status of Terraces and Lynchets in Europe
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Daniel J. Fallu, Andreas Lang, Rosa-Maria Albert, Paolo Tarolli, Sara Cucchiaro, Kristof Van Oost, Pengzhi Zhao, Clive Waddington, Kevin Walsh, Tony Brown, Lisa Snape, Inger Greve Alsos, EGU - European Geoscience Union, and UCL - SST/ELI/ELIC - Earth & Climate
- Subjects
terrace - Abstract
Terraces and lynchets are not only ubiquitous worldwide and within Europe but can provide increasingly important Ecosystem Services (ESs), which may be able to mitigate aspects of climate change. They are also probably a major cause of non-linearity between climate and erosion rates in agricultural systems as noted from alluvial and colluvial studies. In this paper we review the theoretical background of terraces and lynchets, present a modified classification, and show how new techniques are transforming the study of these widespread and often ancient anthropogenic landforms. Indeed the problems of dating terraces and also the time-consuming nature and costly surveys has held back the archaeological study of terraces until now. The applicable suite of techniques available now includes the creation of Digital Terrain Models (DTMs) from Structure from Motion (SfM) photogrammetry, Airborne and Terrestrial Laser Scanning (ALS-TLS); the use of OSL and pOSL, pXRF, FTIR, phytoliths, calcium oxalates from plants and potentially sedaDNA. Examples will be drawn from a recently started ERC project (TerrACE; ERC-2017-ADG: 787790, 2018-2023; https://www.terrace.no/) which is working at over 10 sites in Europe ranging from Norway to Greece.This paper explains the development of a new holistic approach to terrace archaeology driven by a modern conceptualisation of human-landscape relationships, and facilitated by new scientific developments. We explain the rationale for our choice of case study areas, for example, the range of bio-climatic zones. In addition, this multi-regional approach allows us to address contingent regional and local historical/socioeconomic processes; from demographic fluctuations to the development of specific forms of agricultural techniques. Examples of DTM creation, field analyses and selected results will be given from Martleburg in Belgium and sites in Italy. We will then move on to explain how this combination of a comprehensive suite of modern field and laboratory methods and an interpretive strategy informed by the environmental humanities will yield exciting and groundbreaking results.
- Published
- 2020
38. Last Glacial Maximum environmental conditions at Andøya, northern Norway; evidence for a northern ice-edge ecological 'hotspot'
- Author
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Youri Lammers, Jostein Bakke, Aage Paus, Catherine Langdon, Tomasz Goslar, Ludovic Gielly, Per Sjögren, Mary E. Edwards, Melanie J. Leng, Inger Greve Alsos, Willem G.M. van der Bilt, Marie Kristine Føreid Merkel, Torbjørn Alm, and Antony G. Brown
- Subjects
Vascular plant ,010506 paleontology ,Archeology ,010504 meteorology & atmospheric sciences ,medicine.disease_cause ,01 natural sciences ,Pollen ,VDP::Matematikk og Naturvitenskap: 400::Geofag: 450 ,medicine ,Glacial period ,Ecology, Evolution, Behavior and Systematics ,0105 earth and related environmental sciences ,VDP::Mathematics and natural science: 400 ,Global and Planetary Change ,VDP::Mathematics and natural science: 400::Geosciences: 450 ,biology ,Macrofossil ,Geology ,Last Glacial Maximum ,VDP::Matematikk og Naturvitenskap: 400 ,15. Life on land ,biology.organism_classification ,Habitat ,Biological dispersal ,Sedimentary rock ,Physical geography - Abstract
Andøya on the NW coast of Norway is a key site for understanding the Last Glacial Maximum (LGM) in northern Europe. Controversy has arisen concerning the local conditions, especially about the timing and extent of local glacial cover, maximum July temperatures and whether pine and/or spruce could have grown there. We reviewed all existing data and add newly analysed ancient sedimentary DNA (sedaDNA), pollen, macrofossils, geochemistry and stable isotopes from three lake sediment cores from Øvre Æråsvatnet. A total of 23 new dates and age-depth modelling suggests the lake has been ice-free since GI2 (Pinus and Picea sedaDNA was found in all three cores but at such low frequencies that it could not be distinguished from background contamination. LGM samples have an exceptionally high organic matter content, with isotopic values indicating that carbon and nitrogen derive from a marine source. Along with finds of bones of the little auk (Alle alle), this indicates that the lake received guano from an adjacent bird colony.SedaDNA, pollen and macrofossil assemblages were dominated by Poaceae, Brassicaceae and Papaver, but scattered occurrence of species currently restricted to the Low Arctic Tundra Zone (July temperature of 8–9 °C) such as Apiaceae (sedaDNA, 8–9 °C), and Alchemilla alpina (macrofossil, 8–9 °C) were also recorded. The review of >14.7 cal ka BP data recorded 94 vascular plant taxa, of which 38% have a northern limit in Shrub Tundra or more southern vegetation zones. This unusual assemblage likely stems from a combination of proximity to ice-free water in summer, geographical isolation linked with stochastic long-distance dispersal events, and the presence of bird-fertilized habitats. The environmental reconstruction based on all records from the area does not preclude local growth of tree species, as the local climate combined with high nutrient input may have led to periodically suitable environmental ‘hotspot’ conditions.
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- 2020
39. Holocene floristic diversity and richness in northeast Norway revealed by sedimentary ancient<scp>DNA</scp>(seda<scp>DNA</scp>) and pollen
- Author
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Ludovic Gielly, Kari Anne Bråthen, Antony G. Brown, Mary E. Edwards, Francisco Javier Ancin-Murguzur, Tomasz Goslar, Inger Greve Alsos, Peter D. Heintzman, Charlotte Clarke, and Youri Lammers
- Subjects
010506 paleontology ,Archeology ,010504 meteorology & atmospheric sciences ,Environmental change ,Range (biology) ,Ecology ,VDP::Matematikk og Naturvitenskap: 400::Geofag: 450::Stratigrafi og paleontologi: 461 ,Geology ,VDP::Mathematics and natural science: 400::Geosciences: 450::Quaternary geology, glaciology: 465 ,medicine.disease_cause ,01 natural sciences ,Ancient DNA ,VDP::Mathematics and natural science: 400::Geosciences: 450::Stratigraphy and paleontology: 461 ,Pollen ,medicine ,Younger Dryas ,Stadial ,Species richness ,VDP::Matematikk og Naturvitenskap: 400::Geofag: 450::Kvartærgeologi, glasiologi: 465 ,Ecology, Evolution, Behavior and Systematics ,Holocene ,0105 earth and related environmental sciences - Abstract
Source at https://doi.org/10.1111/bor.12357 We present a Holocene record of floristic diversity and environmental change for the central Varanger Peninsula, Finnmark, based on ancient DNA extracted from the sediments of a small lake (sedaDNA). The record covers the period c. 10 700 to 3300 cal. a BP and is complemented by pollen data. Measures of species richness, sample evenness and beta diversity were calculated based on sedaDNA sampling intervals and 1000‐year time windows. We identified 101 vascular plant and 17 bryophyte taxa, a high proportion (86%) of which are still growing within the region today. The high species richness (>60 taxa) observed in the Early Holocene, including representatives from all important plant functional groups, shows that modern shrub‐tundra communities, and much of their species complement, were in place as early as c. 10 700 cal. a BP. We infer that postglacial colonization of the area occurred prior to the full Holocene, during the Pleistocene‐Holocene transition, Younger Dryas stadial or earlier. Abundant DNA of the extra‐limital aquatic plant Callitriche hermaphroditica suggests it expanded its range northward between c. 10 200 and 9600 cal. a BP, when summers were warmer than present. High values of Pinus DNA occur throughout the record, but we cannot say with certainty if they represent prior local presence; however, pollen influx values >500 grains cm−2 a−1 between c. 8000 and 7300 cal. a BP strongly suggest the presence of pine woodland during this period. As the site lies beyond the modern tree limit of pine, it is likely that this expansion also reflects a response to warmer Early Holocene summers.
- Published
- 2018
40. Metabarcoding of modern soil DNA gives a highly local vegetation signal in Svalbard tundra
- Author
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Henrik von Stedingk, Tomasz Goslar, James Haile, Andreas Tribsch, Ludovic Gielly, Nigel G. Yoccoz, Inger Greve Alsos, Catherine Langdon, Heather Binney, Mary E. Edwards, Pierre Taberlet, and Eric Coissac
- Subjects
0301 basic medicine ,Archeology ,Global and Planetary Change ,Ecology ,Soil dna ,Paleontology ,Tundra ,03 medical and health sciences ,030104 developmental biology ,Soil water ,medicine ,Environmental science ,Environmental DNA ,medicine.symptom ,Vegetation (pathology) ,Earth-Surface Processes - Abstract
Environmental DNA retrieved from modern soils (eDNA) and late-Quaternary palaeosols and sediments (aDNA and sedaDNA) promises insight into the composition of present and past terrestrial biotic communities, but few studies address the spatial relationship between recovered eDNA and contributing organisms. Svalbard’s vascular plant flora is well known, and a cold climate enhances preservation of eDNA in soils. Thus, Svalbard plant communities are excellent systems for addressing the representation of plant eDNA in soil samples. In two valleys in the inner fjord region of Spitsbergen, we carried out detailed vegetation surveys of circular plots up to a 4-m radius. One or three near-surface soil samples from each plot were used for extraction and metabarcoding of soil-derived eDNA. Use of PCR replicates and appropriate filtering, plus a relevant reference metabarcode catalogue, provided taxon lists that reflected the local flora. There was high concordance between taxa recorded in plot vegetation and those in the eDNA, but floristic diversity was under-sampled, even at the scale of a 1-m radius plot. Most detected taxa grew within < 0.5–1.0 m of the sampling point. Taxa present in vegetation but not in eDNA tended to occur further from the sampling point, and most had above-ground cover of < 5%. Soil-derived eDNA provides a highly local floristic signal, and this spatial constraint should be considered in sampling designs. For palaeoecological or archaeological studies, multiple samples from a given soil horizon that are spatially distributed across the area of interest are likely to provide the most complete picture of species presence.
- Published
- 2018
41. Shotgun Environmental DNA, Pollen, and Macrofossil Analysis of Lateglacial Lake Sediments From Southern Sweden
- Author
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Inger Greve Alsos, Tanja Slotte, Youri Lammers, Per Unneberg, Barbara Wohlfarth, J. Sakari Salonen, Minna Väliranta, Laura Parducci, Lu Han, Mikkel Winther Pedersen, BioGeoClimate Modelling Lab, Department of Geosciences and Geography, Helsinki Institute of Sustainability Science (HELSUS), Environmental Change Research Unit (ECRU), and Ecosystems and Environment Research Programme
- Subjects
0106 biological sciences ,0301 basic medicine ,1171 Geosciences ,shotgun sequencing (metagenomics) ,lake sediments ,lcsh:Evolution ,medicine.disease_cause ,VDP::Mathematics and natural science: 400::Geosciences: 450::Quaternary geology, glaciology: 465 ,010603 evolutionary biology ,01 natural sciences ,LAST TERMINATION ,EXTRACELLULAR DNA ,EVENTS ,macrofossils remains ,03 medical and health sciences ,Pollen ,lcsh:QH540-549.5 ,medicine ,HOLOCENE ,lcsh:QH359-425 ,Environmental DNA ,Geosciences, Multidisciplinary ,PLANT-COMMUNITIES ,RECORDS ,ancient DNA ,Ecology, Evolution, Behavior and Systematics ,Holocene ,VDP::Matematikk og Naturvitenskap: 400::Geofag: 450::Kvartærgeologi, glasiologi: 465 ,1172 Environmental sciences ,Ecology ,Macrofossil ,Plant community ,Vegetation ,15. Life on land ,Before Present ,environmental DNA ,Multidisciplinär geovetenskap ,READ ALIGNMENT ,030104 developmental biology ,Ancient DNA ,pollen ,SYNCHRONIZATION ,Physical geography ,VEGETATION ,lcsh:Ecology ,Geology - Abstract
Source at https://doi.org/10.3389/fevo.2019.00189. The lake sediments of Hässeldala Port in south-east Sweden provide an archive of local and regional environmental conditions ~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 Allerød (14.1–12.7 ka BP), Younger Dryas (12.7–11.7 ka BP), and Preboreal (
- Published
- 2019
42. DNA metabarcoding—Need for robust experimental designs to draw sound ecological conclusions
- Author
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Inger Greve Alsos, Lucie Zinger, Gentile Francesco Ficetola, Aurélie Bonin, Frédéric Boyer, Marta De Barba, Simon N. Jarman, M. Thomas P. Gilbert, Ian A. Dickie, Leho Tedersoo, Anthony A. Chariton, Bruce E. Deagle, Philip Francis Thomsen, Johan Pansu, Alex J. Dumbrell, Ari Jumpponen, Håvard Kauserud, Holly M. Bik, Eske Willerslev, Pierre Taberlet, Luca Fumagalli, Simon Creer, Eric Coissac, Miklós Bálint, Jan Pawlowski, Ludovic Orlando, Noah Fierer, Laboratoire d'Ecologie Alpine (LECA ), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Biogéosciences [UMR 6282] [Dijon] (BGS), Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, New York University [New York] (NYU), NYU System (NYU), Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Australian Antarctic Division (AAD), Australian Government, Department of the Environment and Energy, emlyon business school, Politecnico di Milano [Milan] (POLIMI), University of Copenhagen = Københavns Universitet (KU), Microbial Evolution Research Group (MERG), Department of Biology [Oslo], Faculty of Mathematics and Natural Sciences [Oslo], University of Oslo (UiO)-University of Oslo (UiO)-Faculty of Mathematics and Natural Sciences [Oslo], University of Oslo (UiO)-University of Oslo (UiO), Section for GeoGenetics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Department of Genetics and Evolution, Université de Genève (UNIGE), University of Tartu, JP was supported by the Marie Skłodowska-Curie actions (TEAM-Coast project, MSCA-GF 750570), Laboratoire d'Ecologie Alpine (LECA), Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Université Joseph Fourier - Grenoble 1 (UJF)-Université Grenoble Alpes (UGA), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS), Laboratoire des Sciences du Numérique de Nantes (LS2N), Université de Nantes - Faculté des Sciences et des Techniques, Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Robotique Et Vivant (ReV), and Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Nantes - Faculté des Sciences et des Techniques
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0106 biological sciences ,replication ,Ecology (disciplines) ,[SDV]Life Sciences [q-bio] ,experimental controls ,Biology ,010603 evolutionary biology ,01 natural sciences ,03 medical and health sciences ,chemistry.chemical_compound ,Dna genetics ,Replication (statistics) ,Genetics ,DNA Barcoding, Taxonomic ,data quality ,Environmental DNA ,Ecology, Evolution, Behavior and Systematics ,Sound (geography) ,ComputingMilieux_MISCELLANEOUS ,030304 developmental biology ,0303 health sciences ,geography ,geography.geographical_feature_category ,Ecology ,Biodiversity ,DNA ,environmental DNA ,chemistry ,Evolutionary biology ,[SDE]Environmental Sciences - Abstract
International audience
- Published
- 2019
43. Lake sedimentary <scp>DNA</scp> accurately records 20 th Century introductions of exotic conifers in Scotland
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Inger Greve Alsos, Per Sjögren, Catherine Langdon, Mary E. Edwards, Ludovic Gielly, Marie Kristine Føreid Merkel, Ian W. Croudace, and Thierry Fonville
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0106 biological sciences ,0301 basic medicine ,Geologic Sediments ,Time Factors ,Taphonomy ,DNA, Plant ,Physiology ,lake sediments ,Plant Science ,environmental DNA (eDNA) ,Biology ,medicine.disease_cause ,010603 evolutionary biology ,01 natural sciences ,03 medical and health sciences ,vegetation change ,Pollen ,VDP::Mathematics and natural science: 400::Zoology and botany: 480 ,medicine ,Afforestation ,sedimentary DNA (sedDNA) ,Repetitive Sequences, Nucleic Acid ,Source area ,Full Paper ,Geography ,Ecology ,Research ,Full Papers ,Models, Theoretical ,Lakes ,Tracheophyta ,030104 developmental biology ,Taxon ,Scotland ,metabarcoding ,Sedimentary rock ,Introduced Species ,Chronology - Abstract
Published version. Source at http://doi.org/10.1111/nph.14199. License CC BY 4.0. Sedimentary DNA (sedDNA) has recently emerged as a new proxy for reconstructing past vegetation, but its taphonomy, source area and representation biases need better assessment. We investigated how sedDNA in recent sediments of two small Scottish lakes reflects a major vegetation change, using well-documented 20th Century plantations of exotic conifers as an experimental system. We used next-generation sequencing to barcode sedDNA retrieved from subrecent lake sediments. For comparison, pollen was analysed from the same samples. The sedDNA record contains 73 taxa (mainly genus or species), all but one of which are present in the study area. Pollen and sedDNA shared 35% of taxa, which partly reflects a difference in source area. More aquatic taxa were recorded in sedDNA, whereas taxa assumed to be of regional rather than local origin were recorded only as pollen. The chronology of the sediments and planting records are well aligned, and sedDNA of exotic conifers appears in high quantities with the establishment of plantations around the lakes. SedDNA recorded other changes in local vegetation that accompanied afforestation. There were no signs of DNA leaching in the sediments or DNA originating from pollen.
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- 2016
44. The regional species richness and genetic diversity of Arctic vegetation reflect both past glaciations and current climate
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Christian Bay, Liv Unn Tveraabak, Jens-Christian Svenning, Loïc Pellissier, Helga Bültmann, Mary S. Wisz, Jonathan Lenoir, Miska Luoto, Peter Christiaan le Roux, Jacob Nabe-Nielsen, Esther Lévesque, Christian Damgaard, Fred J.A. Daniëls, Peder Klith Bøcher, Christian Brochmann, Risto Virtanen, Nigel G. Yoccoz, Kristine Bakke Westergaard, Noémie Boulanger-Lapointe, Niels Martin Schmidt, Olivier Broennimann, Amy L. Breen, Dorothee Ehrich, Andreas Tribsch, Pernille Bronken Eidesen, Lærke Stewart, Ingibjörg S. Jónsdóttir, Inger Greve Alsos, Antoine Guisan, Donald A. Walker, and Peter Schönswetter
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0106 biological sciences ,Global and Planetary Change ,Genetic diversity ,Ecology ,Climate change ,Plant community ,Circumpolar star ,15. Life on land ,Biology ,010603 evolutionary biology ,01 natural sciences ,13. Climate action ,Biological dispersal ,Species richness ,Taxonomic rank ,Arctic vegetation ,Ecology, Evolution, Behavior and Systematics ,010606 plant biology & botany - Abstract
Compilation of the species richness data was made possible through the TFI Networks grant to CD, “Effect Studies and Adaptation to Climate Change,” under the Norforsk initiative (2011 – 2014) which supported two CBIONET-AVA workshops held in Denmark during 2013. The genetic studies were funded by the Research Council of Norway (grant nos. 150322/720 and 170952/V40 to CB).
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- 2016
45. Metabarcoding lake sediments: taphonomy and representation of contemporary vegetation in environmental DNA (eDNA) records
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T Joergensen, Nigel G. Yoccoz, Ludovic Gielly, Inger Greve Alsos, Per Sjögren, Youri Lammers, and Mary E. Edwards
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Vascular plant ,biology ,Ecology ,Biodiversity ,Macrofossil ,biology.organism_classification ,Geography ,Deciduous ,Abundance (ecology) ,Aquatic plant ,medicine ,Environmental DNA ,medicine.symptom ,Vegetation (pathology) - Abstract
Metabarcoding of lake sediments may reveal current and past biodiversity, but little is known about the degree to which taxa growing in the vegetation are represented in environmental DNA (eDNA) records. We analysed composition of lake and catchment vegetation and vascular plant eDNA at 11 lakes in northern Norway. Out of 489 records of taxa growing within 2 m from the lake shore, 17-49% (mean 31%) of the identifiable taxa recorded were detected with eDNA. Of the 217 eDNA records, 73% and 12% matched taxa recorded in vegetation surveys within 2 m and up to about 50 m away from the lakeshore, respectively, whereas 16% were not recorded in the vegetation surveys of the same lake. The latter include taxa likely overlooked in the vegetation surveys or growing outside the survey area. The percentages detected were 61, 47, 25, and 15 for dominant, common, scattered, and rare taxa, respectively. Similar numbers for aquatic plants were 88, 88, 33 and 62%, respectively. Detection rate and taxonomic resolution varied among plant families and functional groups with good detection of e.g. Ericaceae, Roseaceae, deciduous trees, ferns, club mosses and aquatics. The representation of terrestrial taxa in eDNA depends on both their distance from the sampling site and their abundance and is sufficient for recording vegetation types. For aquatic vegetation, eDNA may be comparable with, or even superior to, in-lake vegetation surveys and therefore be used as an tool for biomonitoring. For reconstruction of terrestrial vegetation, technical improvements and more intensive sampling is needed to detect a higher proportion of rare taxa although DNA of some taxa may never reach the lake sediments due to taphonomical constrains. Nevertheless, eDNA performs similar to conventional methods of pollen and macrofossil analyses and may therefore be an important tool for reconstruction of past vegetation.
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- 2018
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- View/download PDF
46. Prevention of microbial species introductions to the Arctic: The efficacy of footwear disinfection measures on cruise ships
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Inger Greve Alsos, Sabine B. Rumpf, and Chris Ware
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0106 biological sciences ,Cruise ,Biosecurity ,Plant Science ,Aquatic Science ,Microbial contamination ,010603 evolutionary biology ,01 natural sciences ,Invasive species ,invasive species ,ddc:570 ,VDP::Matematikk og Naturvitenskap: 400::Zoologiske og botaniske fag: 480::Plantegeografi: 496 ,microorganisms ,lcsh:QH301-705.5 ,disinfection ,Ecology, Evolution, Behavior and Systematics ,Ecology ,010604 marine biology & hydrobiology ,Ecological Modeling ,VDP::Mathematics and natural science: 400::Zoology and botany: 480::Plant geography: 496 ,VDP::Mathematics and natural science: 400::Zoology and botany: 480::Zoogeography: 486 ,VDP::Matematikk og Naturvitenskap: 400::Zoologiske og botaniske fag: 480::Zoogeografi: 486 ,The arctic ,Fishery ,monitoring ,Geography ,lcsh:Biology (General) ,Insect Science ,tourism ,Animal Science and Zoology ,Tourism ,biosecurity - Abstract
Source at https://doi.org/10.3897/neobiota.37.22088. Biosecurity measures are commonly used to prevent the introduction of non-native species to natural environments globally, yet the efficacy of practices is rarely tested under operational conditions. A voluntary biosecurity measure was trialled in the Norwegian high Arctic following concern that non-native species might be transferred to the region on the footwear of travellers. Passengers aboard an expedition cruise ship disinfected their footwear with the broad spectrum disinfectant Virkon S prior to and in-between landing at sites around the remote Svalbard archipelago. The authors evaluated the efficacy of simply stepping through a disinfectant foot bath, which is the most common practice of footwear disinfection aboard expedition cruise ships in the Arctic. This was compared to a more time consuming and little-used method involving drying disinfected footwear, as proposed by other studies. The two practices were evaluated by measuring microbial growth on paired footwear samples before and after disinfection under both conditions. Step-through disinfection did not substantially reduce microbial growth on the footwear. Allowing disinfected footwear to dry, however, reduced the microbial burden significantly to lower levels. Thus, the currently adopted procedures used aboard ships are ineffective at removing microbial burden and are only effective when footwear is given more time to dry than currently granted under operational conditions. These findings underscore results from empirical research performed elsewhere and suggest the need to better relay this information to practitioners. It is suggested that footwear should minimally be wiped dry after step-through disinfection as a reasonable compromise between biosecurity and practicability.
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- 2018
47. Disjunct populations of European vascular plant species keep the same climatic niches
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Mats Dynesius, Carl Johan Dahlberg, Stefanie Reinhardt, Jörg Brunet, Guillaume Decocq, Stefan Dullinger, Jens-Christian Svenning, Gunnar Austrheim, Ann Milbau, Mari Moora, Sylvi M. Sandvik, Risto Virtanen, Safaa Wasof, Olivier Broennimann, W. Scott Armbruster, Wilfried Thuiller, Kari Anne Bråthen, Pascal Vittoz, James D. M. Speed, Kristoffer Hylander, Niklaus E. Zimmermann, John-Arvid Grytnes, Martin Diekmann, Virve Ravolainen, Liv Guri Velle, Fride Høistad Schei, Jonathan Lenoir, Thomas Wohlgemuth, Harald Pauli, Vegar Bakkestuen, Martin Zobel, Miska Luoto, Wolfgang Willner, Arvid Odland, Rasmus Ejrnæs, Antoine Guisan, Jean-Claude Gégout, Bente J. Graae, Kari Klanderud, Bettina Nygaard, Jutta Kapfer, Hans Henrik Bruun, Ingibjörg S. Jónsdóttir, Inger Greve Alsos, H. John B. Birks, Vigdis Vandvik, Liv Unn Tveraabak, and Per Arild Aarrestad
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0106 biological sciences ,Vascular plant ,Ecological niche ,Global and Planetary Change ,010504 meteorology & atmospheric sciences ,Ecology ,biology ,Disjunct distribution ,Niche segregation ,15. Life on land ,Disjunct ,biology.organism_classification ,010603 evolutionary biology ,01 natural sciences ,Environmental niche modelling ,Arctic vegetation ,Ecology, Evolution, Behavior and Systematics ,0105 earth and related environmental sciences ,Global biodiversity - Abstract
Aim Previous research on how climatic niches vary across species ranges has focused on a limited number of species, mostly invasive, and has not, to date, been very conclusive. Here we assess the d ...
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- 2015
48. Microsatellite Markers for Heracleum persicum (Apiaceae) and Allied Taxa: Application of Next-Generation Sequencing to Develop Genetic Resources for Invasive Species Management
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Inger Greve Alsos, Torbjørn Alm, Mohsen Falahati-Anbaran, and Dilli Prasad Rijal
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VDP::Mathematics and natural science: 400::Zoology and botany: 480::Systematic botany: 493 ,Anthriscus sylvestris ,biology ,Heracleum sphondylium ,VDP::Matematikk og Naturvitenskap: 400::Zoologiske og botaniske fag: 480::Systematisk botanikk: 493 ,Plant Science ,biology.organism_classification ,GeneralLiterature_MISCELLANEOUS ,Heracleum sosnowskyi ,Heracleum mantegazzianum ,Heracleum persicum ,Heracleum ,Evolutionary biology ,Genetic structure ,Botany ,ComputingMethodologies_DOCUMENTANDTEXTPROCESSING ,Microsatellite ,Molecular Biology - Abstract
Invasive giant hogweeds are infamous in Europe for causing ecological and economic damage, but genetic resources for their study are limited. We used next-generation sequencing to develop a microsatellite library for Heracleum persicum, a widespread invasive in Nordic countries. In addition, these markers were cross amplified with the closely related Heracleum mantegazzianum, Heracleum sosnowskyi, Heracleum sphondylium, and the putative hybrid H. persicum × H. sphondylium, as well as the more distantly related Anthriscus sylvestris. We designed and validated 164 primer pairs. A cost-effective PCR approach with modified forward primer, reverse primer, and fluorescently labeled universal tail was used to test the functionality of each marker. Twenty-five of thirty markers screened on eight geographically distant samples of H. persicum were polymorphic. The number of alleles was 2–4 whereas the expected and observed heterozygosity varied from 0.06 to 0.84 and 0.0 to 1.0 respectively. The cross-species amplification efficiency was 84–100 %, in which 60–76 % of the cross-species amplified markers were polymorphic for Heracleum taxa including H. persicum × sphondylium. Three out of eight of the cross-amplified markers were polymorphic in Anthriscus sylvestris. Ordination revealed a clear genetic structure of Heracleum taxa. Thus, these markers can serve as important genetic resources for understanding taxonomy, population genetics, and phylogeny of giant hogweeds and their hybrids, which in turn, is expected to contribute to invasive species management.
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- 2014
49. Living on the edge: conservation genetics of seven thermophilous plant species in a high Arctic archipelago
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Inger Greve Alsos, Reidar Elven, Idunn Elisabeth Borgen Skjetne, Anne K. Brysting, and Siri Birkeland
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0106 biological sciences ,0301 basic medicine ,Conservation genetics ,Rare species ,Biodiversity ,islands ,Plant Science ,Kobresia simpliciuscula ,010603 evolutionary biology ,01 natural sciences ,Svalbard ,03 medical and health sciences ,Arctic ,Tofieldia pusilla ,VDP::Matematikk og Naturvitenskap: 400::Basale biofag: 470 ,edge populations ,Amplified fragment length polymorphism (AFLP) ,Genetic diversity ,biology ,Ecology ,biology.organism_classification ,regional red list ,VDP::Mathematics and natural science: 400::Basic biosciences: 470 ,030104 developmental biology ,Population bottleneck ,climate change ,conservation genetics ,geographic locations ,Research Article ,VDP::Matematikk og Naturvitenskap: 400::Zoologiske og botaniske fag: 480 - Abstract
Small and peripheral populations often contain low levels of genetic variation. This may limit their ability to adapt to environmental change, including climate warming. In a recent study published in AoB PLANTS, Birkeland, Skjetne and colleagues show that many rare and threatened plant species in the High Arctic archipelago Svalbard harbour low levels of genetic variation. Most of them are probably relicts from the early Holocene warmer period. They have likely experienced strong genetic founder/bottleneck effects due to climatic limitations. Even though temperatures now are rising, it is highly uncertain whether this will be beneficial for these warmth-demanding species., Small, isolated and/or peripheral populations are expected to harbour low levels of genetic variation and may therefore have reduced adaptability to environmental change, including climate warming. In the Arctic, global warming has already caused vegetation change across the region and is acting as a significant stressor on Arctic biodiversity. Many of the rare plants in the Arctic are relicts from early Holocene warm periods, but their ability to benefit from the current warming is dependent on the viability of their populations. We therefore examined Amplified Fragment Length Polymorphism (AFLP) data from regional red listed vascular plant species in the High Arctic archipelago of Svalbard and reference populations from the main distribution area of: (1) Botrychium lunaria, (2) Carex capillaris ssp. fuscidula, (3) Comastoma tenellum, (4) Kobresia simpliciuscula ssp. subholarctica, (5) Ranunculus wilanderi, (6) Sibbaldia procumbens and (7) Tofieldia pusilla. In addition, we gathered population size data in Svalbard. The Svalbard populations had low genetic diversity and distinctiveness and few or no private markers compared to populations outside the archipelago. This is similar to observations in other rare species in Svalbard and the genetic depletion may be due to an initial founder effect and/or a genetic bottleneck caused by late Holocene cooling. There seems to be limited gene flow from other areas and the Svalbard populations should therefore be considered as demographically independent management units. Overall, these management units have small and/or few populations and are therefore prone to stochastic events which may further increase vulnerability to inbreeding depression, loss of genetic variation, and reduced evolutionary potential. Our results support theory predicting lower levels of genetic diversity in small, isolated and/or peripheral populations and may be of importance for management of other rare plant species in the Arctic.
- Published
- 2017
50. Ancient plant DNA in lake sediments
- Author
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Inger Greve Alsos, Yoshihisa Suyama, Keith Bennett, Jamie R. Wood, Laura Parducci, Mikkel Winther Pedersen, Gentile Francesco Ficetola, and University of St Andrews. Geography & Sustainable Development
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0301 basic medicine ,ancient plant DNA (aDNA) ,Taphonomy ,DNA, Plant ,Bioinformatics ,Physiology ,Sample point ,QH301 Biology ,T-NDAS ,lake sediments ,Plant Science ,high-throughput DNA sequencing ,Biology ,Geologic Sediments ,environmental DNA (eDNA) ,geologic sediments ,shotgun sequencing ,QH301 ,03 medical and health sciences ,Ancient plant DNA (aDNA) ,Abundance (ecology) ,G1 ,lakes ,DNA, Ancient ,Ecology ,taphonomy ,G Geography (General) ,bioinformatics ,High-throuput DNA sequencing ,Lake sediments ,Shotgun sequencing ,DNA plant ,High-Throughput DNA Sequencing ,030104 developmental biology ,Taxon ,Environmental DNA (eDNA) ,pollen ,metabarcoding ,Metabarcoding ,Pollen ,Taxonomic resolution ,fossils ,BDC - Abstract
This work was supported by the Swedish Research Council (grant no. 2013-D0568401), SciLifeLab Stockholm and the Carl Triggers’ Foundation (grant no. 14:371) to L.P., and the Research Council of Norway to I.G.A. (grant no. 213692/F20). 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 aDNA 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 aDNA 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. Postprint
- Published
- 2017
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