10.18710/3CVQAGWang, YuchengYuchengWang0000-0002-7838-226XLundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of CopenhagenPedersen, Mikkel WintherMikkel WintherPedersen0000-0002-7291-8887Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of CopenhagenAlsos, Inger GreveInger GreveAlsos0000-0002-8610-1085UiT The Arctic University of NorwayDe Sanctis, BiancaBiancaDe Sanctis0000-0002-0648-4224Department of Zoology, University of CambridgeRacimo, FernandoFernandoRacimo0000-0002-5025-2607Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of CopenhagenProhaska, AnaAnaProhaska0000-0001-5459-6186Department of Zoology, University of CambridgeCoissac, EricEricCoissac0000-0001-7507-6729UiT The Arctic University of NorwayOwens, Hannah LoisHannah LoisOwens0000-0003-0071-1745Center for Macroecology, Evolution and Climate, GLOBE Institute, University of CopenhagenMerkel, Marie Kristine FøreidMarie Kristine FøreidMerkelUiT The Arctic University of NorwayFernandez-Guerra, AntonioAntonioFernandez-Guerra0000-0002-8679-490XLundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of CopenhagenRouillard, AlexandraAlexandraRouillard0000-0001-5778-6620Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of CopenhagenLammers, YouriYouriLammers0000-0003-0952-2668UiT The Arctic University of NorwayAlberti, AdrianaAdrianaAlberti0000-0003-3372-9423Université Paris-SaclayDenoeud, FranceFranceDenoeud0000-0001-8819-7634Génomique Métabolique, Genoscope, Institut François JacobMoney, DanielDanielMoneyDepartment of Zoology, University of CambridgeRuter, Anthony H.Anthony H.RuterLundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of CopenhagenMcColl, HughHughMcColl0000-0002-7568-4270Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of CopenhagenLarsen, Nicolaj KrogNicolaj KrogLarsen0000-0002-0117-1106Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of CopenhagenCherezova, Anna A.Anna A.Cherezova0000-0002-6199-8164Institute of Earth Sciences, St. Petersburg State UniversityEdwards, Mary E.Mary E.EdwardsSchool of Geography and Environmental Science, University of SouthamptonFedorov, Grigory B.Grigory B.Fedorov0000-0003-2269-4501Institute of Earth Sciences, St. Petersburg State UniversityHaile, JamesJamesHaileLundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of CopenhagenOrlando, LudovicLudovicOrlando0000-0003-3936-1850Centre d'Anthropobiologie et de Génomique de Toulouse, Université Paul SabatierVinner, LasseLasseVinner0000-0002-3081-3702Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of CopenhagenKorneliussen, Thorfinn SandThorfinn SandKorneliussen0000-0001-7576-5380Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of CopenhagenBeilman, David W.David W.BeilmanDepartment of Geography and Environment, University of HawaiiBjørk, Anders A.Anders A.Bjørk0000-0002-4919-792XDepartment of Geosciences and Natural Resource Management, University of CopenhagenCao, JialuJialuCao0000-0001-5359-7072Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of CopenhagenDockter, ChristophChristophDockterCarlsberg Research LaboratoryEsdale, JulieJulieEsdaleCenter for the Environmental Management of Military Lands, Colorado State UniversityGusarova, GalinaGalinaGusarovaUiT The Arctic University of NorwayKjeldsen, Kristian K.Kristian K.Kjeldsen0000-0002-8557-5131Department of Glaciology and Climate, Geological Survey of Denmark and GreenlandMangerud, JanJanMangerud0000-0003-4793-7557Department of Earth Science, University of BergenRasic, Jeffrey T.Jeffrey T.RasicU.S. National Park Service, Gates of the Arctic National Park and PreserveSkadhauge, BirgitteBirgitteSkadhaugeDepartment of Geography and Environment, University of HawaiiSvendsen, John-IngeJohn-IngeSvendsenDepartment of Earth Science, University of BergenTikhonov, AlexeiAlexeiTikhonov0000-0002-7227-5797Zoological Institute, Russian academy of sciencesWincker, PatrickPatrickWinckerGénomique Métabolique, Genoscope, Institut François JacobXing, YingchunYingchunXingResource and Environmental Research Center, Chinese Academy of Fishery SciencesZhang, YubinYubinZhang0000-0003-4920-3100College of Plant Science, Jilin UniversityFroese, Duane G.Duane G.Froese0000-0003-1032-5944Department of Earth and Atmospheric Sciences, University of AlbertaRahbek, CarstenCarstenRahbek0000-0003-4585-0300Center for Macroecology, Evolution and Climate, GLOBE Institute, University of CopenhagenBravo Nogues, DavidDavidBravo Nogues0000-0002-4060-0153Center for Macroecology, Evolution and Climate, GLOBE Institute, University of CopenhagenHolden, Philip B.Philip B.Holden0000-0002-2369-0062School of Environment, Earth and Ecosystem Sciences, The Open UniversityEdwards, Neil R.Neil R.Edwards0000-0001-6045-8804School of Environment, Earth and Ecosystem Sciences, The Open UniversityDurbin, RichardRichardDurbin0000-0002-9130-1006Department of Genetics, University of CambridgeMeltzer, David J.David J.MeltzerLundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of CopenhagenKjær, Kurt H.Kurt H.Kjær0000-0002-8871-5179Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of CopenhagenMöller, PerPerMöllerDepartment of Geology, Quaternary Sciences, Lund UniversityWillerslev, EskeEskeWillerslev0000-0002-7081-6748Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of CopenhagenSupporting data for: Late Quaternary dynamics of Arctic biota revealed by ancient environmental metagenomicsDataverseNO2022Earth and Environmental SciencesMedicine, Health and Life Sciencesplant DNAchloroplast DNAenvironmental DNAnuclear ribosomal DNAphylogenomicpolargenome contigsAlsos, Inger GreveInger GreveAlsosUiT The Arctic University of NorwayUiT The Arctic University of NorwayLaboratoire d’Ecologie AlpineUniv. Grenoble Alpes, Univ. Savoie Mont BlancGenoscope, Institut François JacobInstitut François JacobGenoscopeCEA, CNRSAlsos, Inger GreveInger GreveAlsosCoissac, EricEricCoissacMerkel, Marie K. F.Wang, YuchengYuchengWangAlberti, AdrianaAdrianaAlbertiLammers, YouriYouriLammersDenoeud, FranceFranceDenoeudWincker, PatrickPatrickWinckerUiT The Arctic University of NorwayUiT The Arctic University of NorwayUiT The Arctic University of Norway2019-08-012021-05-282023-02-25Partial DNA sequence assemblies of vascular plant genomes10.1038/s41586-021-04016-x10.3390/plants904043258042332354165523323541963233235418032332354166823323541696233235418202332354193316319244953text/plainapplication/octet-streamapplication/octet-streamapplication/octet-streamapplication/octet-streamapplication/octet-streamapplication/octet-streamapplication/octet-streamtext/plain1.2CC0 1.0<p><b>ALTERNATIVE DOWNLOAD FROM FILESENDER</b> To access the data, click "Read Full Description" [+] and then click <a href="https://filesender.sikt.no/?s=download&token=ccb39bb0-66d5-4e84-94d6-0f8bafb458a3" title="Download URL" target="_blank">here</a></p> <p></p> [Dataset abstract] This dataset contains the assembled genome contigs (whole genome level) of the PhyloNorway plant database used in Wang et al. 2021 Late Quaternary Dynamics of Arctic Biota Revealed by Ancient Environmental Metagenomics. Methods for generating this database can be found in the paper. The 7 fasta files are the database. The PhyloNorway_com_acc2TaxaID.txt supplies a NCBI format acc2TaxaID file matching accession ID to NCBI TaxaID. Additional information about the database can be found in Alsos et al. 2020.<p></p> <p></p> [Article abstract Wang et al. submitted] During the last glacial-interglacial cycle, arctic biota experienced drastic climatic changes, yet the nature, extent and rate of their responses are not fully understood. Here we report the first large-scale environmental DNA metagenomic study of ancient plant and mammal communities using 535 permafrost and lake sediment samples from across the Arctic spanning the last 50,000 years. Additionally, we present 1,541 contemporary plant genome assemblies generated as reference sequences. Our study provides several novel insights into the long-term dynamics of the arctic biota at circumpolar and regional scales. Key findings include: (i) a relatively homogeneous steppe-tundra flora dominated the Arctic during the Last Glacial Maximum, followed by regional divergence of vegetation in the Holocene; (ii) certain grazing animals consistently co-occurred in space and time; (iii) humans appear to have been a minor factor in driving animal distributions; (iv) higher effective precipitation, and an increase in the proportion of wetland plants, show negative effects on animal diversity; (v) the persistence of the steppe-tundra vegetation in northern Siberia allowed the late survival of several now-extinct megafauna species, including woolly mammoth to 3.9±0.2 ka (kilo annum Before Present) and woolly rhinoceros to 9.8±0.2 ka; and (vi) phylogenetic analysis of mammoth eDNA reveals a previously unsampled mitochondrial lineage. Our findings highlight the power of ancient environmental metagenomics to advance understanding of population histories and long-term ecological dynamics.<p></p> <p></p> [Article abstract Alsos et al. 2020] 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.bowtie, 2.3.2AdapterRemoval, 2.3.0DNA sequences of plants collected and deposited at herbarium TROM at Tromsø Museum, Norway.Tromsø, Norway and Paris, FranceThe Research Council of NorwayNorwegian Biodiversity Information CentreThe Research Council of Norway226134/F50Norwegian Biodiversity Information Centre14-14, 70184209