Persistent Identifier
|
doi:10.18710/3CVQAG |
Publication Date
|
2022-03-17 |
Title
| Supporting data for: Late Quaternary dynamics of Arctic biota revealed by ancient environmental metagenomics |
Author
| Wang, Yucheng (Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen) - ORCID: 0000-0002-7838-226X
Pedersen, Mikkel Winther (Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen) - ORCID: 0000-0002-7291-8887
Alsos, Inger Greve (UiT The Arctic University of Norway) - ORCID: 0000-0002-8610-1085
De Sanctis, Bianca (Department of Zoology, University of Cambridge) - ORCID: 0000-0002-0648-4224
Racimo, Fernando (Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen) - ORCID: 0000-0002-5025-2607
Prohaska, Ana (Department of Zoology, University of Cambridge) - ORCID: 0000-0001-5459-6186
Coissac, Eric (UiT The Arctic University of Norway) - ORCID: 0000-0001-7507-6729
Owens, Hannah Lois (Center for Macroecology, Evolution and Climate, GLOBE Institute, University of Copenhagen) - ORCID: 0000-0003-0071-1745
Merkel, Marie Kristine Føreid (UiT The Arctic University of Norway)
Fernandez-Guerra, Antonio (Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen) - ORCID: 0000-0002-8679-490X
Rouillard, Alexandra (Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen) - ORCID: 0000-0001-5778-6620
Lammers, Youri (UiT The Arctic University of Norway) - ORCID: 0000-0003-0952-2668
Alberti, Adriana (Université Paris-Saclay) - ORCID: 0000-0003-3372-9423
Denoeud, France (Génomique Métabolique, Genoscope, Institut François Jacob) - ORCID: 0000-0001-8819-7634
Money, Daniel (Department of Zoology, University of Cambridge)
Ruter, Anthony H. (Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen)
McColl, Hugh (Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen) - ORCID: 0000-0002-7568-4270
Larsen, Nicolaj Krog (Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen) - ORCID: 0000-0002-0117-1106
Cherezova, Anna A. (Institute of Earth Sciences, St. Petersburg State University) - ORCID: 0000-0002-6199-8164
Edwards, Mary E. (School of Geography and Environmental Science, University of Southampton)
Fedorov, Grigory B. (Institute of Earth Sciences, St. Petersburg State University) - ORCID: 0000-0003-2269-4501
Haile, James (Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen)
Orlando, Ludovic (Centre d'Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier) - ORCID: 0000-0003-3936-1850
Vinner, Lasse (Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen) - ORCID: 0000-0002-3081-3702
Korneliussen, Thorfinn Sand (Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen) - ORCID: 0000-0001-7576-5380
Beilman, David W. (Department of Geography and Environment, University of Hawaii)
Bjørk, Anders A. (Department of Geosciences and Natural Resource Management, University of Copenhagen) - ORCID: 0000-0002-4919-792X
Cao, Jialu (Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen) - ORCID: 0000-0001-5359-7072
Dockter, Christoph (Carlsberg Research Laboratory)
Esdale, Julie (Center for the Environmental Management of Military Lands, Colorado State University)
Gusarova, Galina (UiT The Arctic University of Norway)
Kjeldsen, Kristian K. (Department of Glaciology and Climate, Geological Survey of Denmark and Greenland) - ORCID: 0000-0002-8557-5131
Mangerud, Jan (Department of Earth Science, University of Bergen) - ORCID: 0000-0003-4793-7557
Rasic, Jeffrey T. (U.S. National Park Service, Gates of the Arctic National Park and Preserve)
Skadhauge, Birgitte (Department of Geography and Environment, University of Hawaii)
Svendsen, John-Inge (Department of Earth Science, University of Bergen)
Tikhonov, Alexei (Zoological Institute, Russian academy of sciences) - ORCID: 0000-0002-7227-5797
Wincker, Patrick (Génomique Métabolique, Genoscope, Institut François Jacob)
Xing, Yingchun (Resource and Environmental Research Center, Chinese Academy of Fishery Sciences)
Zhang, Yubin (College of Plant Science, Jilin University) - ORCID: 0000-0003-4920-3100
Froese, Duane G. (Department of Earth and Atmospheric Sciences, University of Alberta) - ORCID: 0000-0003-1032-5944
Rahbek, Carsten (Center for Macroecology, Evolution and Climate, GLOBE Institute, University of Copenhagen) - ORCID: 0000-0003-4585-0300
Bravo Nogues, David (Center for Macroecology, Evolution and Climate, GLOBE Institute, University of Copenhagen) - ORCID: 0000-0002-4060-0153
Holden, Philip B. (School of Environment, Earth and Ecosystem Sciences, The Open University) - ORCID: 0000-0002-2369-0062
Edwards, Neil R. (School of Environment, Earth and Ecosystem Sciences, The Open University) - ORCID: 0000-0001-6045-8804
Durbin, Richard (Department of Genetics, University of Cambridge) - ORCID: 0000-0002-9130-1006
Meltzer, David J. (Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen)
Kjær, Kurt H. (Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen) - ORCID: 0000-0002-8871-5179
Möller, Per (Department of Geology, Quaternary Sciences, Lund University)
Willerslev, Eske (Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen) - ORCID: 0000-0002-7081-6748 |
Point of Contact
|
Use email button above to contact.
Alsos, Inger Greve (UiT The Arctic University of Norway) |
Description
| ALTERNATIVE DOWNLOAD FROM FILESENDER To access the data, click "Read Full Description" [+] and then click here
[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. (2021-06-18)
[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. (2021-08-12)
[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. (2020-04-01) |
Subject
| Earth and Environmental Sciences; Medicine, Health and Life Sciences |
Keyword
| plant DNA
chloroplast DNA
environmental DNA
nuclear ribosomal DNA
phylogenomic
polar
genome contigs |
Related Publication
| Wang, Y., Pedersen, M.W., Alsos, I.G. et al. Late Quaternary dynamics of Arctic biota from ancient environmental genomics. Nature 600, 86–92 (2021). doi: 10.1038/s41586-021-04016-x https://doi.org/10.1038/s41586-021-04016-x
Alsos, I. G., et al. (2020). "The treasure vault can be opened: Large-scale genome skimming works well using herbarium and silica gel dried material." Plants (Basel, Switzerland) 9(4): 432. doi: 10.3390/plants9040432 https://doi.org/10.3390/plants9040432 |
Language
| English |
Producer
| UiT The Arctic University of Norway (UiT) https://en.uit.no/
Laboratoire d’Ecologie Alpine (Univ. Grenoble Alpes, Univ. Savoie Mont Blanc) (LECA) https://leca.osug.fr/
Genoscope, Institut François Jacob (CEA, CNRS) https://www.genoscope.cns.fr/ |
Production Date
| 2019-08-01 |
Production Location
| Tromsø, Norway and Paris, France |
Contributor
| Project Leader : Alsos, Inger Greve
Work Package Leader : Coissac, Eric
Data Manager : Merkel, Marie K. F.
Project Member : Wang, Yucheng
Data Curator : Alberti, Adriana
Data Curator : Lammers, Youri
Data Curator : Denoeud, France
Project Member : Wincker, Patrick
Hosting Institution : UiT The Arctic University of Norway
Funder : The Research Council of Norway
Funder : Norwegian Biodiversity Information Centre |
Funding Information
| The Research Council of Norway: 226134/F50
Norwegian Biodiversity Information Centre: 14-14, 70184209 |
Distributor
| UiT The Arctic University of Norway (UiT The Arctic University of Norway) https://dataverse.no/dataverse/uit |
Depositor
| Alsos, Inger Greve |
Deposit Date
| 2021-05-28 |
Data Type
| Partial DNA sequence assemblies of vascular plant genomes |
Software
| bowtie, Version: 2.3.2
BBmap toolkit
AdapterRemoval, Version: 2.3.0 |
Related Dataset
| The raw data of PhyloNorway plant genome database is available at EMBL-ENA with project accession PRJEB43865. Standard barcodes (ITS2, matK and rbcL) are available at BOLDSYSTEMS.org under the name PhyloNorway. |
Other Reference
| Project webpage http://PhyloNorway.no, http://norbol.org |
Data Source
| Herbarium TROM at Tromsø Museum, Norway. |
Origin of Historical Sources
| DNA sequences of plants collected and deposited at herbarium TROM at Tromsø Museum, Norway. |