Supporting data for: Late Quaternary dynamics of Arctic biota revealed by ancient environmental metagenomics

Version 1.2

Wang, Yucheng; Pedersen, Mikkel Winther; Alsos, Inger Greve; De Sanctis, Bianca; Racimo, Fernando; Prohaska, Ana; Coissac, Eric; Owens, Hannah Lois; Merkel, Marie Kristine Føreid; Fernandez-Guerra, Antonio; Rouillard, Alexandra; Lammers, Youri; Alberti, Adriana; Denoeud, France; Money, Daniel; Ruter, Anthony H.; McColl, Hugh; Larsen, Nicolaj Krog; Cherezova, Anna A.; Edwards, Mary E.; Fedorov, Grigory B.; Haile, James; Orlando, Ludovic; Vinner, Lasse; Korneliussen, Thorfinn Sand; Beilman, David W.; Bjørk, Anders A.; Cao, Jialu; Dockter, Christoph; Esdale, Julie; Gusarova, Galina; Kjeldsen, Kristian K.; Mangerud, Jan; Rasic, Jeffrey T.; Skadhauge, Birgitte; Svendsen, John-Inge; Tikhonov, Alexei; Wincker, Patrick; Xing, Yingchun; Zhang, Yubin; Froese, Duane G.; Rahbek, Carsten; Bravo Nogues, David; Holden, Philip B.; Edwards, Neil R.; Durbin, Richard; Meltzer, David J.; Kjær, Kurt H.; Möller, Per; Willerslev, Eske, 2022, "Supporting data for: Late Quaternary dynamics of Arctic biota revealed by ancient environmental metagenomics", https://doi.org/10.18710/3CVQAG, DataverseNO, V1

Learn about Data Citation Standards.

Contact Owner

Dataset Metrics

746 Downloads

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
License/Data Use Agreement	CC0 1.0

Filter by

	1 to 9 of 9 Files	Download
	00_README_Wang_et_al_PhyloNorwayContigs.txt Plain Text - 5.7 KB Published Mar 17, 2022 55 Downloads MD5: 978fea892a6f9cf2a8a5a358073094de Documentation	Preview "00_README_Wang_et_al_PhyloNorwayContigs.txt" Access File File Access Public Download Options Plain Text Download Metadata Data File Citation Download EndNote XML Download RIS Download BibTeX
	PhyloNorwayContigs_1.fasta Unknown - 21.7 GB Published Mar 17, 2022 161 Downloads MD5: e7bbb9e1d722fa31b13ed07bbccdbaa0 Data	Access File File Access Public Download Options Original File Format Download Metadata Data File Citation Download EndNote XML Download RIS Download BibTeX
	PhyloNorwayContigs_2.fasta Unknown - 21.7 GB Published Mar 17, 2022 83 Downloads MD5: 9b5f2e85c1b30800874f6a3c80037eb9 Data	Access File File Access Public Download Options Original File Format Download Metadata Data File Citation Download EndNote XML Download RIS Download BibTeX
	PhyloNorwayContigs_3.fasta Unknown - 21.7 GB Published Mar 17, 2022 75 Downloads MD5: d9047755929b428fd8ac8499ca27dc3c Data	Access File File Access Public Download Options Original File Format Download Metadata Data File Citation Download EndNote XML Download RIS Download BibTeX
	PhyloNorwayContigs_4.fasta Unknown - 21.7 GB Published Mar 17, 2022 68 Downloads MD5: 1e492dc87e1cde414a67280baeb7546e Data	Access File File Access Public Download Options Original File Format Download Metadata Data File Citation Download EndNote XML Download RIS Download BibTeX
	PhyloNorwayContigs_5.fasta Unknown - 21.7 GB Published Mar 17, 2022 53 Downloads MD5: 0c1edbe2c7f15a2d22f59e7aa8211743 Data	Access File File Access Public Download Options Original File Format Download Metadata Data File Citation Download EndNote XML Download RIS Download BibTeX
	PhyloNorwayContigs_6.fasta Unknown - 21.7 GB Published Mar 17, 2022 60 Downloads MD5: d9ffe8b205273d47da94e01a94a6ae64 Data	Access File File Access Public Download Options Original File Format Download Metadata Data File Citation Download EndNote XML Download RIS Download BibTeX
	PhyloNorwayContigs_7.fasta Unknown - 21.7 GB Published Mar 17, 2022 53 Downloads MD5: d46751ed533949b259a123b943e35704 Data	Access File File Access Public Download Options Original File Format Download Metadata Data File Citation Download EndNote XML Download RIS Download BibTeX
	PhyloNorwayContigs_acc2TaxaID.txt Plain Text - 15.2 GB Published Mar 17, 2022 138 Downloads MD5: 5d5c9ea6caa0247b0a77d1e6b0f3129a Data	Preview "PhyloNorwayContigs_acc2TaxaID.txt" Access File File Access Public Download Options Plain Text Download Metadata Data File Citation Download EndNote XML Download RIS Download BibTeX

Citation Metadata

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	Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen0000-0002-7838-226X Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen0000-0002-7291-8887 UiT The Arctic University of Norway0000-0002-8610-1085 Department of Zoology, University of Cambridge0000-0002-0648-4224 Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen0000-0002-5025-2607 Department of Zoology, University of Cambridge0000-0001-5459-6186 UiT The Arctic University of Norway0000-0001-7507-6729 Center for Macroecology, Evolution and Climate, GLOBE Institute, University of Copenhagen0000-0003-0071-1745 Merkel, Marie Kristine FøreidUiT The Arctic University of Norway Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen0000-0002-8679-490X Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen0000-0001-5778-6620 UiT The Arctic University of Norway0000-0003-0952-2668 Université Paris-Saclay0000-0003-3372-9423 Génomique Métabolique, Genoscope, Institut François Jacob0000-0001-8819-7634 Money, DanielDepartment of Zoology, University of Cambridge Ruter, Anthony H.Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen0000-0002-7568-4270 Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen0000-0002-0117-1106 Institute of Earth Sciences, St. Petersburg State University0000-0002-6199-8164 Edwards, Mary E.School of Geography and Environmental Science, University of Southampton Institute of Earth Sciences, St. Petersburg State University0000-0003-2269-4501 Haile, JamesLundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen Centre d'Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier0000-0003-3936-1850 Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen0000-0002-3081-3702 Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen0000-0001-7576-5380 Beilman, David W.Department of Geography and Environment, University of Hawaii Department of Geosciences and Natural Resource Management, University of Copenhagen0000-0002-4919-792X Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen0000-0001-5359-7072 Dockter, ChristophCarlsberg Research Laboratory Esdale, JulieCenter for the Environmental Management of Military Lands, Colorado State University Gusarova, GalinaUiT The Arctic University of Norway Department of Glaciology and Climate, Geological Survey of Denmark and Greenland0000-0002-8557-5131 Department of Earth Science, University of Bergen0000-0003-4793-7557 Rasic, Jeffrey T.U.S. National Park Service, Gates of the Arctic National Park and Preserve Skadhauge, BirgitteDepartment of Geography and Environment, University of Hawaii Svendsen, John-IngeDepartment of Earth Science, University of Bergen Zoological Institute, Russian academy of sciences0000-0002-7227-5797 Wincker, PatrickGénomique Métabolique, Genoscope, Institut François Jacob Xing, YingchunResource and Environmental Research Center, Chinese Academy of Fishery Sciences College of Plant Science, Jilin University0000-0003-4920-3100 Department of Earth and Atmospheric Sciences, University of Alberta0000-0003-1032-5944 Center for Macroecology, Evolution and Climate, GLOBE Institute, University of Copenhagen0000-0003-4585-0300 Center for Macroecology, Evolution and Climate, GLOBE Institute, University of Copenhagen0000-0002-4060-0153 School of Environment, Earth and Ecosystem Sciences, The Open University0000-0002-2369-0062 School of Environment, Earth and Ecosystem Sciences, The Open University0000-0001-6045-8804 Department of Genetics, University of Cambridge0000-0002-9130-1006 Meltzer, David J.Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen0000-0002-8871-5179 Möller, PerDepartment of Geology, Quaternary Sciences, Lund University Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen0000-0002-7081-6748
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.

Geospatial Metadata

Geographic Coverage	Norway Russian Federation Denmark Canada United States

Life Sciences Metadata

Other Organism	Vascular plants
Technology Type	nucleotide sequencing
Technology Platform	Illumina

Dataset Terms

License/Data Use Agreement

Our Community Norms as well as good scientific practices expect that proper credit is given via citation. Please use the data citation shown on the dataset page.

Creative Commons CC0 1.0 Universal Public Domain Dedication. CC0 1.0

	Dataset Version	Summary	Version Note	Contributors	Published on
No records found.

Edit File

This file has already been deleted (or replaced) in the current version. It may not be edited.

Restrict Access

Restricting limits access to published files. People who want to use the restricted files can request access by default. If you disable request access, you must add information about access to the Terms of Access field.

Learn about restricting files and dataset access in the User Guide.

Request Access

Enable access request

You must enable request access or add terms of access to restrict file access.

Terms of Access for Restricted Files

Save Changes

Edit Embargo

The selected file or files have already been published. Contact an administrator to change the embargo date or reason of the file or files.

Edit Retention Period

The selected file or files have already been published. Contact an administrator to change the retention period date or reason of the file or files.

Delete Files

The file will be deleted after you click on the Delete button.

Files will not be removed from previously published versions of the dataset.

Select File(s)

Please select one or more files.

Share Dataset

Share this dataset on your favorite social media networks.

Continue

Dataset Citations

Citations for this dataset are retrieved from Crossref via DataCite using Make Data Count standards. For more information about dataset metrics, please refer to the User Guide.

Sorry, no citations were found.

Inaccessible Files Selected

The selected file(s) may not be downloaded because you have not been granted access or the file(s) have a retention period that has expired or the files can only be transferred via Globus.

You may request access to any restricted file(s) by clicking the Request Access button.

Ineligible Files Selected

The selected file(s) may not be transferred because you have not been granted access or the file(s) have a retention period that has expired or the files are not Globus accessible.

You may request access to any restricted file(s) by clicking the Request Access button.

Download Options

The files selected are too large to download as a ZIP.

You can select individual files that are below the 4.7 GB download limit from the files table, or use the Data Access API for programmatic access to the files.

Select File(s)

Please select a file or files to be downloaded.

Inaccessible Files Selected

The selected file(s) may not be downloaded because you have not been granted access or the file(s) have a retention period that has expired.

Click Continue to download the files you have access to download.

Ineligible Files Selected

Some file(s) cannot be transferred. (They are restricted, embargoed, with an expired retention period, or not Globus accessible.)

Click Continue to transfer the elligible files.

Delete Dataset

Are you sure you want to delete this dataset and all of its files? You cannot undelete this dataset.

Delete Draft Version

Are you sure you want to delete this draft version? Files will be reverted to the most recently published version. You cannot undelete this draft.

Unpublished Dataset Preview URL

Preview URL can only be used with unpublished versions of datasets.

Unpublished Dataset Preview URL

Are you sure you want to disable the Preview URL? If you have shared the Preview URL with others they will no longer be able to use it to access your unpublished dataset.

Delete Files

The file(s) will be deleted after you click on the Delete button.

Files will not be removed from previously published versions of the dataset.

Compute

This dataset contains restricted files you may not compute on because you have not been granted access.

Deaccession Dataset

Are you sure you want to deaccession? This is permanent and the selected version(s) will no longer be viewable by the public.

Deaccession Dataset

Are you sure you want to deaccession this dataset? This is permanent an it will no longer be viewable by the public.

Version Differences Details

Please select two versions to view the differences.

Version Differences Details

Version:
Last Updated:

Select File(s)

Please select a file or files for access request.

Select File(s)

Embargoed files cannot be accessed. Please select an unembargoed file or files for your access request.

Edit Tags

Select existing file tags or create new tags to describe your files. Each file can have more than one tag.

Request Access

You need to Log In to request access.

Dataset Terms

Please confirm and/or complete the information needed below in order to request access to files in this dataset.

This dataset is made available under the following terms. Please confirm and/or complete the information needed below in order to continue.

License/Data Use Agreement

Our Community Norms as well as good scientific practices expect that proper credit is given via citation. Please use the data citation shown on the dataset page.

Creative Commons CC0 1.0 Universal Public Domain Dedication. CC0 1.0

Preview Guestbook

Upon downloading files the guestbook asks for the following information.

Guestbook Name

Collected Data

Account Information

Package File Download

Use the Download URL in a Wget command or a download manager to download this package file. Download via web browser is not recommended. User Guide - Downloading a Dataverse Package via URL

Download URL

https://dataverse.no/api/access/datafile/

Compute Batch

Clear Batch

Dataset	Persistent Identifier	Change Compute Batch

Compute Batch

Submit for Review

You will not be able to make changes to this dataset while it is in review.

Publish Dataset

Are you sure you want to republish this dataset?

Select if this is a minor or major version update.

Minor Release (1.3)

Major Release (2.0)

Publish Dataset

This dataset cannot be published until UiT The Arctic University of Norway is published by its administrator.

Publish Dataset

This dataset cannot be published until UiT The Arctic University of Norway and DataverseNO are published.

Return to Author

Return this dataset to contributor for modification.

Add/Edit a Version Note

Styled Citation