Supporting data for: Late Quaternary dynamics of Arctic biota revealed by ancient environmental metagenomics (doi:10.18710/3CVQAG)

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

doi:10.18710/3CVQAG

DataverseNO

2022-03-17

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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

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

doi:10.18710/3CVQAG

Wang, Yucheng (Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen)

Pedersen, Mikkel Winther (Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen)

Alsos, Inger Greve (UiT The Arctic University of Norway)

De Sanctis, Bianca (Department of Zoology, University of Cambridge)

Racimo, Fernando (Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen)

Prohaska, Ana (Department of Zoology, University of Cambridge)

Coissac, Eric (UiT The Arctic University of Norway)

Owens, Hannah Lois (Center for Macroecology, Evolution and Climate, GLOBE Institute, University of Copenhagen)

Merkel, Marie Kristine Føreid (UiT The Arctic University of Norway)

Fernandez-Guerra, Antonio (Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen)

Rouillard, Alexandra (Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen)

Lammers, Youri (UiT The Arctic University of Norway)

Alberti, Adriana (Université Paris-Saclay)

Denoeud, France (Génomique Métabolique, Genoscope, Institut François Jacob)

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)

Larsen, Nicolaj Krog (Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen)

Cherezova, Anna A. (Institute of Earth Sciences, St. Petersburg State University)

Edwards, Mary E. (School of Geography and Environmental Science, University of Southampton)

Fedorov, Grigory B. (Institute of Earth Sciences, St. Petersburg State University)

Haile, James (Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen)

Orlando, Ludovic (Centre d'Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier)

Vinner, Lasse (Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen)

Korneliussen, Thorfinn Sand (Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen)

Beilman, David W. (Department of Geography and Environment, University of Hawaii)

Bjørk, Anders A. (Department of Geosciences and Natural Resource Management, University of Copenhagen)

Cao, Jialu (Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen)

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)

Mangerud, Jan (Department of Earth Science, University of Bergen)

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)

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)

Froese, Duane G. (Department of Earth and Atmospheric Sciences, University of Alberta)

Rahbek, Carsten (Center for Macroecology, Evolution and Climate, GLOBE Institute, University of Copenhagen)

Bravo Nogues, David (Center for Macroecology, Evolution and Climate, GLOBE Institute, University of Copenhagen)

Holden, Philip B. (School of Environment, Earth and Ecosystem Sciences, The Open University)

Edwards, Neil R. (School of Environment, Earth and Ecosystem Sciences, The Open University)

Durbin, Richard (Department of Genetics, University of Cambridge)

Meltzer, David J. (Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen)

Kjær, Kurt H. (Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen)

Möller, Per (Department of Geology, Quaternary Sciences, Lund University)

Willerslev, Eske (Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen)

Alsos, Inger Greve

Coissac, Eric

Merkel, Marie K. F.

Wang, Yucheng

Alberti, Adriana

Lammers, Youri

Denoeud, France

Wincker, Patrick

UiT The Arctic University of Norway

The Research Council of Norway

Norwegian Biodiversity Information Centre

UiT The Arctic University of Norway

Laboratoire d’Ecologie Alpine

Genoscope, Institut François Jacob

2019-08-01

bowtie

BBmap toolkit

AdapterRemoval

226134/F50

14-14, 70184209

DataverseNO

UiT The Arctic University of Norway

Alsos, Inger Greve

Alsos, Inger Greve

2021-05-28

https://doi.org/10.18710/3CVQAG

Earth and Environmental Sciences, Medicine, Health and Life Sciences, plant DNA, chloroplast DNA, environmental DNA, nuclear ribosomal DNA, phylogenomic, polar, genome contigs

<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.

Norway, Russian Federation, Denmark, Canada, United States

Partial DNA sequence assemblies of vascular plant genomes

Herbarium TROM at Tromsø Museum, Norway.

DNA sequences of plants collected and deposited at herbarium TROM at Tromsø Museum, Norway.

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.

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).

10.1038/s41586-021-04016-x

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).

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.

10.3390/plants9040432

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.

Project webpage http://PhyloNorway.no, http://norbol.org

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00_README_Wang_et_al_PhyloNorwayContigs.txt

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PhyloNorwayContigs_1.fasta

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PhyloNorwayContigs_2.fasta

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PhyloNorwayContigs_3.fasta

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PhyloNorwayContigs_6.fasta

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PhyloNorwayContigs_7.fasta

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PhyloNorwayContigs_acc2TaxaID.txt

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