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


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.

[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.

[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, 2.3.2

AdapterRemoval, 2.3.0

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

Related Identifier
Related Identifier
Metadata Access
Creator Wang, Yucheng (ORCID: 0000-0002-7838-226X); Pedersen, Mikkel Winther ORCID logo; Alsos, Inger Greve ORCID logo; De Sanctis, Bianca ORCID logo; Racimo, Fernando ORCID logo; Prohaska, Ana ORCID logo; Coissac, Eric ORCID logo; Owens, Hannah Lois ORCID logo; Merkel, Marie Kristine Føreid; Fernandez-Guerra, Antonio (ORCID: 0000-0002-8679-490X); Rouillard, Alexandra ORCID logo; Lammers, Youri ORCID logo; Alberti, Adriana ORCID logo; Denoeud, France ORCID logo; Money, Daniel; Ruter, Anthony H.; McColl, Hugh ORCID logo; Larsen, Nicolaj Krog ORCID logo; Cherezova, Anna A. ORCID logo; Edwards, Mary E.; Fedorov, Grigory B. ORCID logo; Haile, James; Orlando, Ludovic ORCID logo; Vinner, Lasse ORCID logo; Korneliussen, Thorfinn Sand ORCID logo; Beilman, David W.; Bjørk, Anders A. (ORCID: 0000-0002-4919-792X); Cao, Jialu ORCID logo; Dockter, Christoph; Esdale, Julie; Gusarova, Galina; Kjeldsen, Kristian K. ORCID logo; Mangerud, Jan ORCID logo; Rasic, Jeffrey T.; Skadhauge, Birgitte; Svendsen, John-Inge; Tikhonov, Alexei ORCID logo; Wincker, Patrick; Xing, Yingchun; Zhang, Yubin ORCID logo; Froese, Duane G. ORCID logo; Rahbek, Carsten ORCID logo; Bravo Nogues, David ORCID logo; Holden, Philip B. ORCID logo; Edwards, Neil R. ORCID logo; Durbin, Richard ORCID logo; Meltzer, David J.; Kjær, Kurt H. ORCID logo; Möller, Per; Willerslev, Eske ORCID logo
Publisher DataverseNO
Contributor Alsos, Inger Greve; UiT The Arctic University of Norway; Laboratoire d’Ecologie Alpine; Genoscope, Institut François Jacob; Coissac, Eric; Merkel, Marie K. F.; Wang, Yucheng; Alberti, Adriana; Lammers, Youri; Denoeud, France; Wincker, Patrick
Publication Year 2022
Funding Reference The Research Council of Norway ; Norwegian Biodiversity Information Centre ; The Research Council of Norway 226134/F50 ; Norwegian Biodiversity Information Centre 14-14, 70184209
Rights CC0 1.0; info:eu-repo/semantics/openAccess;
OpenAccess true
Contact Alsos, Inger Greve (UiT The Arctic University of Norway)
Resource Type Partial DNA sequence assemblies of vascular plant genomes; Dataset
Format text/plain; application/octet-stream
Size 5804; 23323541655; 23323541963; 23323541803; 23323541668; 23323541696; 23323541820; 23323541933; 16319244953
Version 1.2
Discipline Earth and Environmental Science; Environmental Research; Geosciences; Life Sciences; Medicine; Natural Sciences
Spatial Coverage Tromsø, Norway and Paris, France