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Plant sedimentary ancient DNA data from Far East Russia

Citation

Huang, Sichao et al. (2022), Plant sedimentary ancient DNA data from Far East Russia , Dryad, Dataset, https://doi.org/10.5061/dryad.sbcc2fr4k

Abstract

Woody plants are expanding into the Arctic in response to the warming climate. The impact on arctic plants is not well understood due to the limited knowledge about plant assembly rules. Past plant diversity over long time series is rare. Here, we applied sedimentary ancient DNA metabarcoding targeting the P6 loop of the chloroplast trnL gene to a sediment record from Lake Ilirney (central Chukotka, Far Eastern Russia) covering the last 28 thousand years. Our results show that forb-rich steppe-tundra and dwarf-shrub tundra dominated during the cold climate before 14 ka, while deciduous erect-shrub tundra was abundant during the warm period since 14 ka. Larix invasion during the late Holocene substantially lagged behind the likely warmest period between 10 and 6 ka, where the vegetation coverage was densest. We reveal highest richness during 28–23 ka and a second richness peak during 13–10 ka, with both periods being accompanied by low shrub abundance. During the cold period before 14 ka, rich communities were phylogenetically clustered, suggesting low genetic divergence in the communities despite the great number of species. This probably originates from environmental filtering along with niche differentiation due to limited resources under harsh environmental conditions. In contrast, during the warmer period after 14 ka, rich communities were phylogenetically overdispersed. This results from a high number of species which were found to harbor high genetic divergence, likely originating from an erratic recruitment process in the course of warming. Some of our evidence may be of relevance for inferring future arctic plant assembly rules and diversity changes. By analogy to the past, we expect a lagged response of tree invasion. Plant richness may overshoot in the short term; in the long-term, however, the ongoing expansion of deciduous shrubs will eventually result in a phylogenetically more diverse community.

Usage Notes

The dataset is prepared for the manuscript "Plant sedimentary ancient DNA record from Far East Russia covering the last 28 ka reveal different assembly rules in cold and warm climates". It contains the processing of the raw sequencing data using bioinfomatics tools. Below is the detailed data organisation: 
 
1_raw_data: The raw sequencing files
R1 = Forward: 190531_NB501850_A_L1-4_ALRK-5_R1.fastq
R2 = Reverse: 190531_NB501850_A_L1-4_ALRK-5_R2.fastq
 
2_scripts: The metabarcoding pipeline for analyzing the raw sequencing data using OBITools
Data_analyses_using_OBITools.txt
 
3_tagfile: de-multiplex tagged pooled samples
tagfile_SEQRUN.txt
 
4_database: the Arctic and Boreal vascular plant and bryophyte database and reference library
database = arctborbryo_gh.fasta
library = ecochange.zip
 
5_dataset: output of the metabarcoding pipeline and final dataset. The final dataset is filtered as detailed in Supplementary_material Appendix 3.
assigned_SEQRUN_unique_clean_arctborbryo_anno.txt
final_dataset.xlsx

Funding

H2020 European Research Council, Award: 772852

Chinese Scholarship Council, Award: 201708080102

Deutsche Forschungsgemeinschaft, Award: EP 98/3-1