DOI: 10.57760/sciencedb.13553
title: Archived natural DNA samplers reveal multidecadal biodiversity change across the tree of life
title: Archived natural DNA samplers reveal multidecadal biodiversity change across the tree of life

description: Data include the following zip files:Raw Illumina sequencing data marine_Bladderwrack_16S.zip (5.76 GB)marine_Bladderwrack_18S.zip (4.66 GB)marine_Blue_Mussel_16S.zip (7.03 GB)marine_Blue_Mussel_18S.zip (3.04 GB)limnic_Zebramussel_16S.zip (5.71 GB)limnic_Zebramussel_18S.zip (5.82 GB)terrestrial_16S.zip (3.65 GB)terrestrial_COI.zip (11.35 BG)terrestrial_ITS.zip (8.73 GB)including forward (R1) and reverse (R2) reads of each ESB sample and replicate of the respective species and marker that have been sequenced. Reads were processed as described in the methods.OTU tables OTU_tables_marine.zip (3.79 MB)OTU_tables_limnic.zip (2.52 MB)OTU_tables_terrestrial.rar (5.25 MB)each including the OTU tables of all species and markers of the respective ecosystem, i.e. Bladderwrack (Fucus vesiculosus) 16S and 18S as well as Blue Mussel (Mytilus edulis) 16S and 18S for the marine samples, Zebramussel (Dreissena polymorpha) 16S and 18S (the latter being devided into a "Metazoan" dataset and an "Algae" dataset) for the limnic samples and Trees (Fagus sylvatica, Picea abies, Populus nigra) 16S, COI and ITS for the terrestrial samples. The OTU tables represent the "cleaned dataset" (see methods for details) after merging replicates and removing host DNA as well as any non-target DNA.R Codescript_biodiv_ESB.R (96.5 KB)README_script_ESB (3.43 KB)includes the R code for data filtering, data analysis and the non-neutral model for community ecology as well as the simulations. The READ ME file includes information on what the R code does.Supplementary DataSupplementary Data 1: List of all samples used in this study.Supplementary Data 2: Number of samples, OTU count, as well as number of phyla and orders of each taxonomic group per sampled species.Supplementary Data 3: List of all OTUs that match the reference sequence to 100 % over at least 85 % of the amplicon length.Supplementary Data 4: List of functionally annotated fungi found in and on tree leaves and respective trends in occurrence.Supplementary Data 5: Details of the laboratory workflow.The file Supplementary_Data.xlsx contains detailed information about the samples used in this study, zOTUs, functional annotations of fungi and the laboratory workflow.Additional informationSource_Data_Figure_1.txt (1.3 KB)Source_Data_Figure_2.txt (18.1KB)Source_Data_Figure_3.txt (6.6 KB)Source_Data_Figure_4.xlsx (585.8 KB)Source_Data_Figure_5.txt (1.6 KB)Source_Data_Extended_Data_Figure_2.txt (152.4 KB)Source_Data_Extended_Data_Figure_4.xlsx (290.1 KB)Source_Data_Extended_Data_Figure_5.xlsx (533.6 KB)Source_Data_Extended_Data_Figure_6.xlsx (21.6 KB)These files provide the source data for creating the respective plots.sample_sizes_for_depicted_boxplots_and_means.xlsx (26 KB)This file provides the sample sizes underlying box plots and means with error bars in Figures 3B & 4A-D as well as Extended Data Figures 3A-D & 4A+B.
description: Data include the following zip files:Raw Illumina sequencing data marine_Bladderwrack_16S.zip (5.76 GB)marine_Bladderwrack_18S.zip (4.66 GB)marine_Blue_Mussel_16S.zip (7.03 GB)marine_Blue_Mussel_18S.zip (3.04 GB)limnic_Zebramussel_16S.zip (5.71 GB)limnic_Zebramussel_18S.zip (5.82 GB)terrestrial_16S.zip (3.65 GB)terrestrial_COI.zip (11.35 BG)terrestrial_ITS.zip (8.73 GB)including forward (R1) and reverse (R2) reads of each ESB sample and replicate of the respective species and marker that have been sequenced. Reads were processed as described in the methods.OTU tables OTU_tables_marine.zip (3.79 MB)OTU_tables_limnic.zip (2.52 MB)OTU_tables_terrestrial.rar (5.25 MB)each including the OTU tables of all species and markers of the respective ecosystem, i.e. Bladderwrack (Fucus vesiculosus) 16S and 18S as well as Blue Mussel (Mytilus edulis) 16S and 18S for the marine samples, Zebramussel (Dreissena polymorpha) 16S and 18S (the latter being devided into a "Metazoan" dataset and an "Algae" dataset) for the limnic samples and Trees (Fagus sylvatica, Picea abies, Populus nigra) 16S, COI and ITS for the terrestrial samples. The OTU tables represent the "cleaned dataset" (see methods for details) after merging replicates and removing host DNA as well as any non-target DNA.R Codescript_biodiv_ESB.R (96.5 KB)README_script_ESB (3.43 KB)includes the R code for data filtering, data analysis and the non-neutral model for community ecology as well as the simulations. The READ ME file includes information on what the R code does.Supplementary DataSupplementary Data 1: List of all samples used in this study.Supplementary Data 2: Number of samples, OTU count, as well as number of phyla and orders of each taxonomic group per sampled species.Supplementary Data 3: List of all OTUs that match the reference sequence to 100 % over at least 85 % of the amplicon length.Supplementary Data 4: List of functionally annotated fungi found in and on tree leaves and respective trends in occurrence.Supplementary Data 5: Details of the laboratory workflow.The file Supplementary_Data.xlsx contains detailed information about the samples used in this study, zOTUs, functional annotations of fungi and the laboratory workflow.Additional informationSource_Data_Figure_1.txt (1.3 KB)Source_Data_Figure_2.txt (18.1KB)Source_Data_Figure_3.txt (6.6 KB)Source_Data_Figure_4.xlsx (585.8 KB)Source_Data_Figure_5.txt (1.6 KB)Source_Data_Extended_Data_Figure_2.txt (152.4 KB)Source_Data_Extended_Data_Figure_4.xlsx (290.1 KB)Source_Data_Extended_Data_Figure_5.xlsx (533.6 KB)Source_Data_Extended_Data_Figure_6.xlsx (21.6 KB)These files provide the source data for creating the respective plots.sample_sizes_for_depicted_boxplots_and_means.xlsx (26 KB)This file provides the sample sizes underlying box plots and means with error bars in Figures 3B & 4A-D as well as Extended Data Figures 3A-D & 4A+B.