Millennia of metacommunity diversification and homogenization captured by sedimentary ancient DNA
Data files
Sep 11, 2025 version files 1.93 MB
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README.md
22.82 KB
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Rijal_et_al_Diversity_analysis.zip
1.58 MB
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Supplementary_Table_S1.xlsx
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Abstract
Alpha (𝝰), beta (𝝱), gamma (𝛄), and zeta (𝛇) diversity metrics are complementary in their information, yet insight from this complementarity has yet to be explored. Here, we use postglacial lake sediments for reconstructing plant metacommunity diversity patterns using all four metrics. Based on sedimentary ancient DNA data, we find that the metacommunity both diversified (𝝱spatial) and homogenized (𝛇) over millennia of ecosystem development, alongside rising taxon richness at both community (𝝰) and metacommunity (𝛄) levels. In contrast, the temporal turnover of taxa (𝝱temporal) declined, both at the community and metacommunity level. With taxon appearances exceeding disappearances, this suggests the co-existence of taxa in the communities increased. However, the shared taxa in the metacommunity (ζ) showed a continuously high temporal turnover, suggesting the taxa contributing to the metacommunity homogenization were largely transient. That communities have homogenized but remained distinctively different over millennia highlights the importance of individual communities in sustaining metacommunity biodiversity.
Plant diversity change over millennia
Supplementary data: Supplementary_Table_S1.xlsx
Table S1: This table contains terrestrial plant data used for diversity calculation in this stud,y including associated metadata.
Columns:
Lakes: Name of the lakes
Lake code: Codes for the lakes
Latitude: Latitudinal position of a lake
Longitude: Longitudinal position of a lake
Sample code: 9 digit sample code composed of project abbreviation (EG for Ecogen)
followed by lake code (10 for Nordvivatnet) followed by type of sediment core
(L for large Nesje cores and M for multisampler) followed by 3 digits depth in cm
Median calibrated years before present: The median value of 14C dates after
calibration
Holocene periods: Formal division of the Holocene where samples aged older than
11700 years are categorized as the Late Glacial
Saliceae to Diplophyllum.taxifolium: Terrestrial plant taxa used in this study (0 and 1 indicate absence and presence of taxa respectively).
Rijal_et_al_Diversity_analysis.zip: This folder includes R project with all the necessary R codes for reproducing data analysis and figures 3 to 6 included in the manuscript.
Diversity_analysis_20250822.Rproj: This is the RStudio project file for opening the entire project in RStudio.
Rijal_et_al_2025_Alpha_Gamma_Beta_Zeta_analyses.R: This file includes all the R scripts used to generate figures included in the manuscript except Figures 01 and 02. Figures 3-6 are produced within the R project folder in .png format after running theses codes.
Supplementary_Table_S1.xlsx: Main input file for all the analyses as described above.
Lat_Long_UTM_dat_10_lakes.csv: This file contains UTM coordinates for 10 lakes included in this study. UTM coordinates were used while calculating Euclidean distance used in Figure 06.
Intermediate files: Following files were generated as the intermediate files to use in subsequent plots as generation of these data takes very long time.
Resampled_mean_gamma_20250428.csv: Gamma diversity value calculated using minimum three lakes per 500-years interval was used in Figure 03 as "Gamma adjusted" and all values in Supplementary figure S2.
Resampled_mean_beta_20250428.csv: Beta diversity value for metacommunity calculated using minimum two lakes per 500-years interval was used in Figure 04 as "Metacommunity" and all values in Supplementary figure S2.
Resampled_mean_zeta_20250426.csv: Mean zeta diversity values based on 100 sub-sampling were plotted in Supplementary figure S3.
Supplementary_Table_S2-S7.xlsx: Uploaded to Zenodo as supplementary information and contains README sheets which has the descriptions of the respective sheet
The data used in this study was initially published by Rijal et al. 2021 and further updated by Alsos et al. 2022. The terrestrial plant data used in this study are available as the supplementary material in Alsos et al. 2022.