DOI: 10.5061/dryad.np5hqc03c
title: Reconstruction of marimo population dynamics over 200 years using molecular markers and fossil plankton remains

description: Recent efforts have focused on reconstructing the historical abundance of
 unfossilized organisms using environmental DNA preserved in sediments
 (sedDNA). This information is crucial for understanding long-term changes
 in ecosystems. However, because sedDNA is prone to degradation, its
 quantification may not always provide accurate estimates of past
 abundances. To address this issue, we developed a novel method to correct
 for sedDNA degradation by incorporating plankton remains and applied it to
 estimate the historical abundance of marimo—large spherical colonies of
 the green alga Aegagropila brownie (formerly A. linnaei)—in Lake Akan,
 Japan, which is the only known habitat for large marimo. We first
 quantified marimo sedDNA in lake sediments dating back over 200 years. We
 then used our new method to estimate historical changes in their abundance
 from sedDNA. Analyses revealed that marimo were historically 10-100 times
 more abundant than they are today, but that their abundance declined in
 the early 20th century when influxes of muddy water and water level
 fluctuations occurred due to deforestation and the operation of a
 hydroelectric power plant. These findings align with historical eyewitness
 accounts, indicating that, when corrected for degradation using fossilized
 remains, sedDNA can be a powerful tool for reconstructing the past
 abundance of unfossilized organisms.
description: # Reconstruction of marimo population dynamics over 200 years using
 molecular markers and fossil plankton remains ## **Description of the data
 and file structure** This folder contains the data for the article:
 Authors: Jotaro Urabe, Isamu Wakana, Hajime Ohtsuki, Masayuki K. Sakata,
 Yurie Ohtake, Ryotaro Ichige, Michinobu Kuwae, Toshifumi Minamoto Title:
 Reconstruction of marimo population dynamics over 200 years using
 molecular markers and fossil plankton remains. Published in *Environmental
 DNA* Comments and requests should be addressed to Jotaro
 Urabe: [urabe@tohoku.ac.jp](mailto:urabe@tohoku.ac.jp) or [jurabe07@gmail.com](mailto:jurabe07@gmail.com) When and where used, please cite this data set as Urabe, et al. (2025). Reconstruction of marimo population dynamics over 200 years using molecular markers and fossil plankton remains [Dataset]. Dryad. https://doi.org/10.5061/dryad.np5hqc03c ## File list ### **File name: Marimo\_data.csv** Dataset used to reconstruct the marimo population and its symbiont cyanobacterial population in Lake Akan. Sample Sample number Mid-depth Mid-depth of the sliced sample (cm) Year_Time Estimated year Elapsed_Year Estimated year elapsed MAR Mass accumulation rate (g/cm^2/yr) 18S_Copy_Number Marimo 18S rRNA copy number (number/cm^2) 23S_Copy_Number Cyanobacterial 23S rRNA copy number (number/cm^2) 18S_flux Marimo 18S rRNA copy number flux (number/cm^2/yr) 23S_flux Cyanobacterial 23S rRNA copy number flux (number/cm^2/yr) log_18S_ME log-transformed marimo 18S rRNA copy number flux estimated by the best model log_18S_M_H log-transformed upper 95% CI value of marimo 18S rRNA copy number flux estimated by the best model log_18S_M_L log-transformed lower 95% CI value of marimo 18S rRNA copy number flux estimated by the best model log_23S_ME log-transformed Cyanobacterial 23S rRNA copy number flux estimated by the best model log_23S_M_H log-transformed upper 95% CI value of Cyanobacterial 23S rRNA copy number flux estimated by the best model log_23S_M_L log-transformed lower 95% CI value of Cyanobacterial 23S rRNA copy number flux estimated by the best model ### **File name: Environment\_data.csv** Data set used for environmental analysis in Lake Akan Mid-depth Mid-depth of the sliced sample (cm) Year Estimated year Mass_accumulation_rate Mass accumulation rate (g/cm^2/yr) TP Total phosphorus concentration (micro g /cm^2) Chl+Phao Chlorophyll-a + pheophytin concentration (micro g /cm^2) TP_flux Fulx of total phosphorus concentration (micro g /cm^2/yr) Chl+pPhao_flux Flux of chlorophyll-a + pheophytin (micro g /cm^2/yr) ### **File name: Dating\_data.csv** Data used for chronological analysis and estimation of mass accumulation rate. U_Depth Upper surface depth of the sliced sample (cm) L_Depth Lower surface depth of the sliced sample (cm) Mid_Depth Mid-depth of the sliced sample (cm) Pb-210 Radioactivity (Bq/g) 1SD_Pb-210 Standard deviation of Pb-210 Pb-214 Radioactivity (Bq/g) 1SD_Pb-214 Standard deviation of Pb-214 Cs-137 Radioactivity (Bq/g) 1SD_Cs-137 Standard deviation of CS-137 Excess_Pb-210 Radioactivity (Bq/g) 1SD_Excess_Pb-210 Standard deviation of excess Pb-210 CRS-based_age Year at mid-mass depth 1SD_CRS-based_age Standard deviation of CSR-based_age Mass_accmulation_rate Mass accumulation rate (g/cm^2/yr) 1SD_Mass_accmulation_rate Standard deviation of Mass accumulation rate Tephra Presence of Tephra ### **File name: Environment\_data.csv** Data used for environmental analysis in Lake Akan Mid-depth Mid-depth of the sliced sample (cm) Year Estimated year Mass_accumulation_rate Mass accumulation rate (g/cm^2/yr) TP Total phosphorus concentration (micro g /cm^2) Chl+Phao Chlorophyll-a + pheophytin concentration (micro g /cm^2) TP_flux Fulx of total phosphorus concentration (micro g /cm^2/yr) Chl+pPhao_flux Flux of chlorophyll-a + pheophytin (micro g /cm^2/yr) ### **File name: Daphnia\_data.csv** Data set used to construct a best-fit model of factors correcting for sedDNA degradation rate. Sample Sample number Mid-depth Mid-depth of the sliced sample (cm) Year Estimated year Elapsed_Year Estimated year elapsed Abdominal_Claw flux Flux of Daphnia's abdominal claw number (number /cm^2/yr) 12S flux Daphnia 12S rRNA copy number flux (number/cm^2/yr)