gmmDenoise_Paper

Overview

This repository includes several directories containing the R code used in the analyses presented in Koseki et al. (2025). Below is a brief overview of each directory:

• Example_1/ Contains scripts for analyzing stream fish community eDNA data from Nakagawa et al. (2018). The analysis serves as an illustrative example of how gmmDenoise can be used to derive accurate intraspecific diversity estimates and population genetic inferences.

• Example_2/ Contains scripts for another example analysis using gmmDenoise. This example uses estuarine fish community eDNA data from Ahn et al. (2020).

• Example_comp_fig/ Contains a script to create a set of histograms illustrating the effect of the stringency-controlling parameter of UNOISE3 on the read count distributions of amplicon sequence variants (ASVs) obtained in Example_1 and Example_2.

• PCR_Artifact_Sim/ Includes scripts for simulating eDNA metabarcoding processes, including PCR, to analyze the read count distributions of true sequences and artifacts derived from them.

• gmmDenoise_Test_1/ Contains scripts used to evaluate the performance of gmmDenoise with mock eDNA data of Plecoglossus altivelis from Tsuji, Miya et al. (2020).

• gmmDenoise_Test_2/ Contains scripts for another performance test of gmmDenoise using stream eDNA data of P. altivelis from Tsuji, Maruyama et al. (2020).

Each script in these directories includes a brief header and inline comments explaining its purpose and usage. The core gmmDenoise package is available at the following repository: https://github.com/YSKoseki/gmmDenoise.

References

• Ahn, H., Kume, M., Terashima, Y., Ye, F., Kameyama, S., Miya, M., Yamashita, Y., & Kasai, A. (2020). Evaluation of fish biodiversity in estuaries using environmental DNA metabarcoding. PLOS ONE, 15(10), e0231127.
• Koseki, Y., Takeshima, H., Yoneda, R., Katayanagi, K., Ito, G., & Yamanaka, H. (2025). gmmDenoise: a new method and R package for high-confidence sequence variant filtering in environmental DNA amplicon analysis. Molecular Ecology Resources. Advance online publication. https://doi.org/10.1111/1755-0998.70023.
• Nakagawa, H., Yamamoto, S., Sato, Y., Sado, T., Minamoto, T., & Miya, M. (2018). Comparing local‐ and regional‐scale estimations of the diversity of stream fish using eDNA metabarcoding and conventional observation methods. Freshwater Biology, 63(6), 569–580.
• Tsuji, S., Maruyama, A., Miya, M., Ushio, M., Sato, H., Minamoto, T., & Yamanaka, H. (2020). Environmental DNA analysis shows high potential as a tool for estimating intraspecific genetic diversity in a wild fish population. Molecular Ecology Resources, 20(5), 1248–1258.
• Tsuji, S., Miya, M., Ushio, M., Sato, H., Minamoto, T., & Yamanaka, H. (2020). Evaluating intraspecific genetic diversity using environmental DNA and denoising approach: A case study using tank water. Environmental DNA, 2(1), 42–52.

Funding

This work was supported by JSPS KAKENHI Grant Numbers JP21K12329, JP22K14908, and JP25K02038.