Sakata et al. Fish SedDNA Extraction Protocol v1

Variations of this standardised protocol have been used by Masayuki K. Sakata and colleagues to successfully extract fish eDNA from modern and historic Japanese lake and river sediments. The method has been used to recover fish species composition data from modern surface sediments from a lake (Sakata et al., 2020) and a small, natural river (Sakata et al., 2021). It has also been applied to detect target fish species in lake sediments up to 100 years old (Sakata et al., 2022). This extraction method represents a consolidation of the methods applied in the following publications: Sakata, M. K., Yamamoto, S., Gotoh, R. O., Miya, M., Yamanaka, H., & Minamoto, T. (2020). Sedimentary eDNA provides different information on timescale and fish species composition compared with aqueous eDNA. Environmental DNA, 2(4), 505– 518. https://doi.org/10.1002/edn3.75 Sakata, M. K., Watanabe, T., Maki, N., Ikeda, K., Kosuge, T., Okada, H., … Minamoto, T. (2021). Determining an effective sampling method for eDNA metabarcoding: a case study for fish biodiversity monitoring in a small, natural river. Limnology, 22(2), 221–235. https://doi.org/10.1007/s10201-020-00645-9 Sakata, M.K., Tsugeki, N., Kuwae, M., Ochi, N., Hayami, K., Osawa, R., Morimoto, T., Yasashimoto, T., Takeshita, D., Doi, H., & Minamoto, T. (2022). Fish environmental DNA in lake sediment overcomes the gap of reconstructing past fauna in lake ecosystems. bioRxiv, https://doi.org/10.1101/2022.06.16.496507