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Title: Comparing local- and regional-scale estimations of the diversity of stream fish using eDNA metabarcoding and conventional observation methods
Authors: Nakagawa, Hikaru  kyouindb  KAKEN_id
Yamamoto, Satoshi
Sato, Yukuto
Sado, Tetsuya
Minamoto, Toshifumi
Miya, Masaki
Author's alias: 中川, 光
山本, 哲史
佐藤, 行人
佐土, 哲也
源, 利文
宮, 正樹
Keywords: assemblage pattern
environmental DNA
metabarcoding
MiFish primers
stream fish
Issue Date: Jun-2018
Publisher: Wiley-Blackwell
Journal title: Freshwater Biology
Volume: 63
Issue: 6
Start page: 569
End page: 580
Abstract: 1. We present a performance evaluation of environmental DNA (eDNA) metabarcoding with MiFish-U/E primers to investigate local and regional diversities of stream fish species to examine potential effectiveness, limits and future remedies of this technique in large-scale monitoring. We hypothesised that eDNA inferences are more consistent with fish assemblages observed upstream than downstream due to a directional flow of river water. 2. River water was sampled at 102 sites in 51 rivers around Lake Biwa in the central part of Honshu Island, Japan, within 10 person-days, and fish species compositions inferred from eDNA and existing observational data were compared. Observation sites were chosen from the observational data that were within a certain distance (buffer range) of a water-sampling site along a river trajectory. The hypothesis of the detection bias of eDNA towards upstream assemblage was tested by comparing results with all of the observational data, data from a higher elevation and data from a lower elevation. The Jaccard dissimilarity index was plotted between the observational data and the eDNA estimates against the buffer range; the buffer range with minimum dissimilarity was chosen. 3. When using existing observational data from within 6 km upstream of the eDNA sampling sites, the eDNA results were the most consistent with the observational data and inferred 86.4% of the species reported (38/44), as well as two additional species. eDNA results also showed patterns consistent with known upstream–downstream turnover of related species and biogeographical assemblage patterns of certain species. 4. Our 10-person-days survey using the metabarcoding technique enabled us to obtain as much regional fish diversity data including the hypothesised pattern of eDNA detection with an upstream bias as the accumulated observational data obtained through greater amounts of time, money and labour. The problems regarding false-positive/negative detection were suggested in our survey; however, these should be decreased or removed by modifying the sampling methods and experimental procedures in future works. Therefore, we concluded this new tool to enable monitoring that has never been implemented, such as cross-nation, and even whole-Earth monitoring with the data at yearly, seasonal or finer temporal scales.
Description: 琵琶湖周辺河川の魚が丸わかり --環境DNA分析で40種の魚の生息場所が明らかに--. 京都大学プレスリリース. 2018-02-28.
Following sentence in the abstract was corrected from "3. When using existing observational data from within 6 km upstream of the eDNA sampling sites, the eDNA results were the most consistent with the observational data and inferred 88.6% of the species reported (38/44), as well as two additional species." to "3. When using existing observational data from within 6 km upstream of the eDNA sampling sites, the eDNA results were the most consistent with the observational data and inferred 86.4% of the species reported (38/44), as well as two additional species.(L38–40)" in the published article.
Rights: This is the accepted version of the following article: [Hikaru Nakagawa, Satoshi Yamamoto, Yukuto Sato, Tetsuya Sado, Toshifumi Minamoto, Masaki Miya. Comparing local‐ and regional‐scale estimations of the diversity of stream fish using eDNA metabarcoding and conventional observation methods. Freshwater Biology (2018), 63, 6, 569-580.], which has been published in final form at https://doi.org/10.1111/fwb.13094. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving.
The full-text file will be made open to the public on 01 May 2019 in accordance with publisher's 'Terms and Conditions for Self-Archiving'.
This is not the published version. Please cite only the published version. この論文は出版社版でありません。引用の際には出版社版をご確認ご利用ください。
URI: http://hdl.handle.net/2433/230967
DOI(Published Version): 10.1111/fwb.13094
Related Link: http://www.kyoto-u.ac.jp/ja/research/research_results/2017/180228_1.html
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