Overwintering fish community in ice-covered environments in Hokkaido, Japan, inferred from environmental DNA

The overwintering ecology of fish in the seasonal ice zones (SIZs) remains largely unexplored owing to methodological limitations. Environmental DNA (eDNA) can reveal the distribution and diversity of fish species in various aquatic environments, thereby offering a possible solution to the methodological limitations of SIZ studies. Therefore, we aimed to detect the overwintering fish community in the ice-covered Saroma-ko Lagoon, located on the Okhotsk Sea coast of Hokkaido, and its inflow, using eDNA metabarcoding. eDNA extracted from under-ice seawater collected from the lagoon yielded 28 fish taxa, predominantly Clupea pallasii based on the relative DNA read abundance. Dissimilarity analysis suggested short-term temporal variations in eDNA composition in under-ice seawater, even at the same site. Nineteen fish taxa, predominantly Tribolodon brandtii and T. hakonensis, were detected in the eDNA extracted from under-ice river water. The high dissimilarity between eDNA results from unde..., Study site
The Saroma-ko Lagoon is an enclosed coastal lagoon with a surface area of 151.59 km2 and a maximum depth of 22 m. It is connected to the southern part of the Sea of Okhotsk by two inlets (Figure 1). The water mass of the eastern part of the lagoon consists primarily of Okhotsk Sea water, with freshwater input from the Saromabetsu River (Nomura et al., 2009). The sediments in the lagoon consist primarily of silt and sand (Nishihama & Hoshikawa, 1992). Almost the entire surface of the lagoon is covered with sea ice from early January to early April (Shirasawa et al., 2005). A weak but steady horizontal and vertical current (<0.02 m/s) likely driven by tidal fluctuations is observed beneath the sea ice (Nomura et al., 2024). The lagoon has moderate fish diversity (49 species) and is a composite of coastal marine fish (e.g., Clupea pallasii, Sebastes spp., Pleuronectidae spp.) and brackish water fish (e.g., Mugil cephalus) (Ministry of the Environment, Japan, 1993). Fish f..., , # Overwintering fish community in ice-covered environments in Hokkaido, Japan, inferred from environmental DNA

[https://doi.org/10.5061/dryad.rn8pk0pnn](https://doi.org/10.5061/dryad.rn8pk0pnn)

## Description of the data and file structure

This repository contains the data and R script required to reproduce the main results of the manuscript, as well as a prototype of the figures and tables. Raw sequence data files were deposited in the DNA Data Bank of Japan (DDBJ) Sequence Read Archive (DRA) as DRA014723 and DRA018892.

### Files and variables

#### File: Metadata.zip

This ZIP file includes the following metadata and supporting data for the analysis.

##### Sampling\_detail.csv

Detailed information of eDNA sampling.

* *Sample_ID*: ID for each eDNA sample.
* *Filter_ID*: ID for the filter to process the sample.
* *Description*: Description of the eDNA source.
* *Sampler*: The type of water sampler used to collect the seawater.
* *Station*: The name of the sampling station.
* *Lat...,

受限于方法学局限，季节性冰区（seasonal ice zones, SIZs）内鱼类的越冬生态学研究迄今仍未得到充分探索。环境DNA（environmental DNA, eDNA）能够揭示各类水生环境中鱼类物种的分布与多样性，因此有望解决季节性冰区鱼类研究面临的方法学瓶颈。为此，本研究借助环境DNA元条形码测序（eDNA metabarcoding）技术，对位于北海道鄂霍次克海沿岸的冰覆盖佐吕间湖（Saroma-ko Lagoon）及其入水口的越冬鱼类群落进行检测。从该潟湖冰下采集的海水中提取的环境DNA共检测出28个鱼类类群，基于DNA读长相对丰度来看，优势类群为太平洋鲱（Clupea pallasii）。相似性分析结果显示，即便在同一采样点位，冰下海水的环境DNA组成也存在短期时间动态变化。从冰下河水提取的环境DNA中则检测出19个鱼类类群，优势类群为布氏三块鱼（Tribolodon brandtii）和哈氏三块鱼（T. hakonensis）。二者之间的环境DNA检测结果存在极高的异质性[原文截断]，研究区域：
佐吕间湖是一处封闭型沿岸潟湖，表面积达151.59平方千米，最大水深22米。该潟湖通过两处水道与鄂霍次克海南部海域相连（图1）。潟湖东部的水团主要由鄂霍次克海水构成，同时有佐吕别川（Saromabetsu River）注入的淡水（Nomura等，2009）。该潟湖的沉积物以粉砂和砂为主（Nishihama & Hoshikawa，1992）。每年1月初至4月初，该潟湖几乎全部表面都会被海冰覆盖（Shirasawa等，2005）。海冰下方存在一股微弱但稳定的水平与垂直流（流速小于0.02 m/s），推测其由潮汐波动驱动（Nomura等，2024）。该潟湖的鱼类多样性中等（共记录49种），涵盖沿岸海洋鱼类（如太平洋鲱Clupea pallasii、平鲉属Sebastes spp.、鲽科Pleuronectidae spp.）以及咸淡水鱼类（如鲻Mugil cephalus）（日本环境省，1993）。该潟湖的鱼类组成[原文截断]，# 基于环境DNA解析日本北海道冰覆盖环境中的鱼类越冬群落
[https://doi.org/10.5061/dryad.rn8pk0pnn](https://doi.org/10.5061/dryad.rn8pk0pnn)
## 数据与文件结构说明
本数据集仓库包含复现论文核心结果所需的原始数据与R脚本，以及图表与表格的原型文件。原始测序数据文件已提交至日本DNA数据库（DNA Data Bank of Japan, DDBJ）序列读取归档库（Sequence Read Archive, DRA），存档编号为DRA014723与DRA018892。
### 文件与变量说明
#### 文件：Metadata.zip
该压缩包包含本分析所需的各类元数据与辅助数据。
##### Sampling_detail.csv
eDNA采样的详细信息。
* *Sample_ID*：每个eDNA样本的唯一标识编号。
* *Filter_ID*：处理样本所用滤膜的编号。
* *Description*：eDNA样本来源的详细说明。
* *Sampler*：采集海水所用的水样采集器类型。
* *Station*：采样站位的名称。
* *Lat...[原文截断]