Study on fish species diversity in the East China Sea in summer based on environmental DNA technology
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摘要: 为了解东海海域主要鱼类群落的种类组成，监测和保护其多样性，本研究利用环境DNA技术对东海鱼类进行物种多样性分析。通过海水样本的采集，环境DNA提取、扩增和高通量测序分析，从东海14个站点的环境DNA样本中共检测出2纲，23目，29科，42属，44种海水鱼类，大部分种类在东海传统渔业资源调查中均有出现。其中，相对丰度较高的物种为赤鼻棱鳀（Thryssa kammalensis）、蓝点马鲛（Scomberomorus niphonius）、日本鲐（Scomber japonicus）、小黄鱼（Larimichthys polyactis）和鲻（Mugil cephalus）。站点间α多样性差异较大，总体上呈现近海站点生物多样性高，远海站点生物丰度高的特点。研究结果表明，环境DNA技术可以作为传统渔业资源调查的补充，也可以对东海海域鱼类物种多样性及空间分布进行快速检测。Abstract: To understand the species composition of the dominant fish species communities in the East China Sea and to monitor and protect their diversity, environmental DNA technology to analyze the species diversity of fish in the East China Sea was used in this study. Through the collection of seawater samples, eDNA extraction, amplification and high-throughput sequencing analysis, a total of 44 species of marine fishes in 2 classes, 23 orders, 29 families and 42 genera were detected, and most of the species were found in the traditional fishery resources survey in the East China Sea. Among them, the species with high relative abundance were red nose anchovy (Thryssa kammalensis), blue-spotted horse mackerel (Scomberomorus niphonius), Japanese mackerel (Scomber japonicus), small yellowtail (Larimichthys polyactis) and mullet (Mugil cephalus). The alpha diversity among stations was significant difference, and generally showed high biodiversity at coastal stations and high biological abundance at offshore stations. The results suggested that environmental DNA technology could quickly explore the diversity and spatial distribution of fish species in the East China Sea, as an effective supplementary to traditional fisheries resource monitoring.
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Key words:
- environmental DNA /
- East China Sea /
- biodiversity /
- fish
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图 2 东海鱼类OTU划分和分类地位鉴定结果
Fig. 2 Result of OTU division and classification taxon identification of fish in the East China Sea
图 3 各采样站点优势鱼类物种组成
Fig. 3 The composition of dominant fish species at each sampling station
图 4 东海不同采样站点（每条线代表一个站点）物种α多样性指数稀疏曲线
Fig. 4 Sparse curve of species alpha diversity index at different sampling stations (each line represents a different station) in the East China Sea
图 5 东海水域不同采样站点共有OTU的花瓣图
Fig. 5 Petal map of OTU shared by different sampling stations in the East China Sea
图 6 各优势鱼种在不同采样站点的相对丰度
Fig. 6 Relative abundance of dominant fish species at different sampling stations
图 7 环境DNA检出的东海鱼类物种组成热图
样本按照物种组成数据的欧式距离进行UPGMA聚类，并根据聚类结果排列；物种按照其组成数据的Pearson相关性系数矩阵进行UPGMA聚类，并根据聚类结果排列；不同色标代表不同物种在不同样本中的表达量，色标数值通过物种丰度数据取Z值获得，由绿到棕表示对应样本中该种丰度逐渐降低
Fig. 7 Heat map of fish species composition in the East China Sea detected by eDNA
Samples are clustered by UPGMA according to the euclidean distance of species composition data, and arranged according to the clustering results; UPGMA clustering is carried out according to Pearson correlation coefficient matrix of species composition data, and arranged according to the clustering results; different color codes represent the expression of different species in different samples, and the value of color codes is obtained by taking Z value of species abundance data, and from green to brown, the abundance in corresponding samples gradually decreases
表 1 各站点的序列量（eDNA）结果
Tab. 1 Sequence quantity (eDNA) results of each station
样本
编号输入 拼接 过滤 去除嵌合体 去除稀有个体 ES1 49 783 44 714 44 391 42 432 42 408 ES2 46 901 41 393 40 861 38 840 38 805 ES3 40 025 32 226 31 836 28 594 28 582 ES4 51 372 46 714 46 342 44 584 44 577 ES5 48 368 42 888 42 569 38 711 38 693 ES6 40 211 36 323 36 045 35 215 35 191 ES7 45 536 37 148 36 896 33 504 33 477 ES8 42 894 38 350 37 916 36 222 36 206 ES9 39 905 35 718 35 365 33 794 33 779 ES10 36 894 34 166 33 866 33 029 33 025 ES11 47 798 42 483 42 025 40 463 40 452 ES12 48 212 44 930 44 405 42 827 42 818 ES13 57 782 52 829 52 126 50 612 50 594 ES14 61 182 52 154 51 314 48 608 48 582 注：表中第二列为原始数据中能同时匹配到正向和反向引物的序列量；第三列为拼接后的序列量；第四列为去除低质量序列后的数据量；第五列为聚类后去除嵌合体后序列量，即为高质量序列量；第六列为去除singleton OTUs（在所有样本中绝对丰度为1的OTU）后的序列量。 
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表 2 东海环境DNA检出的鱼类物种
Tab. 2 Fish species detected by eDNA in the East China Sea
目 科 属 种 Anguilliformes Muraenesocidae Muraenesox 褐海鳗 Muraenesox bagio 海鳗 Muraenesox cinereus Aulopiformes Synodontidae Harpadon 龙头鱼 Harpadon nehereus Carangaria Polynemidae Polydactylus 黑斑多指马鲅 Polydactylus sextarius Carangiformes Carangidae Trachurus 日本竹筴鱼 Trachurus japonicus Centrarchiformes Terapontidae Rhynchopelates 尖突吻䱨 Rhynchopelates oxyrhynchus Clupeiformes Clupeidae Konosirus 斑鰶 Konosirus punctatus Sardinops 远东拟沙丁鱼 Sardinops melanostictus Engraulidae Encrasicholina 银灰半棱鳀 Encrasicholina punctifer Engraulis 日本鳀 Engraulis japonicus Setipinna 太的黄鲫 Setipinna taty Thryssa 赤鼻棱鳀Thryssa kammalensis 黄吻棱鳀 Thryssa vitrirostris Pristigasteridae Ilisha 鳓 Ilisha elongata Elopiformes Elopidae Elops 夏威夷海鲢 Elops hawaiensis Eupercaria Sciaenidae Chrysochir 尖头黄鳍牙鱛 Chrysochir aureus Larimichthys 小黄鱼 Larimichthys polyactis Pennahia 银姑鱼 Pennahia argentata Labriformes Labridae Scarus 青点鹦嘴鱼 Scarus ghobban Mugiliformes Mugilidae Mugil 鲻 Mugil cephalus Myctophiformes Myctophidae Benthosema 七星底灯鱼 Benthosema pterotum Diaphus 帕尔眶灯鱼 Diaphus parri Ophidiiformes Ophidiidae Hoplobrotula 棘鼬鳚 Hoplobrotula armata Pempheriformes Lateolabracidae Lateolabrax 中国花鲈 Lateolabrax maculatus Perciformes Pholidae Pholis 方氏锦鳚 Pholis fangi Triglidae Chelidonichthys 棘绿鳍鱼 Chelidonichthys spinosus Pleuronectiformes Cynoglossidae Cynoglossus 焦氏舌鳎 Cynoglossus joyneri Paraplagusia 日本须鳎 Paraplagusia japonica Pleuronectidae Pleuronichthys 木叶鲽 Pleuronichthys cornutus Priacanthiformes Priacanthidae Polydactylus 长尾大眼鲷 Priacanthus tayenus Scombriformes Centrolophidae Hyperoglyphe 日本栉鲳 Hyperoglyphe japonica Psenopsis 刺鲳 Psenopsis anomala Scombridae Auxis 双鳍舵鲣 Auxis rochei Scomber 日本鲐 Scomber japonicus Scomberomorus 蓝点马鲛 Scomberomorus niphonius Thunnus 长鳍金枪鱼 Thunnus alalunga Trichiuridae Trichiurus 日本带鱼 Trichiurus japonicus Spariformes Sparidae Acanthopagrus 黑棘鲷 Acanthopagrus schlegelii Stomiiformes Sternoptychidae Polyipnus 闪电烛光鱼 Polyipnus stereope Syngnathiformes Callionymidae Repomucenus 饰鳍斜棘鴨 Repomucenus ornatipinnis Tetraodontiformes Balistidae Canthidermis 疣鳞鲀 Canthidermis maculata Uranoscopiformes Uranoscopidae Uranoscopus 日本 Uranoscopus japonicus Xenocephalus 青 Xenocephalus elongatus Carcharhiniformes Carcharhinidae Carcharhinus 镰状真鲨 Carcharhinus falciformis
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表 3 东海鱼类物种相对丰度的α多样性指数
Tab. 3 Alpha diversity index of relative abundance of fish species in the East China Sea
样本编号 α多样性指数 Chao1
指数Observed
species指数Pielou
均匀度指数Shannon
多样性指数Simpson
多样性指数ES1 136.067 110.9 0.114 603 0.778 447 0.146 170 ES2 141.298 118.8 0.194 134 1.338 000 0.279 125 ES3 66.306 52.5 0.155 547 0.888 807 0.210 343 ES4 87.058 70.4 0.076 428 0.469 034 0.087 745 ES5 180.581 158.0 0.179 919 1.313 980 0.260 339 ES6 146.008 131.1 0.103 214 0.726 042 0.137 918 ES7 179.801 156.1 0.120 015 0.874 447 0.159 080 ES8 123.483 104.2 0.055 219 0.370 140 0.060 713 ES9 96.789 73.4 0.052 500 0.325 372 0.055 633 ES10 52.628 41.3 0.031 302 0.168 019 0.028 676 ES11 128.553 113.0 0.174 276 1.188 490 0.266 132 ES12 76.652 65.1 0.240 004 1.445 680 0.358 558 ES13 97.967 84.7 0.085 121 0.545 044 0.099 298 ES14 155.352 140.8 0.396 211 2.827 730 0.644 819
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