INVESTIGATING THE FISH DIVERSITY IN ERHAI LAKE BASED ON ENVIRONMENTAL DNA METABARCODING
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摘要: 研究使用环境DNA宏条形码(eDNA metabarcoding)检测洱海鱼类多样性, 探索适用于洱海鱼类多样性监测和保护的新方法。通过水样采集、过滤、eDNA提取、遗传标记扩增、测序与生物信息分析的环境DNA宏条形码标准化分析流程, 从洱海16个采样点中获得可检测的9个采样点数据, 共检测出17种鱼类, 其中土著种5种、外来种12种; 鲫(Carassius auratus)、鳙(Hypophthalmichthys nobilis)、麦穗鱼(Pseudorasbora parva)、泥鳅(Misgurnus anguillicaudatus)和食蚊鱼(Gambusia affinis)为优势种。研究结果表明虽然环境DNA宏条形码无法完全替代传统的鱼类监测方法, 但作为一种新兴的生物多样性监测手段, 其可用于快速检测洱海鱼类多样性及其空间分布。Abstract: In recent years, environmental DNA metabarcoding (eDNA metabarcoding) has been widely utilized in fish diversity assessments due to its cost-effective and non-invasive strategies with increased sensitivity. To explore new methods for monitoring and protecting Erhai Lake’s fish diversity, this study first used eDNA metabarcoding to detect fish diversity of Erhai Lake. This study used a standardized process of eDNA metabarcoding analysis, including water collection, water filtration, eDNA extraction, genetic marker amplification, sequencing and bioinformatic analyses. A total of 17 fish species were detected from 9 sampling sites, including 5 native species and 12 non-native species. Five species (Carassius auratus, Hypophthalmichthys nobilis, Pseudorasbora parva, Misgurnus anguillicaudatus, and Gambusia affinis) were the dominant species. Although eDNA metabarcoding cannot completely replace traditional methods, it can be used as a supplementary tool to efficiently assess and monitor fish diversity and species distribution patterns in Erhai Lake.
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Keywords:
- eDNA metabarcoding /
- Non-invasive sampling /
- Species detection /
- Fish diversity
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图 3 湖中线和湖岸样品的鱼类相对序列丰度
Figure 3. Relative sequence abundances of fish detected in the samples from midline and shoreline
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图 4 基于物种存在情况(a)和序列丰度(b)统计的鱼类组成相似性
Figure 4. PCoA of the similarity in fish composition based on species occurrence (a) and read counts (b) across sampling sites
表 1 基于环境DNA宏条形码在洱海9个采样点检测到的鱼类物种
Table 1 List of fish species detected by eDNA metabarcoding at each of 9 sampling sites in Erhai Lake
目Order 科Family 种Species 采样点Sampling site M1 M2 M4 S7 S8 S9 S10 S11 S12 Totalb 鲤形目Cypriniformes 鲤科Cyprinidae 棒花鱼Abbottina rivularis √ √ √ 3 鲫Carassius auratus √ √ √ √ √ √ √ √ √ 9 草鱼Ctenopharyngodon idella √ √ √ √ √ √ √ √ √ 9 䱗Hemiculter leucisculus √ √ √ √ 4 鲢Hypophthalmichthys molitrix √ √ √ √ √ √ √ √ √ 9 鳙Hypophthalmichthys nobilis √ √ √ √ √ √ √ √ √ 9 青鱼Mylopharyngodon piceus √ √ √ √ √ √ √ 7 麦穗鱼Pseudorasbora parva √ √ √ √ √ √ √ √ √ 9 高体鳑鲏Rhodeus ocellatus √ 1 中华鳑鲏Rhodeus sinensis √ 1 光唇裂腹鱼Schizothorax lissolabiatus √ √ √ √ √ √ √ √ √ 9 大理裂腹鱼*Schizothorax taliensis √ √ √ √ √ √ √ √ √ 9 云南裂腹鱼Schizothorax yunnanensis √ √ √ √ √ √ √ √ √ 9 鳅科Cobitidae 泥鳅Misgurnus anguillicaudatus √ √ √ √ √ √ √ √ √ 9 鳉形目Cyprinodontiformes 胎鳉科Poeciliidae 食蚊鱼Gambusia affinis √ √ √ √ √ √ √ √ √ 9 鲈形目Perciformes 鰕虎鱼科Gobiidae 波氏吻鰕虎鱼Rhinogobius cliffordpopei √ √ √ 3 鲇形目Siluriformes 胡子鲇科 Clariidae 胡子鲇Clarias fuscus √ √ 2 总计Totala 11 13 12 13 12 12 13 13 12 注: a各采样点检出物种总数; b各物种被检测到的次数; *土著特有物种Note: a The total number of detected species at each sampling site; b the occurrence times of each species; * endemic species 
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表 2 洱海中9个采样点的物种序列数
Table 2 The number of reads detected for each species at each of 9 sampling sites in Erhai Lake
物种Species 各采样点物种序列数Read counts of each species at each site M1 M2 M4 S7 S8 S9 S10 S11 S12 棒花鱼Abbottina rivularis 0 132 0 12 0 0 0 0 13 鲫Carassius auratus 83019 64044 54860 73393 77478 33081 69019 94723 78890 草鱼Ctenopharyngodon idella 3087 5223 91 176 319 638 158 3501 64 䱗Hemiculter leucisculus 0 29 0 94 59 0 0 26 0 鲢Hypophthalmichthys molitrix 299 139 336 836 252 328 276 169 135 鳙Hypophthalmichthys nobilis 44433 48136 34080 39974 52195 17890 48014 56174 32261 青鱼Mylopharyngodon piceus 25 23 20 15 10 29 10 0 0 麦穗鱼Pseudorasbora parva 22938 20990 16093 34047 31005 10435 31787 26806 39718 高体鳑鲏Rhodeus ocellatus 0 0 0 0 0 0 11 0 0 中华鳑鲏Rhodeus sinensis 0 0 0 0 0 0 7212 0 0 光唇裂腹鱼Schizothorax lissolabiatus 1498 18 133 101 72 152 46 83 44 大理裂腹鱼Schizothorax taliensis 1389 348 3160 1137 296 1898 156 3572 1909 云南裂腹鱼Schizothorax yunnanensis 563 6292 1956 1549 2919 883 3605 2580 1888 泥鳅Misgurnus anguillicaudatus 62968 128069 93358 83273 118837 32269 114806 112284 136729 食蚊鱼Gambusia affinis 23933 25304 11263 19958 23052 5983 28785 21715 17344 波氏吻鰕虎鱼Rhinogobius cliffordpopei 0 0 0 0 0 1798 0 5285 5204 胡子鲇Clarias fuscus 0 0 12 0 0 0 0 81 0 总序列数Total reads 244150 298745 215362 254564 306490 105384 303885 326996 314197
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表 3 基于传统方法监测到的洱海鱼类资源状况
Table 3 Fish species composition detected by conventional monitoring methods in different years
年份Year 物种数量Species number 优势种Dominant species 总数Total 土著种 外来种 20世纪50年代 17[14, 17]/18[13] 17/18 0 大理裂腹鱼、云南裂腹鱼、大眼鲤、杞麓鲤、洱海四须鲃、鲫、泥鳅、中华青鳉、黄鳝 20世纪80年代 25[14]/32[18]/
34[13]11/17/
1814/15/
16杞麓鲤、鲫、青鱼、鲢、草鱼、棒花鱼、团头鲂、麦穗鱼、中华鳑鲏、兴凯鱊、波氏吻鰕虎鱼、太湖新银鱼 20世纪90年代 19[14]/32[13] 6/17 13/15 鲫、草鱼、鲢、鳙、团头鲂、麦穗鱼、中华鳑鲏、兴凯鱊、棒花鱼、波氏吻鰕虎鱼、子陵吻鰕虎鱼、太湖新银鱼 2009年 26[17]/23[12] 8/5 18/18 鲢、鳙、团头鲂、䱗、太湖新银鱼、波氏吻鰕虎鱼、子陵吻鰕虎鱼、麦穗鱼 2009—
2011年30[13] 14 16 鲢、鳙、团头鲂、太湖新银鱼 2014—
2015年24[18] 5 19 鲫、鲤、鲢、䱗、太湖新银鱼 2018年 33[15] 17 16 鲫、鲤、鲢、鳙、草鱼、青鱼、鰕虎鱼、麦穗鱼
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