The efficacy of DNA barcoding in the classification, genetic differentiation, and biodiversity assessment of benthic macroinvertebrates

Yihao Ge; Chengxing Xia; Jun Wang; Xiujie Zhang; Xufa Ma; Qiong Zhou

doi:10.1002/ece3.7470

The efficacy of DNA barcoding in the classification, genetic differentiation, and biodiversity assessment of benthic macroinvertebrates

Ecol Evol. 2021 Apr 4;11(10):5669-5681. doi: 10.1002/ece3.7470. eCollection 2021 May.

Authors

Yihao Ge^{1

2

3}, Chengxing Xia^{1

2}, Jun Wang^{1

3}, Xiujie Zhang^{1

2}, Xufa Ma^{1

2}, Qiong Zhou^{1

2}

Affiliations

¹ Key Laboratory of Freshwater Animal Breeding Ministry of Agriculture and Rural Affair/Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction Ministry of Education College of Fisheries Huazhong Agricultural University Wuhan China.
² Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt Ministry of Education Wuhan China.
³ The Key Laboratory of Aquatic Biodiversity and Conservation Institute of Hydrobiology Chinese Academy of Sciences Wuhan China.

Abstract

Macroinvertebrates have been recognized as key ecological indicators of aquatic environment and are the most commonly used approaches for water quality assessment. However, species identification of macroinvertebrates (especially of aquatic insects) proves to be very difficult due to the lack of taxonomic expertise in some regions and can become time-consuming. In this study, we evaluated the feasibility of DNA barcoding for the classification of benthic macroinvertebrates and investigated the genetic differentiation in seven orders (Insecta: Ephemeroptera, Plecoptera, Trichoptera, Diptera, Hemiptera, Coleoptera, and Odonata) from four large transboundary rivers of northwest China and further explored its potential application to biodiversity assessment. A total of 1,144 COI sequences, belonging to 176 species, 112 genera, and 53 families were obtained and analyzed. The barcoding gap analysis showed that COI gene fragment yielded significant intra- and interspecific divergences and obvious barcoding gaps. NJ phylogenetic trees showed that all species group into monophyletic species clusters whether from the same population or not, except two species (Polypedilum. laetum and Polypedilum. bullum). The distance-based (ABGD) and tree-based (PTP and MPTP) methods were utilized for grouping specimens into Operational Taxonomic Units (OTUs) and delimiting species. The ABGD, PTP, and MPTP analysis were divided into 177 (p = .0599), 197, and 195 OTUs, respectively. The BIN analysis generated 186 different BINs. Overall, our study showed that DNA barcoding offers an effective framework for macroinvertebrate species identification and sheds new light on the biodiversity assessment of local macroinvertebrates. Also, the construction of DNA barcode reference library of benthic macroinvertebrates in Eurasian transboundary rivers provides a solid backup for bioassessment studies of freshwater habitats using modern high-throughput technologies in the near future.

Keywords: DNA barcoding; benthic macroinvertebrates; biodiversity assessment; species identification.