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Aquatic Insects Biodiversity and eDNA Monitoring

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A special issue of Insects (ISSN 2075-4450).

Deadline for manuscript submissions: 31 July 2026 | Viewed by 17522

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Dr. Xiao-Long Lin

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Guest Editor

College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China
Interests: biosgeography; Chironomidae; ecology; systematics; eDNA; mitogenome; molecular phylogeny
Special Issues, Collections and Topics in MDPI journals

Dr. Mathew Seymour

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Guest Editor

School of Biological Sciences, Faculty of Science, The University of Hong Kong, Hong Kong 999077, China
Interests: aquatic insects; environmental DNA; molecular ecology; conservation biology; molecular tool development

Dr. Xin-Yu Ge

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Guest Editor

College of Life Sciences, Tianjin Normal University, Tianjin 300387, China
Interests: Trichoptera; taxonomy; mitogenome; phylogenomics; environmental DNA; diversity

Special Issue Information

Dear Colleagues,

Although numerous past studies have made significant progress in elucidating the diversity, phylogeny, evolution, and ecology of aquatic insects, there is still a vast amount of knowledge to be gained regarding uncertain taxonomic groups and their phylogenetic relationships. Aquatic insects stand as indispensable sentinels, monitoring changes in freshwater ecosystems and offering vital insights into environmental alterations. However, the success of biological monitoring in these delicate ecosystems critically depends on taxonomic expertise. To address these challenges, DNA-based methods emerge as powerful tools for accurately identifying aquatic insects. Specifically, eDNA metabarcoding, coupled with sensitive, cost-effective, and rapidly advancing DNA sequencing technologies, holds immense importance in biodiversity monitoring and environmental policy formulation.

This Special Issue aims to gather high-quality, original research that further illuminates our understanding of aquatic insect biodiversity, evolution, and ecology. We eagerly await submissions in the fields of both traditional and molecular taxonomy, eDNA metabarcoding, phylogeny, ecology, and biogeography. We encourage contributions that explore novel applications of these methodologies, especially those that advance our knowledge of aquatic insect taxonomy and ecology and their role in freshwater ecosystems. By compiling a collection of cutting-edge research, we hope to pave the way for a deeper understanding and appreciation of these vital organisms.

Dr. Xiao-Long Lin
Dr. Mathew Seymour
Dr. Xin-Yu Ge
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 250 words) can be sent to the Editorial Office for assessment.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Insects is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

aquatic insects
biodiversity
systematics
DNA barcode
eDNA metabarcoding
ecology
evolution

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Published Papers (11 papers)

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Research

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14 pages, 14777 KB

Open AccessArticle

Decoding Biodiversity in Baiyangdian Lake: A DNA Barcode Reference Library for Aquatic Insects

by Ya-Jun Qiao, Ze-Peng Wang, Meng-Yu Lv, Pei-Dong Su, Tong Wu, Hai-Feng Xu, Yu-Fan Li, Xiao-Long Lin and Chun-Hui Zhang

Insects 2026, 17(1), 60; https://doi.org/10.3390/insects17010060 - 1 Jan 2026

Viewed by 986

Abstract

Freshwater ecosystems are among the most vulnerable habitats worldwide, and reliable biodiversity assessment is essential for their conservation. Baiyangdian Lake, the largest freshwater lake in northern China, has undergone severe ecological degradation but is now experiencing recovery through restoration efforts. To provide a molecular basis for monitoring biodiversity, we constructed a COI DNA barcode reference library of aquatic insects from Baiyangdian Lake. From January 2023 to May 2025, systematic sampling across representative habitats yielded 315 high-quality sequences covering 104 species, 74 genera, and 33 families within eight insect orders. Diptera, particularly Chironomidae, showed the highest diversity, followed by Odonata. Phylogenetic analysis using maximum likelihood resolved all orders and families as well-supported monophyletic groups, demonstrating strong congruence with morphological taxonomy. Genetic distance analysis revealed a pronounced barcode gap, with mean intraspecific divergence of 0.46% and nearest-neighbor divergence exceeding 15%, confirming the discriminatory power of COI for species identification. Accumulation curves indicated that genus-level diversity is largely captured, while species-level diversity, especially among Diptera, remains incompletely revealed. This study provides the first comprehensive DNA barcode reference library for Baiyangdian aquatic insects, supporting ecological restoration evaluation, eDNA applications, and regional biodiversity conservation strategies. Full article

(This article belongs to the Special Issue Aquatic Insects Biodiversity and eDNA Monitoring)

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76 pages, 34149 KB

Open AccessArticle

Two New Species and First Stage Associations for Two Other Species of the Cincticostella nigra (Uéno, 1928) Complex (Ephemeroptera, Ephemerellidae) from Yunnan, China, with Discussion About Cincticostella Allen, 1971 Species Complexes Based on Winged Stages

by Yi-Fei Feng, Yan-Chang Zi, Cheng-Fa Zhao, Yuan Mu, Xian-Fu Li and Luke M. Jacobus

Insects 2025, 16(12), 1221; https://doi.org/10.3390/insects16121221 - 29 Nov 2025

Viewed by 1211

Abstract

Four species of the Cincticostella nigra (Uéno, 1928) complex (Ephemeroptera, Ephemerellidae) from Yunnan, China are described based on egg chorionic structure and nymph and winged stages, including C. wangi Selvakumar Martynov & Subramanian, 2021, C. funki Martynov, Selvakumar, Palatov & Vasanth, 2021, and two new species, viz., Cincticostella xiazhi Zi, Li & Jacobus, sp. nov. and Cincticostella yushui Zi, Li & Jacobus, sp. nov. The egg and winged stages of C. wangi and C. funki are described for the first time. Eggs of all four species have macroreliefs generally similar to one another and to other species in the genus. Male imagoes have preliminary species-level differences in the median convex lobes of the styliger plate and the shapes of the penis lobes themselves. The current delimitation of four complexes of Cincticostella is briefly discussed based on the nymph and winged stages. A partial phylogenetic reconstruction of Cincticostella based on the COI gene illustrates relations of representatives of the four complexes on the one hand and distinct delimitation of C. wangi, C. funki, C. xiazhi, sp. nov., and C. yushui, sp. nov. on the other. An updated list of species of Cincticostella is provided, along with a new key for the identification of nymphs of the C. nigra complex, which are distinguished primarily based on features of the abdominal terga, mesothoracic projections, tarsal claws, labrum emargination, setation of femora, and body color. Full article

(This article belongs to the Special Issue Aquatic Insects Biodiversity and eDNA Monitoring)

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21 pages, 115665 KB

Open AccessArticle

Report on Leg Sensilla of Notonectidae (Hemiptera, Heteroptera)

by Meng-Yao Fan and Tong-Yin Xie

Insects 2025, 16(10), 1048; https://doi.org/10.3390/insects16101048 - 14 Oct 2025

Viewed by 1026

Abstract

Notonectidae belongs to the infraorder Nepomorpha within the order Hemiptera. The aim of this study was to analyze the morphological types and arrangement of leg sensilla in Anisops, Enithares and Notonecta. A variety of sensilla are distributed on the legs. These sensilla are responsible for receiving signals from the external environment. Mechanoreceptors exhibit the highest diversity. Using a scanning electron microscope, ten types of sensilla were identified on the legs of seventeen species from Notonectidae. Basic types of mechanoreceptors, including sensilla trichodea (ST1, ST2), sensilla chaetica (SCh1, SCh2), sensilla basiconica (SB2) and sensilla campaniformia (SCa), were distributed across all the studied species. In Anisops, sensilla arch-shaped (SAr) and sensilla spoon-shaped (SSp) were reported for the first time. Additionally, six subtypes of ST were distinguished in Anisops, among which ST3, ST4, ST5 and ST6 are unique. In Enithares and Notonecta, sensilla styloconica (SS) were observed; these sensilla are hypothesized to function as both mechanoreceptors and gustatory receptors. Beyond mechanoreceptors, we also identified thermo-hygroreceptors—sensilla ampullacea (SA) and sensilla coeloconica (SCo)—as well as a potential olfactory sensilla type, namely, sensilla placodea multilobated (SPM). These findings suggest that Notonectidae leg sensilla play an important role in the perception of aquatic environments and prey localization. Full article

(This article belongs to the Special Issue Aquatic Insects Biodiversity and eDNA Monitoring)

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27 pages, 12102 KB

Open AccessArticle

Genome Annotation of Molting-Related Protein-Coding Genes in Propsilocerus akamusi Reveals Transcriptomic Responses to Heavy Metal Contamination

by Wenbin Liu, Anmo Zhou, Ziming Shao, Jiaxin Nie, Chuncai Yan, Shaobo Gao and Yiwen Wang

Insects 2025, 16(6), 636; https://doi.org/10.3390/insects16060636 - 17 Jun 2025

Cited by 1 | Viewed by 1515

Abstract

The exoskeleton of insects, known as the cuticle, necessitates regular renewal during molting and metamorphosis, with chitin being its primary structural component. Consequently, the molting and metamorphosis processes in insects are characterized by periodic degradation and synthesis of chitin, which are tightly regulated by juvenile hormone (JH) and 20-hydroxyecdysone (20E). Propsilocerus akamusi, a species that plays a crucial role in freshwater ecosystems, demonstrates remarkable resilience to environmental pollutants, including metallic elements found in industrial waste. In this investigation, we systematically analyzed and summarized the metabolic pathways associated with JH, 20E, chitin, and heavy metal transport in P. akamusi. Based on previous genome assembly, we conducted a systematic annotation and functional analysis of genes involved in these metabolic pathways in P. akamusi. This was achieved by querying conserved domains using Pfam and SMART, as well as identifying gene-specific classical consensus regions through amino acid sequence alignment using DNAMAN. Through our validation, a total of 109 genes were definitively categorized into four distinct metabolic pathways: 27 genes were involved in the JH metabolic pathway, 24 in the 20E metabolic pathway, 27 in the chitin metabolic pathway, and 31 in metal transport pathways. A total of 30 genes failed our validation and were temporarily excluded. Furthermore, through RNA sequencing (RNA-seq)-based transcriptome analysis, we observed that under copper (Cu) stress, the expression levels of the majority of genes participating in these metabolic pathways in P. akamusi were altered. This finding suggests that copper exposure influences the molting process in P. akamusi. Full article

(This article belongs to the Special Issue Aquatic Insects Biodiversity and eDNA Monitoring)

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61 pages, 29845 KB

Open AccessArticle

Ameletus Mayflies (Ephemeroptera: Ameletidae) of the Eastern Nearctic

by David H. Funk

Insects 2025, 16(5), 530; https://doi.org/10.3390/insects16050530 - 16 May 2025

Viewed by 2737

Abstract

Fourteen Ameletus species are recognized in the eastern Nearctic (south of the Artic zone), including six described as new. Keys to adult males and full-grown larvae are provided. Taxonomic decisions were based on morphologic and genetic evidence. Their justification is discussed in depth and four species groups are proposed. The vast majority of Ameletus encountered in the eastern Nearctic are members of one of three triploid, clonal parthenogenetic species, at least two of which are of hybrid origin. Bisexual progenitors of the parthenogens were inferred using a combination of mitochondrial and nuclear genetic markers. The parthenogens likely arose during the Late Pleistocene when glacial advances brought previously allopatric species/populations into contact, and as glaciers retreated the parthenogens rapidly expanded their range while the sexual lineages remained in presumed glacial refugia. Although parthenogenesis is relatively common in Ephemeroptera, these Ameletus represent the first known cases of polyploidy and hybrid origin. Full article

(This article belongs to the Special Issue Aquatic Insects Biodiversity and eDNA Monitoring)

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26 pages, 42762 KB

Open AccessArticle

Diversity and the Origin of Perlodinella Klapálek 1912 (Plecoptera: Perlodidae) in Qinghai Province, China

by Qing-Bo Huo, Shi-Xiong Fan, Ya-Fei Zhu and Yu-Zhou Du

Insects 2025, 16(5), 520; https://doi.org/10.3390/insects16050520 - 14 May 2025

Cited by 1 | Viewed by 1588

Abstract

The article presents integrative research of the perlodid genus Perlodinella in Qinghai Province, northwestern China. P. tatunga Wu, 1973 is considered a junior synonym of P. kozlovi Klapálek, 1912, with a further description of intraspecific morphological variability, while P. unimacula Klapálek, 1912 is considered to be nomen dubium. The COI barcodes of the three valid species in Qinghai, P. epiproctalis (Zwick, 1997), P. kozlovi Klapálek, 1912, and P. microlobata Wu, 1938 are firstly sequenced, enabling adult–larva matching and the analysis of genetic diversity. The larval morphology of P. kozlovi and P. microlobata is described for the first time. Additionally, the biology, ecological adaptability, and fungal infections of Perlodinella are firstly recorded with an environment-related comparison. The discussion of the origin and immigration of the genus is also provided. Full article

(This article belongs to the Special Issue Aquatic Insects Biodiversity and eDNA Monitoring)

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10 pages, 2859 KB

Open AccessArticle

Conservation and Variability in Mitochondrial Genomes of Perlodidae: Insights from Comparative Mitogenomics

by Xiao Yang, Qing-Bo Huo, Abdur Rehman, Ya-Fei Zhu and Yu-Zhou Du

Insects 2025, 16(3), 245; https://doi.org/10.3390/insects16030245 - 26 Feb 2025

Cited by 1 | Viewed by 1104

Abstract

The mitochondrial genomes of three stoneflies, e.g., Tibetisoperla wangluyui Huo and Du, 2021, Perlodinella kozlovi Klapálek, 1912 and Perlodinella epiproctalis (Zwick, 1997), were sequenced in this study, with lengths 16,043 bp, 16,024 bp, and 16,071 bp, respectively. Each mitogenome contained 37 genes including 22 tRNAs, two ribosomal RNAs, 13 protein-coding genes (PCGs), and a noncoding control region (CR). In general, standard ATN start and TAN termination codons were evident in the PCGs. Meanwhile, in this paper, three newly published mitochondrial genomes and 11 existing mitochondrial genomes of the Perlodidae from NCBI were analyzed. Among the 13 PCGs in the mitochondrial genome of Perlodidae, the lengths of atp6, atp8, cox2, cox3, cytb, nad1, nad2, nad3, and nad4 are exactly the same, and the length of cox1 is 1536–1569 bp. The length of nad4L is 297, but the length of Arcynopteryx dichroa is 300. The length of nad5 ranges from 1732 bp to 1752 bp, while that of nad6 ranges from 525 bp to 534 bp. The length of rrnL is between 1292 and 391 bp, and the length of rrnS is between 793 and 869 bp. In addition, we found that atp8 in Isoperlinae started with GTG as a start codon but in Perlodinae, it started with ATG. Despite these advances, mitochondrial genome data from the Perlodidae are still needed. Full article

(This article belongs to the Special Issue Aquatic Insects Biodiversity and eDNA Monitoring)

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18 pages, 4018 KB

Open AccessArticle

Gone with Water or Mountain: The Population Genetic Diversity of Rhopalopsole sinensis Yang and Yang, 1993 in China

by Qing-Bo Huo, Yu-Ben Yang, Anna Eichert and Yu-Zhou Du

Insects 2025, 16(3), 244; https://doi.org/10.3390/insects16030244 - 26 Feb 2025

Cited by 3 | Viewed by 1091

Abstract

Rhopalopsole sinensis Yang and Yang, 1993 is one of the most widely distributed stoneflies in southern China. In this study, the genetic structure of nine different geographical populations of R. sinensis was studied based on three datasets of the 18S, COI and ITS2 genes. The phylogenetic trees showed that there had been a great degree of genetic differentiation among its nine geographical populations, but the hypothesis of random mating did not support the formation of reproductive isolation among different geographical populations, indicating that R. sinensis did not form cryptic species. The establishment of the 18S gene and ITS2 gene supports the population of (Guangdong + Shaanxi + Sichuan + Guizhou + Fujian) as independent branches, while the population of (Anhui + Zhejiang + Hunan) is another branch. The establishment of COI gene tree supports (Shaanxi + Sichuan + Guizhou + Fujian) as one branch, while the other independent branch is composed of (Anhui + Zhejiang + Guangxi + Hunan + Guangdong) groups. The possible reasons for this situation based on geography and biology are discussed. Our results provide the first reference for the genetic differentiation in Chinese Rhopalopsole stoneflies. Full article

(This article belongs to the Special Issue Aquatic Insects Biodiversity and eDNA Monitoring)

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14 pages, 4128 KB

Open AccessArticle

New Mitogenomes from the Genus Ablabesmyia (Diptera: Chironomidae, Tanypodiinae): Characterization and Phylogenetic Implications

by Wen-Bin Liu, Wen-Xuan Pei, Ya-Ning Tang, Jia-Xin Nie, Wei Cao, Cheng-Yan Wang and Chun-Cai Yan

Insects 2025, 16(2), 178; https://doi.org/10.3390/insects16020178 - 7 Feb 2025

Viewed by 1572

Abstract

(1) Background: The insect mitogenome encodes essential genetic components and serves as an effective marker for molecular identification and phylogenetic analysis in insects due to its small size, maternal inheritance, and rapid evolution. The morphological identification of Ablabesmyia is challenging, particularly for non-experts. Thus, there is an increasing need for molecular data to improve classification accuracy and phylogenetic analysis. (2) Methods: Our analysis encompassed eight species of Ablabesmyia, a single species of Conchapelopia, one species of Denopelopia, and one species of Thienemannimyia, all originating from China. We then performed a comprehensive analysis of the nucleotide composition, sequence length, and evolutionary rate. (3) Results: All newly assembled mitogenomes displayed a negative GC-skew, indicating a cytosine bias, while most exhibited a positive AT-skew, reflecting an adenine and thymine abundance. All thirteen protein-coding genes (PCGs) featured the conventional start codon ATN, aligning closely with the typical mitochondrial start codon observed in insects. The evolutionary rates of these PCGs can be ordered as follows: ND2 > ATP8 > ND6 > ND4 > ND5 > ND3 > ND4L > ND1 > CYTB > COIII > ATP6 > COII > COI. (4) Conclusions: These newly sequenced mitogenomes exhibit structural features and nucleotide compositions that closely align with those of previously reported Chironomidae species, marking a significant expansion of the chironomid mitogenome database. Full article

(This article belongs to the Special Issue Aquatic Insects Biodiversity and eDNA Monitoring)

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13 pages, 5330 KB

Open AccessArticle

Mitogenomics Provide New Phylogenetic Insights of the Family Apataniidae (Trichoptera: Integripalpia)

by Xinyu Ge, Jingyuan Wang, Haoming Zang, Lu Chai, Wenbin Liu, Jiwei Zhang, Chuncai Yan and Beixin Wang

Insects 2024, 15(12), 973; https://doi.org/10.3390/insects15120973 - 6 Dec 2024

Cited by 6 | Viewed by 2133

Abstract

The family Apataniidae consists of two subfamilies, Apataniinae and Moropsychinae. Currently, there are 204 valid species of Apataniidae, which are widely distributed throughout the northern hemisphere. The larvae typically inhabit cold-water environments, and they serve as biological indicators for monitoring the health of freshwater ecosystems. The phylogenetic relationships within Apataniidae are not fully understood. Moreover, the available molecular data of Apataniidae are still limited. Herein, we provided the mitochondrial genomes of eight apataniid species and compared them with the published mitochondrial genomes of Apataniidae. The nine newly obtained sequences ranged from 15,070 bp to 16,737 bp in length. The results of the nonsynonymous with synonymous substitution rates displayed that ATP8 had the highest evolutionary rate, while COXI exhibited the lowest. The ND4L may be an effective molecular marker for the classification of the Apataniidae. Based on the published mitogenomes, we constructed a phylogenetic tree for Limnephiloidea and conducted a preliminary analysis of its advanced phylogeny. The ML and BI analyses recover the monophyly of Apataniidae and Limnephilidae. Except for PCG, BI tree based on other matrices consistently showed the topology: (Apataniana + (Moropsyche + (Apatidelia + Apatania))). The taxonomic status of Apatania and Apatidelia were also preliminarily explored. The mitochondrial genome of Apataniidae provides critical genomic resources for understanding the phylogenetic relationships of Apataniidae. Full article

(This article belongs to the Special Issue Aquatic Insects Biodiversity and eDNA Monitoring)

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Review

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31 pages, 2139 KB

Open AccessReview

Aquatic Diptera in Phytotelmata of Bromeliaceae and Zingerberales

by Barbara L. Hayford, Marcella M. Jurotich, Heera Malik and Caroline S. Chaboo

Insects 2026, 17(3), 280; https://doi.org/10.3390/insects17030280 - 4 Mar 2026

Viewed by 860

Abstract

Phytotelmata are small, plant-held water pools that support unique assemblages of fauna and flora. Aquatic Diptera are a significant component of these microecosystems. Based on an exhaustive review of over 100 years of published literature, a global database of phytotelmata-associated aquatic Diptera with Bromeliaceae and Zingiberales (7 families) was compiled to explore diversity and ecology and identify gaps in the research. This database is designed to provide a valuable baseline and to serve as an objective, informed tool for future monitoring and research. A total of 4979 unique associations between aquatic Diptera larvae and 117 species in 26 genera of Bromeliaceae and 27 species in 10 genera across 6 families of Zingiberales were assembled in the database. These reported aquatic Diptera span 369 species, 80 genera, and 14 families, and include taxa with diverse ecological roles as detritivores, filter feeders, predators, and prey. Mosquitoes (Culicidae) had the greatest number of documented species (227), and non-biting midges (Chironomidae) had the greatest number of documented genera (26) in the dataset. Several mosquito vectors (e.g., Anopheles, Aedes, and Culex) also complete their life cycles in these habitats, although records of vector mosquitoes compose only 6% of the assembled data. Because phytotelmata provide year-round aquatic refugia, they sustain regional aquatic Diptera diversity yet are threatened by habitat loss and other anthropogenic pressures. Furthermore, despite the important role of phytotelmata in freshwater ecology, diversity in these ephemeral freshwater habitats remains under-documented. This comprehensive analysis of existing literature establishes the first global baseline for aquatic Diptera in phytotelmata and offers a foundation for biodiversity assessments, conservation strategies, and future ecological research. Full article

(This article belongs to the Special Issue Aquatic Insects Biodiversity and eDNA Monitoring)

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