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Insects
Special Issues
Aquatic Insects Biodiversity and eDNA Monitoring
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Aquatic Insects Biodiversity and eDNA Monitoring

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

Deadline for manuscript submissions: 31 December 2025 | Viewed by 3718

Special Issue Editors

Dr. Xiao-Long Lin

E-Mail Website
Guest Editor
College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China
Interests: biogeography; Chironomidae; ecology; systematics; eDNA; mitogenome; molecular phylogeny
Special Issues, Collections and Topics in MDPI journals
Dr. Mathew Seymour

E-Mail Website
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

E-Mail Website
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 100 words) can be sent to the Editorial Office for announcement on this website.

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 (6 papers)

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Research

61 pages, 29845 KiB  
Article
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 292
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 [...] Read more.
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 KiB  
Article
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
Viewed by 209
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 [...] Read more.
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 KiB  
Article
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
Viewed by 467
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 [...] Read more.
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 KiB  
Article
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
Viewed by 477
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 [...] Read more.
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 KiB  
Article
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 713
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. [...] Read more.
(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 KiB  
Article
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 3 | Viewed by 983
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 [...] Read more.
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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