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Fishes
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Molecular Phylogeny and Taxonomy of Aquatic Animals
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Molecular Phylogeny and Taxonomy of Aquatic Animals

A special issue of Fishes (ISSN 2410-3888). This special issue belongs to the section "Taxonomy, Evolution, and Biogeography".

Deadline for manuscript submissions: 10 August 2026 | Viewed by 2000

Special Issue Editors

Dr. Pedro F. Amorim

E-Mail Website
Guest Editor
Laboratory of Systematics and Evolution of Teleost Fishes, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro CEP 21941-902, Brazil
Interests: biodiversity; biogeography; conservation; evolution; genetics; ichthiology; systematics; taxonomy; zoology
Dr. José Leonardo de Oliveira Mattos

E-Mail Website
Guest Editor
Laboratory of Systematics and Evolution of Teleost Fishes, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro CEP 21941-902, Brazil
Interests: taxonomy; systematics; neotropical; catfishes; cichlids; fish biodiversity; conservation
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The journal Fishes is pleased to announce this Special Issue, ‘Molecular Phylogeny and Taxonomy of Aquatic Animals’. This Special Issue will provide a valuable opportunity to deepen our understanding of the evolutionary relationships among the diverse aquatic lineages that form a major component of global biodiversity.

From the depths of marine trenches to the headwaters of high-altitude rivers, aquatic organisms exhibit extraordinary diversity, occupying a wide range of ecological niches and displaying fascinating morphological, behavioral, and genetic adaptations. However, despite this richness, large gaps remain in our knowledge of the phylogenetic history of many aquatic groups. These gaps represent a significant challenge for fields such as systematics, taxonomy, conservation biology, and biogeography, where accurate evolutionary frameworks are essential for progress.

With this Special Issue, we aim to advance our current understanding of the evolution and classification of aquatic animals by publishing original research articles, short communications, perspectives, reviews, and mini-reviews. For this aim, we invite you to present new insights into the evolutionary relationships among aquatic lineages worldwide, and also promote the application of this knowledge in studies addressing biogeography, ecology, integrative taxonomy, species delimitation, phylogeography, and the use of molecular tools for conservation and biodiversity assessment.

We invite you to join us in advancing the science of aquatic biodiversity and shaping future research in this vital field.

Dr. Pedro F. Amorim
Dr. José Leonardo de Oliveira Mattos
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. Fishes 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

  • biodiversity
  • biogeography
  • conservation
  • distribution
  • evolution
  • genetics
  • ichthiology
  • systematics
  • taxonomy
  • zoology
 

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Published Papers (3 papers)

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Research

11 pages, 3800 KB  
Communication
DNA Barcoding Analysis of Meretrix Clams (Bivalvia: Veneridae) Around Hainan Island, China
by Hongrui Chen, Mingjie Liu, Yu Sun, Minghua Sun, Zhifeng Gu and Yi Yang
Fishes 2026, 11(4), 195; https://doi.org/10.3390/fishes11040195 - 25 Mar 2026
Viewed by 476
Abstract
This study aimed to assess the species diversity and genetic structure of Meretrix clams around Hainan Island using mitochondrial cytochrome c oxidase subunit I (COI) DNA barcoding. The genus Meretrix is a common and economically important group of bivalves in the intertidal zones [...] Read more.
This study aimed to assess the species diversity and genetic structure of Meretrix clams around Hainan Island using mitochondrial cytochrome c oxidase subunit I (COI) DNA barcoding. The genus Meretrix is a common and economically important group of bivalves in the intertidal zones of Hainan Island, widely distributed in estuarine and nearshore sandy habitats and playing a significant role in local fisheries and aquaculture. In recent years, studies on Meretrix in Hainan have mainly focused on morphological identification and species records from limited coastal areas; however, due to the high phenotypic plasticity of shell morphology and the relatively subtle differences among species, traditional morphology-based identification remains challenging. Meanwhile, molecular systematic investigations of Meretrix in Hainan are still limited, particularly systematic studies using DNA barcoding to assess species diversity and geographic distribution patterns. A total of 141 individuals were collected from ten intertidal sites. Four species were identified—M. lyrata, M. lamarckii, M. meretrix and M. petechialis—with interspecific genetic distances (17.6–22.7%) far exceeding intraspecific variation (0.3–0.9%). Phylogenetic analysis based on COI sequences clearly distinguished four Meretrix species from the waters around Hainan Island, with each species forming a well-supported monophyletic clade, supporting their status as independent evolutionary lineages. In addition, two markedly divergent genetic lineages were detected within M. petechialis, suggesting that this species may possess a relatively complex population structure, one of which is typically found in northern Chinese waters, suggesting possible human-mediated introduction. Species richness was higher on the eastern coast, potentially influenced by regional hydrodynamic conditions. This study provides baseline DNA barcode data for Meretrix species in Hainan and supports the need for integrative management of this economically important resource. Full article
(This article belongs to the Special Issue Molecular Phylogeny and Taxonomy of Aquatic Animals)
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17 pages, 3316 KB  
Article
A Preliminary Study of the Mitochondrial Genome of Leptobotia rotundilobus: Structural Characteristics and Insights into the Phylogeny of Leptobotinae
by Yuting Hu, Guoqing Duan, Huaxing Zhou, Huan Wang and Amei Liu
Fishes 2026, 11(3), 162; https://doi.org/10.3390/fishes11030162 - 12 Mar 2026
Viewed by 353
Abstract
Leptobotia rotundilobus is a newly described species in the subfamily Leptobotinae (Teleostei: Cypriniformes), which is endemic to China. Research on this recently discovered species is preliminary, characterized by limited baseline data and the absence of a fully sequenced mitochondrial genome. To elucidate the [...] Read more.
Leptobotia rotundilobus is a newly described species in the subfamily Leptobotinae (Teleostei: Cypriniformes), which is endemic to China. Research on this recently discovered species is preliminary, characterized by limited baseline data and the absence of a fully sequenced mitochondrial genome. To elucidate the structural features of the mitochondrial genome of L. rotundilobus, we performed whole-genome sequencing using next-generation sequencing technology and analyzed its genomic composition, gene content, and structural variation through genome assembly and bioinformatics. The complete circular sequence, spanning 16,593 bp, comprises 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a typical control region (D-loop), all arranged in the canonical order. The overall base composition of the genome was determined to be 30.8% adenine (A), 24.4% thymine (T), 28.6% cytosine (C), and 16.2% guanine (G). This A+T bias (55.2%) is consistent with the mitochondrial genomes of other Leptobotia, which may affect secondary structure. The ratio of non-synonymous (Ka) to synonymous substitutions (Ks) of 13 PCGs of 16 Leptobotinae species is far less than 1 (0.012–0.063), indicating strong negative or purifying selection on the mitogenome in these species. Moreover, to investigate the phylogenetic relationships within the subfamily Leptobotinae, particularly within the genus Leptobotia, we constructed multiple phylogenetic trees of the mitogenome and concatenated 13 PCGs of 39 sequences with Sinibotia superciliaris as an outgroup. The phylogentic trees using the maximum likelihood (ML) and Bayesian inference (BI) methods consistently indicate that: (1) after correcting the species identification error, L. rotundilobus is closely related to L. micra; and (2) the species of Leptobotia and Parabotia each form a monophyletic group. This study provides new insights into the taxonomy and phylogenetic relationships of Leptobotinae, with a particular focus on the genus Leptobotia, thereby contributing to the clarification of the systematics, origin, and evolution of Botiidae. Full article
(This article belongs to the Special Issue Molecular Phylogeny and Taxonomy of Aquatic Animals)
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15 pages, 1569 KB  
Article
Integrative COI Barcoding and Species Delimitation in Echinodermata from Vietnam
by Tran My Linh, Nguyen Chi Mai, Pham Thi Hoe, Le Quang Trung, Nguyen Tuong Van, Luu Xuan Hoa, Hoang Dinh Chieu, Pham Tran Dinh Nho, Nguyen Kim Thoa, Le Quynh Lien and Do Cong Thung
Fishes 2026, 11(1), 15; https://doi.org/10.3390/fishes11010015 - 27 Dec 2025
Viewed by 712
Abstract
Echinoderms are marine invertebrates that play important roles in structuring marine benthic ecosystems. DNA barcoding has become a valuable tool for species identification; however, reference DNA barcode libraries for echinoderms remain incomplete. This study aims to: (i) develop a COI-5′ reference dataset for [...] Read more.
Echinoderms are marine invertebrates that play important roles in structuring marine benthic ecosystems. DNA barcoding has become a valuable tool for species identification; however, reference DNA barcode libraries for echinoderms remain incomplete. This study aims to: (i) develop a COI-5′ reference dataset for echinoderms from Vietnam by integrating DNA barcodes with morphological data; (ii) evaluate species resolution and barcode gaps using multiple analytical approaches; (iii) assess the consistency of species assignments from BOLD and GenBank for echinoderms collected in Vietnam; (iv) make barcode data publicly available to support global reference database development. Thirty-two echinoderm specimens representing 16 species were analyzed for COI-5′ sequences, and BLAST assignments were highly concordant with those from GenBank and BOLD. Integrative validation confirmed that all taxa were monophyletic in the Neighbor Joining Tree, formed single OTUs in Cluster Sequences, and exhibited clear barcode gaps greater than 3% to the nearest-neighbor species. These results provided species-level resolution for 75% and genus-level resolution for 90% of the records. The dataset, spanning four classes, eight orders, and eleven families, enhances barcode coverage and contributes records (ProcessIDs. BINs; GenBank accessions) to public repositories. This study delivers the first curated COI-5′ reference library, supporting regional baselines for taxonomy, conservation, and biodiversity assessment. Full article
(This article belongs to the Special Issue Molecular Phylogeny and Taxonomy of Aquatic Animals)
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