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Animals
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Mitochondrial Markers in Aquatic Animals: Evolution, Adaptation, and Conservation
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Mitochondrial Markers in Aquatic Animals: Evolution, Adaptation, and Conservation

A special issue of Animals (ISSN 2076-2615). This special issue belongs to the section "Animal Genetics and Genomics".

Deadline for manuscript submissions: 31 December 2026 | Viewed by 3242

Editors

Dr. Chenghe Sun

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Guest Editor
College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
Interests: molecular ecology; conservation genetics; gut microbiota; biodiversity genomics; bioinformatics; conservation genetics
Dr. Lei Xu

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Guest Editor
South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
Interests: biogeography; molecular phylogeny; population genetics; molecular ecology; biodiversity; DNA barcode; fish conservation
Dr. Yangliang Gu

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Guest Editor
National Key Laboratory of Water Environmental Simulation and Pollution Control, South China Institute of Environmental Sciences, Ministry of Ecology and Environment, Guangzhou 510530, China
Interests: molecular phylogeny; population genetics; molecular ecology; biodiversity; DNA barcode; fish conservation

Special Issue Information

Dear Colleagues,

Mitochondrial markers provide a critical lens into understanding evolutionary processes, adaptive mechanisms, and physiological functions in organisms. The mitogenomes of aquatic animals exhibit remarkable diversity and distinctive evolutionary traits. As key components of diverse ecosystems, these animals are increasingly threatened by habitat fragmentation, climate change, and anthropogenic pressures. Advances in genomic technologies, particularly the integration of mitochondrial and population genomics, offer powerful tools for deciphering the evolutionary history, adaptive potential, and conservation strategies of aquatic animals.

This Special Issue aims to compile and highlight recent progress in the mitochondrial and population genomics of aquatic animals, spanning comparative genomics, evolutionary mechanisms, conservation genetics, and management practices. We welcome submissions addressing, but not limited to, the following topics:

  • Comparative mitogenomics in aquatic animals, elucidating phylogenetic relationships and adaptive evolution.
  • Effects of mitogenome variation on aquatic animal health, adaptation, and environmental responses.
  • Mitochondrial–nuclear genome interactions and their functional roles in aquatic animal physiology and development.
  • Population genomics for aquatic animal conservation, including demographic reconstruction, effective population size estimation, adaptive introgression, and hybridization risk assessment.
  • Applications of environmental DNA (eDNA) and genomic tools in monitoring, conservation, and management of aquatic animal diversity.

We invite original research articles, comprehensive reviews, and short communications to collectively advance the field of aquatic animal mitochondrial and conservation genomics.

Dr. Chenghe Sun
Dr. Lei Xu
Dr. Yangliang Gu
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-anonymized peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Animals is an international peer-reviewed open access semimonthly 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 2400 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

  • mitogenomes
  • mitochondrial genome
  • molecular evolution
  • genetic diversity
  • phylogenetic analyses
  • conservation genetics
  • aquatic animals genetics
  • aquatic animals conservation
  • genetic markers
  • population genomics

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Published Papers (4 papers)

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Research

19 pages, 1929 KB  
Article
Phylogeography of Cranoglanis (Teleostei: Cranoglanididae) Reveals Discordance Between Nominal Species and Maternal Lineages: A Broadly Distributed Clade Co-Occurring with a Cryptic Endemic in the Pearl River
by Xing-Pu Huang, Yan-Qiao Li, Tong Wu, Qi Huang, Ling-Lin Wan, Shao-Lin Xie, Ji-Xing Zou, Gui-Feng Wei and Qun Zhang
Animals 2026, 16(11), 1648; https://doi.org/10.3390/ani16111648 - 28 May 2026
Viewed by 1042
Abstract
The species limits of Cranoglanis remain controversial despite their relevance to freshwater fish conservation in southern China. We analyzed mitochondrial cytochrome b sequences from 203 individuals representing seven geographic populations across the Pearl, Red, and Nandujiang drainages to test species validity, assess genetic [...] Read more.
The species limits of Cranoglanis remain controversial despite their relevance to freshwater fish conservation in southern China. We analyzed mitochondrial cytochrome b sequences from 203 individuals representing seven geographic populations across the Pearl, Red, and Nandujiang drainages to test species validity, assess genetic structure, and infer demographic history. Phylogenetic and haplotype network analyses recovered two deeply divergent lineages: a widespread Clade A distributed across all three drainages and a geographically restricted Clade B confined to the middle Xijiang system of the Pearl River Basin. The traditionally recognized Pearl River, Hainan, and Red River nominal taxa all fell within Clade A rather than forming three independent maternal lineages. Within Clade A, differentiation between the Yuanjiang–Red River and Pearl River populations was low, whereas the Nandujiang population showed significant differentiation and extremely low nucleotide diversity. Divergence dating estimated separation between Clades A and B at 4.9183 Ma. Both lineages showed signals consistent with historical demographic expansion. Our results support recognition of two evolutionarily significant units within Cranoglanis and identify the Nandujiang population as a priority for conservation, while the taxonomic status of Clade B requires further testing with nuclear and morphological evidence. Full article
(This article belongs to the Special Issue Mitochondrial Markers in Aquatic Animals: Evolution, Adaptation, and Conservation)
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19 pages, 10539 KB  
Article
Complete Mitochondrial Genomes of Two Species of the Genus Loricaria (Loricariidae: Loricariinae) and Its Phylogenetic Implications
by Xiaoli Zhang, Shuya Liu and Liping Chen
Animals 2026, 16(10), 1537; https://doi.org/10.3390/ani16101537 - 18 May 2026
Viewed by 835
Abstract
Loricaria, the type genus of the armored catfish family Loricariidae, is a species-depauperate lineage in the subfamily Loricariinae, with only 18 valid species formally recognized to date. However, the extremely high morphological homogeneity across congeners of this genus has long posed great [...] Read more.
Loricaria, the type genus of the armored catfish family Loricariidae, is a species-depauperate lineage in the subfamily Loricariinae, with only 18 valid species formally recognized to date. However, the extremely high morphological homogeneity across congeners of this genus has long posed great obstacles to accurate taxonomic delimitation when relying solely on phenotypic traits. In this study, we newly sequenced and fully annotated the complete mitochondrial genomes (mitogenomes) of L. parnahybae and L. simillima. The two assembled mitogenomes are 16,581 bp and 16,371 bp in length respectively, both carrying the conserved vertebrate mitochondrial gene set consisting of 37 functional units (22 transfer RNA genes, 13 protein-coding genes (PCGs), 2 ribosomal RNA genes) and 1 non-coding control region. Among Protein Control Genes, only the Cox1 gene uses GTG as the start codon, whereas the remaining 12 PCGs initiate with ATG. The observed stop codons include TAA, as well as the incomplete stop codons TA and T. We reconstructed phylogenetic trees using both maximum likelihood and Bayesian inference methods, based on a dataset covering mitogenome sequences of 22 Loricariidae species and 2 outgroup taxa. Phylogenetic analyses consistently supported the monophyly of Loricariinae, Hypostominae, and Hypoptopomatinae. These results clarify the evolutionary position of L. simillima and L. parnahybae within Loricariidae and will contribute to elucidating the complex phylogenetic relationships among Loricariidae species. Full article
(This article belongs to the Special Issue Mitochondrial Markers in Aquatic Animals: Evolution, Adaptation, and Conservation)
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16 pages, 5231 KB  
Article
Mitogenome Characteristics and Phylogenetic Analysis of Six Apistogramma Species
by Xiao-Die Chen, Wei Hu, Xiao Ma, Cheng-He Sun and Chang-Hu Lu
Animals 2026, 16(8), 1178; https://doi.org/10.3390/ani16081178 - 12 Apr 2026
Viewed by 427
Abstract
The Neotropical cichlid genus Apistogramma represents one of the most taxonomically diverse and ecologically significant groups of South American freshwater fishes, yet its evolutionary history and species boundaries remain poorly understood due to a lack of comprehensive genomic resources. To address this gap, [...] Read more.
The Neotropical cichlid genus Apistogramma represents one of the most taxonomically diverse and ecologically significant groups of South American freshwater fishes, yet its evolutionary history and species boundaries remain poorly understood due to a lack of comprehensive genomic resources. To address this gap, this study investigated the complete mitogenomic characteristics of six representative Apistogramma species (A. agassizii, A. allpahuayo, A. baenschi, A. nijsseni, A. resticulosa, and A. cacatuoides) to establish a robust molecular framework for species identification and phylogenetic reconstruction. The results showed that Apistogramma mitogenomes are highly conserved. All six Apistogramma species exhibited significant AT bias. Selection pressure analysis revealed that the Ka/Ks ratios for all 13 protein-coding genes were between 0 and 1, indicating that these genes were under purifying selection. Differential site analysis identified nad5, cox1, and nad4 as ideal molecular markers for rapid Apistogramma species identification owing to higher proportions of variable sites. Phylogenetic analysis recovered Apistogramma as a strongly supported monophyletic clade (BP = 100, PP = 1.00), within which A. nijsseni clustered with A. baenschi and A. cacatuoides with A. agassizii. These internal phylogenetic relationships are consistent with the calculated genetic distances and previous morphological groupings. These findings provide an important theoretical basis and data support for rapid species identification, genetic evolutionary research, and divergence time estimation within Apistogramma. Full article
(This article belongs to the Special Issue Mitochondrial Markers in Aquatic Animals: Evolution, Adaptation, and Conservation)
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18 pages, 6734 KB  
Article
Mitochondrial Cyt b Reveals Low Diversity and Basin-Scale Population Structure in Black Carp (Mylopharyngodon piceus) from the Yangtze, Pearl and Red River Basins
by Yan-Qiao Li, Xing-Pu Huang, Dan Li, Tong Wu, Xiao-Yan Fu, Yu-Ning Zhang, Qi Huang, Gui-Feng Wei, Ling-Lin Wan and Qun Zhang
Animals 2026, 16(5), 768; https://doi.org/10.3390/ani16050768 - 1 Mar 2026
Cited by 1 | Viewed by 497
Abstract
The black carp (Mylopharyngodon piceus) is an ecologically and economically important freshwater fish native to China and neighbouring regions, but its wild stocks have declined sharply in recent decades. We analysed mitochondrial cytochrome b (Cyt b) sequences from 100 individuals collected [...] Read more.
The black carp (Mylopharyngodon piceus) is an ecologically and economically important freshwater fish native to China and neighbouring regions, but its wild stocks have declined sharply in recent decades. We analysed mitochondrial cytochrome b (Cyt b) sequences from 100 individuals collected in 2008–2009 from four Yangtze River, two Pearl River and one Red River populations to assess genetic diversity and structure as a pre-ban baseline for maternal lineages. Sixteen polymorphic sites defined 17 haplotypes, with a single dominant haplotype (Hap2) shared across all populations. Haplotype diversity was high but nucleotide diversity low, and neutrality tests together with mismatch-distribution analyses were consistent with a recent Late Pleistocene demographic expansion. Pairwise FST values ranged from negligible differentiation among middle–lower Yangtze populations to pronounced differentiation between the upstream Yangtze population (SS) and middle–lower populations and between the Yangtze and the combined Pearl–Red basins, whereas Pearl and Red River populations showed no significant divergence and high mitochondrial homogeneity, consistent with substantial historical connectivity. Overall, the Cyt b data indicate low mitochondrial diversity and shallow but significant inter-basin structuring, providing preliminary mtDNA-based evidence that Yangtze and Pearl–Red populations represent candidate conservation and management units, and highlighting the need for nuclear genomic markers and contemporary sampling to refine drainage-scale units and evaluate recent management effects. Full article
(This article belongs to the Special Issue Mitochondrial Markers in Aquatic Animals: Evolution, Adaptation, and Conservation)
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