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Genetics and Evolutionary Biology of Aquatic Organisms
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Genetics and Evolutionary Biology of Aquatic Organisms

A special issue of Biology (ISSN 2079-7737). This special issue belongs to the section "Evolutionary Biology".

Deadline for manuscript submissions: 15 November 2026 | Viewed by 6045

Special Issue Editors

Dr. Qianhong Gu

E-Mail Website
Guest Editor
College of Life Sciences, Hunan Normal University, Changsha 410081, China
Interests: population genetics; biogeography; evolutionary biology; conservation genetics; phylogenetics
Dr. Liang Guo

E-Mail Website
Guest Editor
College of Life Sciences, Hunan Normal University, Changsha 410081, China
Interests: sex determining; sex chromosome; sex-determining gene; turnover of sex-determining gene or sex chromosome
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Aquatic organisms represent a critical component of global biodiversity. Thriving in highly diverse habitats—from high-altitude lakes to deep-sea trenches—they display extraordinary genetic and phenotypic diversity, offering a powerful natural laboratory for investigating adaptive evolution and speciation. Aquatic ecosystems face severe threats from overfishing, pollution, and climate change, with over 30% of species at risk of extinction. Studying their genetic diversity and adaptive mechanisms is crucial for informing targeted conservation strategies, such as designing protected areas based on genetic structure. Aquatic environments, characterized by both ​isolation​ (e.g., geographic barriers in lakes and rivers) and ​connectivity​ (e.g., ocean-current-mediated gene flow), offer an ideal system for studying diverse modes of speciation. Amid global warming-induced water temperature rise and ocean acidification, aquatic organisms' adaptive capacity is pivotal for climate resilience. Studying rapid adaptive evolution facilitates predicting species persistence and informs early warning systems in ecosystem management. Moreover, adaptations to extreme conditions—including high-altitude hypoxia and deep-sea high pressure—harbor unique genetic insights into life's responses to environmental stress. Studies in these areas not only clarify evolutionary mechanisms under "life extremes" but also provide valuable insights for biomedical research, environmental conservation, and sustainable aquatic resource utilization.

We sincerely invite global researchers to submit original research papers, reviews, perspectives, and brief reports, contributing novel insights into the genetics and evolutionary biology of aquatic organisms. Manuscripts must adhere to rigorous scientific standards, demonstrate innovation, and be supported by sufficient data and sound theoretical analysis.

This Special Issue seeks to showcase cutting-edge research advances in the genetics and evolutionary biology of aquatic organisms. Research areas may include (but are not limited to) the following:

  • Genomics and molecular evolution;
  • Mechanisms of adaptation;
  • Fish functional genetics;
  • Fish quantitative genetics;
  • Phylogenetics and taxonomy;
  • Fish molecular evolution and selection pressure;
  • Fish macroevolution and biogeography;
  • Evolutionary developmental biology (evo-devo);
  • Genetic breeding;
  • Population genetics;
  • ​Mechanisms of speciation;
  • ​Conservation of genetic resources​;
  • Convergent evolution;
  • Fish epigenetic evolution;
  • ​Phylogeography;
  • Mechanisms of formation of important traits in fish.

Dr. Qianhong Gu
Dr. Liang Guo
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. Biology 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 2700 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

  • population genetics
  • conservation genetics
  • biodiversity
  • comparative genomics
  • polyploidization
  • rapid adaptation
  • population genetic divergence
  • thermal tolerance
  • hypoxia adaptation
  • deep-sea pressure adaptation
  • convergent evolution
  • molecular clock
  • phylogeography
  • population genetic structure
  • divergence time
  • inbreeding depression
  • genetic diversity
  • genomic selection
  • genome assembly
  • transcriptomics
  • population genomics

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Published Papers (5 papers)

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Research

17 pages, 3888 KB  
Article
Mitogenomic Phylogeny and Adaptive Evolution of Snailfishes (Liparidae) Reveal Correlation Between tRNA Rearrangements and Deep-Sea Colonization
by Ruxiang Wang, Ang Li, Shuai Che, Huan Wang and Shufang Liu
Biology 2026, 15(4), 295; https://doi.org/10.3390/biology15040295 - 7 Feb 2026
Viewed by 638
Abstract
The snailfish family (Liparidae) represents one of the most rapidly speciating and ecologically diverse lineages of marine fishes, with species distributed across a broad bathymetric range from intertidal zones to the hadal depths. Despite their ecological and evolutionary significance, phylogenetic relationships and adaptive [...] Read more.
The snailfish family (Liparidae) represents one of the most rapidly speciating and ecologically diverse lineages of marine fishes, with species distributed across a broad bathymetric range from intertidal zones to the hadal depths. Despite their ecological and evolutionary significance, phylogenetic relationships and adaptive mechanisms within Liparidae remain poorly resolved due to morphological conservatism, phenotypic plasticity, and limited genomic resources due to challenges such as sampling difficulties and a reliance on partial mtDNA markers. In this study, we sequenced, assembled, and annotated the complete mitochondrial genomes of two snailfish species, Liparis chefuensis and Liparis tanakae, collected from the Yellow Sea. The mitogenome of L. chefuensis is 18,870 bp in length, encoding 13 protein-coding genes (PCGs), 2 rRNAs, and 22 tRNAs, while that of L. tanakae spans 17,485 bp and contains 13 PCGs, 2 rRNAs, and 23 tRNAs. Phylogenetic reconstruction based on the concatenated sequences of 13 mitochondrial PCGs from 15 liparid species revealed that L. chefuensis clusters within the subgenus Lyoliparis, contradicting its previous classification under Careliparis and suggesting a need for taxonomic reassessment. Notably, we identified distinct patterns of tRNA gene rearrangement in the cluster between ND2 and COI, which suggest a link to both phylogeny and habitat depth. Shallow-water species (<30 m) possess the tRNATrp-tRNATyr-tRNAAla-tRNAAsn-tRNACys (WYANC) arrangement, whereas deep-water species (>100 m) display the derived tRNATrp-tRNAAsn-tRNACys-tRNATyr-tRNAAla-tRNACys/tRNAAla (WNCYAC/A) configurations. These rearrangements are hypothesized to originate from tandem duplication events followed by random gene loss, potentially reflecting adaptive evolution to deep-sea environments. Additionally, L. tanakae exhibits a markedly higher number of non-canonical G–U and A–C base pairs in its tRNA secondary structures, indicating substantial structural divergence. Our findings not only provide essential mitogenomic resources for snailfish systematics and species identification but also propose that tRNA rearrangements in mitochondrial genomes may serve as genomic innovations facilitating deep-sea colonization. This study enhances our understanding of mitochondrial genome evolution and environmental adaptation in marine fishes. Full article
(This article belongs to the Special Issue Genetics and Evolutionary Biology of Aquatic Organisms)
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18 pages, 3041 KB  
Article
Comparative Transcriptome Sequencing Analysis Revealed Key Pathways and Hub Genes Related to Gill Raker Development in Silver Carp (Hypophthalmichthys molitrix)
by Xiaohui Li, Ziyang Geng, Cui Feng and Hongwei Liang
Biology 2025, 14(12), 1797; https://doi.org/10.3390/biology14121797 - 17 Dec 2025
Viewed by 737
Abstract
The silver carp (Hypophthalmichthys molitrix) is a filter-feeding fish species, characterized by significant morphological transformations in its filter-feeding apparatus, particularly the gill rakers, which are closely associated with dietary changes throughout its development. Despite the importance of these morphological innovations, the [...] Read more.
The silver carp (Hypophthalmichthys molitrix) is a filter-feeding fish species, characterized by significant morphological transformations in its filter-feeding apparatus, particularly the gill rakers, which are closely associated with dietary changes throughout its development. Despite the importance of these morphological innovations, the molecular mechanisms driving these changes remain largely unexplored. To investigate this, we employed an integrative approach combining scanning electron microscopy (SEM) and comparative transcriptomics to examine the gill rakers at five critical developmental stages (6, 15, 30, 45, and 60 days post-hatching, dph). SEM analysis revealed a structural evolution from sparse, bump-like protrusions to a dense, interlocking mesh. Simultaneously, transcriptomic analysis identified 10,184 differentially expressed genes (DEGs), which showed significant enrichment in pathways such as Focal Adhesion, ECM-Receptor Interaction, and the PI3K-Akt Signaling Pathway. Gene Set Enrichment Analysis (GSEA) indicated a coordinated upregulation of collagen and integrin gene families during the early developmental transition (6 vs. 15 dph), highlighting their crucial role in the formation of the sieve structure. This study reveals the molecular mechanisms of gill raker development in silver carp, providing initial insights into genetic regulation of morphology for ecological adaptation. The findings connect developmental biology, evolutionary biology, and ecology. Full article
(This article belongs to the Special Issue Genetics and Evolutionary Biology of Aquatic Organisms)
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15 pages, 1094 KB  
Article
Genetic Diversity and Structure for Conservation Genetics of Goldeye Rockfish Sebastes thompsoni (Jordan and Hubbs, 1925) in South Korea
by Kang-Rae Kim, Keun-Sik Kim and Sung Jin Yoon
Biology 2025, 14(11), 1559; https://doi.org/10.3390/biology14111559 - 6 Nov 2025
Cited by 1 | Viewed by 1154
Abstract
Sebastes thompsoni is a cold-water rockfish of commercial and ecological value off the coast of Korea, requiring conservation management. We analyzed seven microsatellite loci to assess genetic diversity, population structure, and historical effective population size (Ne) of five populations obtained [...] Read more.
Sebastes thompsoni is a cold-water rockfish of commercial and ecological value off the coast of Korea, requiring conservation management. We analyzed seven microsatellite loci to assess genetic diversity, population structure, and historical effective population size (Ne) of five populations obtained from the South and East Seas of Korea in 2018. The observed heterozygosity (HO = 0.759–0.816) was higher than previously reported, and none of the STRUCTURE, DAPC, or AMOVA analyses detected geographic differentiation among samples from the South and East coasts of Korea, indicating a single population within these coasts. There was genetic flow between the five groups, with migration rates ranging from 4.1 to 19.11. However, the current Ne of all populations is estimated to be <1000, and VarEff-based reconstructions indicate a recent, severe bottleneck following an expansion approximately 600–1200 years ago (100–200 generations ago). This suggests that genetic diversity loss may persist in the future due to long-term habitat loss, fishing pressure, and ocean current fluctuations. Therefore, S. thompsoni should be established as a single management unit covering the Korean Peninsula coast, and habitat protection, overfishing control, genetic management type resource release using various mother and broodstock, and periodic genetic monitoring should be promoted. This study provides evidence to guide efforts to secure long-term genetic resilience and sustainable management of S. thompsoni in Korean coastal waters. Full article
(This article belongs to the Special Issue Genetics and Evolutionary Biology of Aquatic Organisms)
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20 pages, 3060 KB  
Article
Molecular Phylogenetics of Seven Cyprinidae Distant Hybrid Lineages: Genetic Variation, 2nNCRC Convergent Evolution, and Germplasm Implications
by Ziyi Wang, Yaxian Sun, Ting Liao, Hui Zhong, Qianhong Gu and Kaikun Luo
Biology 2025, 14(11), 1527; https://doi.org/10.3390/biology14111527 - 30 Oct 2025
Viewed by 1341
Abstract
Distant hybridization is key to trait innovation and speciation, with Cyprinidae hybrid phylogeny helping to clarify diversification mechanisms. Yet, a major gap persists in Cyprinidae studies: the stabilization mechanisms of interspecific distant hybrid lineages. To address this, we systematically analyzed the molecular phylogeny [...] Read more.
Distant hybridization is key to trait innovation and speciation, with Cyprinidae hybrid phylogeny helping to clarify diversification mechanisms. Yet, a major gap persists in Cyprinidae studies: the stabilization mechanisms of interspecific distant hybrid lineages. To address this, we systematically analyzed the molecular phylogeny of seven Cyprinidae distant hybrid lineages and their parental species, using an integrative genetic framework encompassing four mitochondrial genes (Cytb, COI, 16S rRNA, D-loop) and five nuclear genes (EGR2b, IRBP2, RAG1, RAG2, RH2). Homologous sequences of 41 representative Cyprinidae species (85 samples) were retrieved from GenBank to supplement the dataset. Phylogenies were reconstructed from concatenated sequences, complemented by haplotype networks. Intra-/interspecific divergence was quantified using two mitochondrial genes (COI, Cytb) and two nuclear (RAG1, RH2). The results showed that these hybrid lineages exhibited variation patterns analogous to other Cyprinidae species. Both ML and BI trees reconstructed exhibited congruent topologies with high support (bootstrap/BPP > 80%), resolving genus/species-level relationships. While most hybrids clustered intermediately between their parental species, they typically displayed maternal affinity. A notable exception was the 2nNCRC (a homodiploid hybrid from Cyprinus carpio ♀ × Megalobrama amblycephala ♂), which displayed convergent evolution toward Carassius auratus. COI-based K2P genetic distance analysis revealed 2nNCRC had a much closer relationship with C. auratus (0.0119) than with its parents (0.1249 to C. carpio, 0.1552 to M. amblycephala). These nine genes elucidate the genetic relationships between Cyprinid hybrid lineages and progenitors, serving as pivotal molecular markers for parentage tracing and genetic dissection of distant hybridization mechanisms. The integrated mitochondrial–nuclear marker system in this study advances understanding of cytonuclear coadaptation and the stabilization of interspecific distant hybrid lineages in Cyprinidae. Specifically, it provides a precise tool for parentage tracing, Cyprinid germplasm conservation, and targeted regulation of hybrid breeding—laying a foundation for exploring hybrid speciation and developing elite aquaculture germplasms. Full article
(This article belongs to the Special Issue Genetics and Evolutionary Biology of Aquatic Organisms)
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16 pages, 6472 KB  
Article
Research on the Mechanism of Hypoxia Tolerance of a Hybrid Fish Using Transcriptomics and Metabolomics
by Yuhua Tang, Jiayi Yang, Chunchun Zhu, Hong Zhang, Li Hu, Wenting Rao, Xinxin Yu, Ming Wen, Min Tao and Shaojun Liu
Biology 2025, 14(10), 1462; https://doi.org/10.3390/biology14101462 - 21 Oct 2025
Cited by 2 | Viewed by 1669
Abstract
The novel hybrid fish BTB, derived from crossing blunt snout bream (Megalobrama amblycephala, BSB) and topmouth culter (Culter alburnus, TC), exhibits markedly hypoxia tolerance in aquaculture. In this study, hypoxic treatment experiments confirmed that, comparing to its original parent [...] Read more.
The novel hybrid fish BTB, derived from crossing blunt snout bream (Megalobrama amblycephala, BSB) and topmouth culter (Culter alburnus, TC), exhibits markedly hypoxia tolerance in aquaculture. In this study, hypoxic treatment experiments confirmed that, comparing to its original parent BSB, the tolerance to low oxygen of BTB increased by 20.0%. Furthermore, a comparative analysis of the transcriptome and metabolome was performed using gill tissues from BTB exposed to normoxic and hypoxic conditions. Under hypoxic conditions, BTB displayed adaptive modifications in gill lamellae and hemocytes. Transcriptomic profiling identified 789 differentially expressed genes (DEGs), with 298 upregulated and 491 downregulated, enriched in pathways including apoptosis, NK cell-mediated cytotoxicity, MAPK/TNF/Toll-like receptor signaling, and HIF-1/FoXO signaling pathways. Twelve hypoxia-related candidate genes (egln3, im_7150988, znf395a, hif-1an, mknk2b, pck2, ero1a, igfbp-1a, vhl, bpifcl, egln1a, and ccna1) were screened and validated as potential contributors to hypoxia tolerance. Metabolomics analysis revealed a total of 108 differential metabolites (78 upregulated and 30 downregulated), predominantly linked to Arginine and proline metabolism, Ether lipid metabolism, Arachidonic acid metabolism, and Glycerophospholipid metabolism. Association analysis of transcriptomics and metabolomics revealed that the DEGs and DMs were enriched in the pathways of glycerophospholipid metabolism, ether lipid metabolism, arachidonic acid metabolism, and arginine and proline metabolism. In summary, BTB exhibited relatively high hypoxia tolerance, and 12 candidate genes related to hypoxia tolerance were identified. These findings laid a foundation for further investigation into the mechanisms of hypoxia tolerance improvement in hybrid fish. Full article
(This article belongs to the Special Issue Genetics and Evolutionary Biology of Aquatic Organisms)
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