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 1905

Special Issue Editors


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Guest Editor
College of Life Sciences, Hunan Normal University, Changsha 410081, China
Interests: population genetics; biogeography; evolutionary biology; conservation genetics; phylogenetics

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
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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

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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 (3 papers)

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Research

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
Viewed by 455
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
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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
Viewed by 675
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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