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21 pages, 2346 KB

Open AccessArticle

Genetic Analysis of Mixed Individuals Reveals Different Spawning Populations of the Tetrapturus pfluegeri (Longbill Spearfish) in the Western Atlantic Ocean

by Suhaila Karim Khalil Jaser, Caio Augusto Perazza, Rodrigo Rodrigues Domingues, Freddy Arocha, Eric Hallerman and Alexandre Wagner Silva Hilsdorf

Fishes 2026, 11(4), 253; https://doi.org/10.3390/fishes11040253 - 21 Apr 2026

Viewed by 435

Abstract

Populations of several billfish species are declining due to overfishing and bycatch, and fundamental aspects of their biology and population dynamics remain poorly understood. We provide the first assessment of the population genetic structure of longbill spearfish (Tetrapturus pfluegeri) in the [...] Read more.

Populations of several billfish species are declining due to overfishing and bycatch, and fundamental aspects of their biology and population dynamics remain poorly understood. We provide the first assessment of the population genetic structure of longbill spearfish (Tetrapturus pfluegeri) in the western Atlantic Ocean. We screened variation at 12 nuclear microsatellite loci (n = 144) and mitochondrial DNA control region sequences (mtCR, n = 177). Both marker types revealed three genetically differentiated clusters, with mean values for microsatellites showing differentiation of F_ST = 0.136 and D_EST = 0.201, and for mtCR F_ST = 0.645. Microsatellite markers demonstrated moderate-to-high genetic diversity, with a mean allelic richness of 6.73 alleles per locus, moderate heterozygosities (Ho = 0.446, He = 0.604), and a positive inbreeding coefficient (F_IS = 0.22) across the three sample collection sites. The overall estimated effective population size was 789.2 (95% CI: 246.7–∞). The mtCR exhibited 96 haplotypes, with high haplotype (0.989 ± 0.003) and nucleotide (0.025 ± 1.3%) diversities. We found higher mean relatedness within clusters than among them, supporting the interpretation of population subdivision and the Wahlund effect. Tajima’s D and Fu’s Fs were negative across all localities, with significant values observed along the Brazilian coast but not in the Caribbean Sea. These neutrality test results, together with low Harpending’s raggedness indices from DNA sequence mismatch distributions, are consistent with historical demographic expansion. Our findings establish a genetic baseline for fishery monitoring and management, contributing to the conservation of T. pfluegeri populations in the western Atlantic Ocean. Full article

(This article belongs to the Special Issue Conservation and Population Genetics of Fishes)

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13 pages, 2433 KB

Open AccessArticle

Development of a Two-Set Multiplex PCR System for Rapid Discrimination of Seven Commercially Important Cuttlefish Species Using COI-Derived SNP Markers

by Chun Mae Dong, Mi-Nan Lee, Hee Jeong Park, Hyo Sun Jung, Eun Soo Noh, In Joon Hwang, Jung-Ha Kang and Eun-Mi Kim

Fishes 2026, 11(4), 226; https://doi.org/10.3390/fishes11040226 - 12 Apr 2026

Viewed by 372

Abstract

Reliable identification of seafood species is critical for fisheries management and product authentication, especially when morphological characteristics are lost during processing. In this study, a multiplex PCR system was developed to distinguish seven cuttlefish species (six Sepia spp. and Sepiella inermis) commercially [...] Read more.

Reliable identification of seafood species is critical for fisheries management and product authentication, especially when morphological characteristics are lost during processing. In this study, a multiplex PCR system was developed to distinguish seven cuttlefish species (six Sepia spp. and Sepiella inermis) commercially distributed in the Korean seafood market. Species identity was first confirmed by amplifying a mitochondrial cytochrome c oxidase subunit I (COI) fragment (~658 bp) using universal primers (LCO1490/HCO2198), showing 99–100% sequence similarity to corresponding GenBank reference sequences. Analysis of genetic variation based on a 530 bp aligned region demonstrated complete interspecific differentiation without shared haplotypes among species. The number of haplotypes per species ranged from 5 to 21, with haplotype diversity values between 0.667 and 1.000. An extended COI fragment (~1200 bp) was further analyzed to identify diagnostic interspecific variation for marker development. Seven diagnostic single-nucleotide polymorphism (SNP) sites were identified and used to design species-specific forward primers with diagnostic nucleotides positioned at the 3′ termini. Distinct amplicons (220–1099 bp) were generated and clearly resolved by agarose gel electrophoresis. Because simultaneous amplification of all seven primer pairs reduced amplification efficiency, the assay was divided into two multiplex sets. Under optimized conditions (56 °C), each species produced a single expected band without cross-amplification. This multiplex PCR system provides a rapid and sequencing-free approach for reliable species discrimination and can be effectively applied to fisheries monitoring and seafood authentication in commercial supply chains. Full article

(This article belongs to the Special Issue Conservation and Population Genetics of Fishes)

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16 pages, 1170 KB

Open AccessArticle

Geographical Traceability of Anguilla japonica from Different Habitats Successfully Achieved Using Muscle Elemental Fingerprint Analysis

by Chao Song, Chengyao Yang, Yijia Li, Dongyu Song, Xiaorong Huang, Sikai Wang, Feng Zhao and Hong Tao

Fishes 2026, 11(1), 68; https://doi.org/10.3390/fishes11010068 - 22 Jan 2026

Viewed by 380

Abstract

Anguilla japonica is a catadromous fish, and the Yangtze River Estuary serves as a crucial passage for A. japonica migrating downstream to the sea. A large number of adult A. japonica appear on the market during the peak migration period. Due to the [...] Read more.

Anguilla japonica is a catadromous fish, and the Yangtze River Estuary serves as a crucial passage for A. japonica migrating downstream to the sea. A large number of adult A. japonica appear on the market during the peak migration period. Due to the lack of effective discrimination basis, it is difficult to distinguish the source of samples in market supervision. Therefore, there is an urgent need to trace the origin of A. japonica from different water bodies. This study analyzed muscle elemental fingerprints of 21 elements to determine the geographical origin of A. japonica. The results showed that A. japonica from different habitats had distinct elemental compositions in their muscles. Specifically, A. japonica from estuary waters (EW) was characterized by significantly higher levels of V and Hg compared to other water bodies. Na was identified as a key discriminant element among different habitats, with its content significantly increasing in river waters (RW), EW, and offshore waters (OW), respectively. Discriminant analysis selected four discriminant elements (V, Hg, Na and Cu) from 21 elemental compositions, among which V, Hg, and Na were the three key distinguishing elements. Based on the composition of these four discriminant elements in the muscles of A. japonica from different habitats, hierarchical cluster analysis (HCA), orthogonal partial least squares discriminant analysis (OPLS-DA), and linear discriminant analysis (LDA) were applied and validated, successfully achieving rapid and accurate origin tracing and verification for new samples, achieving 100% classification accuracy. Therefore, the application of muscle EFA can achieve the geographical traceability of A. japonica from different habitats. The analytical method and verification process for origin tracing established in this study can be successfully applied to market supervision for tracing the origin of samples with unknown sources. Full article

(This article belongs to the Special Issue Conservation and Population Genetics of Fishes)

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16 pages, 5564 KB

Open AccessArticle

Assessing Genetic Diversity and Population Structure of the Endangered Freshwater Fish Gobiobotia brevibarba for Conservation Genetics in Korea

by Keun-Sik Kim, Kang-Rae Kim and In-Chul Bang

Fishes 2026, 11(1), 4; https://doi.org/10.3390/fishes11010004 - 20 Dec 2025

Viewed by 841

Abstract

The endangered freshwater fish Gobiobotia brevibarba is endemic to Korea and threatened by habitat disturbance in major river systems. We investigated four wild populations from the Han River basin (IJR, BHR, NHR) and the Geum River basin (GR) using eleven microsatellite loci to [...] Read more.

The endangered freshwater fish Gobiobotia brevibarba is endemic to Korea and threatened by habitat disturbance in major river systems. We investigated four wild populations from the Han River basin (IJR, BHR, NHR) and the Geum River basin (GR) using eleven microsatellite loci to assess genetic diversity, population structure, and contemporary gene flow. All populations showed relatively high genetic diversity (H_O = 0.709–0.800, H_E = 0.707–0.803) and no evidence of inbreeding, although bottleneck signals under the infinite allele mutation model were detected in IJR and BHR. Contemporary effective population size was large in IJR (N_e = 2463) and moderate in NHR (N_e = 467), whereas estimates for BHR and GR were imprecise. Genetic differentiation was very low within the Han River basin (F_ST = 0.009–0.027) but weak and significant between Han and Geum (F_ST = 0.085–0.096), and clustering analyses (STRUCTURE, DAPC, find.cluster) consistently supported K = 2, separating Han from Geum River. Gene flow analyses indicated extremely limited interbasin gene flow (<4%) but asymmetric contemporary migration from BHR into both IJR and NHR; all other migration rates were similarly low. These results show that G. brevibarba currently maintains high genetic diversity and two basin-level genetic clusters, underscoring the need to manage Han and Geum River populations as separate units and conserve riffle habitats and longitudinal connectivity. Full article

(This article belongs to the Special Issue Conservation and Population Genetics of Fishes)

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14 pages, 2777 KB

Open AccessArticle

Genomic Structure and Hybridization Patterns of Brown Trout (Salmo trutta L.) in the Aosta Valley Using ddRAD-seq, mtDNA-CR, and LDH-C1* Markers

by Edo D’Agaro, Pierpaolo Gibertoni and Stefano Esposito

Fishes 2025, 10(11), 578; https://doi.org/10.3390/fishes10110578 - 10 Nov 2025

Viewed by 680

Abstract

The aim of this research was to characterize the genetic structure of brown trout species complex populations in nine river basins in the Aosta Valley and neighbouring regions in northern Italy. We used a combined analysis of nuclear lactate dehydrogenase (LDH-C1*), [...] Read more.

The aim of this research was to characterize the genetic structure of brown trout species complex populations in nine river basins in the Aosta Valley and neighbouring regions in northern Italy. We used a combined analysis of nuclear lactate dehydrogenase (LDH-C1*), mitochondrial DNA-CR (control region) (mtDNA-CR) sequences and ddRAD-seq-generated single-nucleotide polymorphism. In this way, we estimated the degree of hybridization of wild populations with the Atlantic-derived hatchery lineage. The results of the genetic analyses showed a complex genetic structure with different levels of introgression at the respective sampling sites. The mitochondrial lineages (Atlantic (AT), Mediterranean (ME), Adriatic (AD), and Marmoratus (MA)) were present with varying percentages across the sampling sites. Data analysis using the Admixture v.1.3.0 software allowed the identification of four distinctive cluster units in the Aosta Valley. For the Vertosan River, we identified a distinct native population and a level of hybridization close to zero. In terms of conservation, this population with a distinct native lineage represents a high priority for protection and serves as a reservoir for the entire western north Italian alpine zone. Some interventions to support conservation actions within the study area can be envisaged. Full article

(This article belongs to the Special Issue Conservation and Population Genetics of Fishes)

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14 pages, 1723 KB

Open AccessEditor’s ChoiceArticle

High Connectivity in the Deep-Water Pagellus bogaraveo: Phylogeographic Assessment Across Mediterranean and Atlantic Waters

by Martina Spiga, Giusy Catalano, Federica Piattoni, Alice Ferrari, Carolina Johnstone, Kenza Mokhtar-Jamaï, Montse Pérez, Fabio Fiorentino, Manuel Hidalgo and Alessia Cariani

Fishes 2025, 10(10), 527; https://doi.org/10.3390/fishes10100527 - 17 Oct 2025

Viewed by 856

Abstract

The Blackspot Seabream, Pagellus bogaraveo, is a commercially valuable species widely distributed in the northeastern Atlantic and Mediterranean. Its biology makes it vulnerable to overfishing, but its population structure and ontogenetic migration strategy remain unclear. Building on previous work based on microsatellite [...] Read more.

The Blackspot Seabream, Pagellus bogaraveo, is a commercially valuable species widely distributed in the northeastern Atlantic and Mediterranean. Its biology makes it vulnerable to overfishing, but its population structure and ontogenetic migration strategy remain unclear. Building on previous work based on microsatellite markers, we expanded the investigation by analysing the mitochondrial Control Region (CR) to complement nuclear data. We analysed 199 specimens from 13 sites and combined the new CR sequences with 129 published records to achieve the broadest coverage in terms of biogeographic and genetic data. We calculated genetic diversity and performed AMOVA, pairwise ΦST comparisons, and multivariate analyses. Eighty-eight haplotypes were identified, showing high haplotype diversity (Hd = 0.767–0.945) and moderate nucleotide diversity (π = 0.0026–0.0054). Most genetic variation occurred within populations, and overall analyses indicated genetic homogeneity. However, pairwise analysis and AMOVA confirmed significant differentiation of the Azores population. These results confirm extensive genetic connectivity throughout the Atlantic–Mediterranean range of P. bogaraveo, likely due to a combination of large larval dispersal and a common spawning migration strategy, but identify the Azores as a genetically distinct unit. This highlights the need to consider both large-scale connectivity and local divergence in fisheries management. Full article

(This article belongs to the Special Issue Conservation and Population Genetics of Fishes)

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22 pages, 4857 KB

Open AccessArticle

eDNA Metabarcoding Reveals the Depth-Structured Variation of Coral Reef Fish

by Jinfa Zhao, Lin Lin, Yong Liu, Teng Wang, Yu Liu, Yayuan Xiao, Jianzhong Shen, Hongyu Xie, Hai Huang and Qiuying Han

Fishes 2025, 10(5), 209; https://doi.org/10.3390/fishes10050209 - 2 May 2025

Cited by 3 | Viewed by 3555

Abstract

Global coral reef ecosystems face various levels of disturbance pressure. Understanding the depth-structured variation in coral reef fish communities can help us to better grasp and predict the adaptive changes of the ecosystem under different stressors. This study applied eDNA metabarcoding technology to [...] Read more.

Global coral reef ecosystems face various levels of disturbance pressure. Understanding the depth-structured variation in coral reef fish communities can help us to better grasp and predict the adaptive changes of the ecosystem under different stressors. This study applied eDNA metabarcoding technology to analyze the spatial distribution of the coral reef fish at various depths (0 m, 5 m, 10 m, 15 m, 20 m, 30 m, 40 m, 50 m, and 60 m) within the Xisha Islands of China. The results indicated that the eDNA technology detected a total of 213 amplicon sequence variants (ASVs), including 33 species that were not identified using traditional methods. Herbivorous fish generally dominated in relative abundance across different depths. Moreover, the similarity among depth groups was largely absent, and significant differences existed in fish assemblages across depth gradients, consistent with the unique depth preferences of fish microhabitats. Importantly, our findings revealed distinct depth-structured variation among different functional groups of coral reef fish. Large carnivorous fish initially increased and then decreased along the depth gradient from 0 to 60 m, with a turning point around 20 m, while large herbivorous fish displayed the opposite trend. Small carnivorous and small herbivorous fish consistently declined along the same depth gradient. Additionally, the Margalef index (D) and Function richness (FRic) both displayed a consistent downward trend with increasing depth, while the Shannon–Wiener index (H′), Pielou index (J′), Quadratic entropy (RaoQ), Functional dispersion (FDis), and Functional evenness (FEve) initially increased and then decreased, peaking around 20 m. This study revealed that eDNA metabarcoding is an effective tool for evaluating coral reef fish biodiversity, community composition, and spatial distribution. It enhances our understanding of distribution dynamics and offers valuable insights for coral reef conservation and restoration efforts. Full article

(This article belongs to the Special Issue Conservation and Population Genetics of Fishes)

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16 pages, 3515 KB

Open AccessArticle

Variations of Length–Weight Relationships for Six Fish Species from the Lower Yarlung Zangbo River Catchment, Tibet, China

by Huiping Ding, Mantang Xiong, Yang Yang, Tian Zhong, Feng Chen, Yutian Gong, Dongya Zhang, Sijin Jiang and Zhiming Zhang

Fishes 2025, 10(2), 56; https://doi.org/10.3390/fishes10020056 - 29 Jan 2025

Cited by 1 | Viewed by 1636

Abstract

The lower reaches of the Yarlung Zangbo River are one of the most important biodiversity hotspots worldwide. With the rapid economic development in the area coupled with global climate change, the fish resources and diversity of this region are experiencing serious threats. Basic [...] Read more.

The lower reaches of the Yarlung Zangbo River are one of the most important biodiversity hotspots worldwide. With the rapid economic development in the area coupled with global climate change, the fish resources and diversity of this region are experiencing serious threats. Basic biological information on most fishes in the river is limited, restricting the conservation of local fish resources. This study aimed to provide estimates of length–weight relationships (LWRs) for six fish species from the lower Yarlung Zangbo River catchment, Tibet, China. From 2023 to 2024, 4034 specimens belonging to two families, five genera, and six species were collected using various types of fishing techniques. The LWRs of five species, namely Schizothorax curvilabiatus, Schizothorax molesworthi, Pseudecheneis sulcata, Parachiloglanis hodgarti, and Exostoma labiatum were reported for the first time to FishBase, except Garra tibetana. The b values calculated from the LWRs ranged between 2.738 and 3.172, and the r² values for all LWRs estimates ranged from 0.931 to 0.989. Sexual variations of LWRs were observed in S. molesworthi and P. sulcata; seasonal variations were detected in S. curvilabiatus, S. molesworthi, G. tibetana, P. sulcata, and P. hodgarti; and geographical differences were discovered in S. molesworthi, G. tibetana, P. sulcate, P. hodgarti, and E. labiatum. Additionally, this study updated information for FishBase by providing a new record of maximum standard length for S. curvilabiatus, S. molesworthi, G. tibetana, and P. hodgarti and a new record of total length for P. sulcata. The findings of this study are essential for the management and conservation of locally indigenous fish and fisheries. Full article

(This article belongs to the Special Issue Conservation and Population Genetics of Fishes)

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