In the face of accelerating environmental change, overexploitation of marine resources and habitat degradation, the study of population genetics has emerged as a crucial tool for understanding species resilience, evolutionary potential and for providing information for effective conservation strategies. At the core of population genetics lies the quantification of genetic variation within and amongst populations, providing insights into historical demography, gene flow and the adaptive capacity of species under both natural and anthropogenic pressures (Islam et al. 2022, Sun et al. 2022). In particular, in marine systems, where many species exhibit high dispersal capabilities and complex life cycles, genetic data are essential for identifying population structure that is not always evident from morphology or geography alone.

The yellowfin seabream (Acanthopagrus latus), a member of the family Sparidae, is a protandrous hermaphrodite fish widely distributed across the Indo-West Pacific Region, from Japan and China to the coasts of Southeast Asia and northern Australia. It is of high commercial value in both capture fisheries and aquaculture and plays a significant ecological role in estuarine and nearshore environments (Wang et al. 2020, Tang et al. 2023). In Vietnam, A. latus is a vital component of artisanal fisheries, particularly in coastal provinces of the Central Region. However, increasing fishing pressure, habitat contraction due to coastal development and pollution pose threats to its long-term sustainability (Yan et al. 2021, Peng et al. 2023). Despite its economic importance, knowledge of the population genetic structure and evolutionary history of A. latus in Vietnam remains limited.

Mitochondrial DNA (mtDNA) and, specifically, the control region (mtCR), has been widely used to assess intraspecific genetic variation in marine organisms due to its high mutation rate, lack of recombination and maternal inheritance. This marker allows for the detection of historical demographic events, such as population expansions, contractions or bottlenecks (Duong et al. 2023). In the case of A. latus, previous studies have revealed cryptic genetic lineages and population structuring across its distribution range, suggesting that, despite high dispersal potential, population connectivity may be limited by environmental factors, ocean currents or habitat discontinuities (Islam et al. 2022, Li et al. 2025). In addition, recent advancements in phylogeographic analysis and Bayesian modelling now enable the reconstruction of species’ demographic histories in unprecedented detail. Tools, such as Bayesian Skyline Plots (BSP) and haplotype network analyses, help to visualise past population dynamics and identify potential refugia or expansion fronts, providing crucial context for conservation planning (Bouckaert et al. 2019, Cheng et al. 2019). Moreover, fixation indices (Fst) and AMOVA provide statistical quantification of genetic differentiation across spatial scales, offering insights into the extent of gene flow and the potential existence of evolutionarily significant units. The application of population genetics to conservation biology is particularly vital for marine fishes, where traditional stock assessment methods may fail to detect underlying genetic structure or demographic history. Genetic data can provide information for the design of marine protected areas, guide restocking programmes and help assess the risks of inbreeding or genetic erosion in exploited populations (Liu et al. 2021). In this context, understanding the genetic structure of A. latus populations in Central Vietnam not only contributes to basic evolutionary knowledge, but also has direct implications for sustainable fisheries management, stock enhancement programmes and habitat conservation efforts.

The Vietnamese coastline represents a dynamic and ecologically diverse region influenced by monsoonal cycles, freshwater inputs and complex current systems, such as the Kuroshio and North Equatorial Currents. These oceanographic factors likely play a pivotal role in shaping the genetic structure of coastal marine species through larval dispersal and connectivity (Nguyen et al. 2022). Central Vietnam’s monsoonal cycles, with distinct wet (September–December) and dry (January–August) seasons, induce pronounced seasonal variations in precipitation, river discharge and coastal hydrology. These variations result in fluctuating salinity, temperature and nutrient levels, which profoundly influence the distribution, reproduction and survival of coastal marine species like A. latus (Nguyen et al. 2013, Do et al. 2018, Tran et al. 2022). Furthermore, estuarine and coastal environments, characterised by significant salinity fluctuations during the rainy season, function as essential nursery grounds for aquatic organisms including A. latus (Truong et al. 2010, Do 2022). Interconnected with seagrass beds and mangrove forests, these estuaries enhance regional biodiversity, providing vital habitats that support the life cycles of numerous aquatic species (Nguyen et al. 2022).

Yet, localised retention mechanisms, such as estuarine nursery dependency or habitat specificity, may act in opposition to homogenising forces, resulting in genetic differentiation at surprisingly fine geographic scales (Wang et al. 2024). A. latus exhibits a strong preference for estuarine environments for juvenile development, where low salinity, abundant food resources and sheltered conditions provide optimal nursery grounds (Sourinejad et al. 2015, Tran et al. 2019). This estuarine nursery dependency can result in self-recruitment, where larvae remain in or return to their natal estuaries rather than dispersing widely via ocean currents (Pattrick and Strydom 2014, Tang et al. 2023). Moreover, coastal geomorphology, such as bays, estuaries and offshore islands, can create hydrodynamic barriers, such as eddies or retention zones, that disrupt larval dispersal (Pineda et al. 2007). In Central Vietnam, the intricate coastlines of provinces like Hue, Nghe An and Quang Binh result in significant implications for marine biodiversity and fisheries management (Tran and Le 2012). The coastline is highly irregular, characterised by numerous bays, river estuaries and lagoons, such as the Ca Estuary in Nghe An and the Gianh, Nhat Le Estuary in Quang Binh and the Tam Giang-Cau Hai Lagoon in Hue. This lagoon, with its narrow inlets and complex network of channels, creates a semi-enclosed environment with weak tidal currents and limited exchange with the open sea (Tran et al. 2010, Hoang and Tran 2020). The nearshore currents at the estuaries of the Ca River, Gianh River and Nhat Le River are strongly influenced by the monsoon regime, exhibiting an irregular and low-amplitude tidal regime (Tran and Nguyen 2014, Nguyen et al. 2021, Tran et al. 2024). These localised disruptions can lead to subtle genetic differentiation, even in species with high dispersal potential. Thus, a comprehensive understanding of both broad-scale connectivity and local genetic structuring is critical for predicting the responses of A. latus to ongoing environmental changes.

In this study, we investigated the genetic diversity, structure and demographic history of A. latus populations distributed across Central Vietnam, using mtCR sequences and a suite of population genetic analyses. Specifically, we aimed to: 1) quantify levels of genetic variation within and amongst regions; 2) determine whether population structuring exists along the Central Vietnamese coast; and 3) reconstruct the evolutionary history of A. latus populations to detect historical demographic events such as bottlenecks or expansions. The findings of this study not only fill a critical gap in our understanding of A. latus population genetics in Vietnam, but also provide essential data for the development of regionally informed conservation and fishery management policies.

Sample collection total DNA extraction

DNA amplification and sequencing protocols

Phylogenetic evaluation

Genetic diversity and population structure pattern

Phylogenetic relationships of A. latus based on the mtCR

From 125 sequences, 90 haplotypes were identified, with no dominant haplotype observed. Of these, 71 haplotypes were unique, while 19 were shared: 17 haplotypes were shared between two populations and two haplotypes were shared amongst three populations. A Bayesian phylogenetic tree analysis, based on the mtCR haplotypes of A. latus (Fig. 1), revealed three main clades. The first clade, belonging to haplogroup A, encompassed the majority of individuals from the sampled population. The second clade comprised 19 haplotypes assigned to haplogroup B. The third clade, corresponding to haplogroup C, formed a distinct group closely related to haplogroup B, consisting of five A. latus individuals. Notably, certain A. latus haplotypes, such as 76, 3 and 90, exhibited monophyletic divergence and did not cluster closely with any of the aforementioned haplogroups, indicating unique genetic characteristics and these remained unclassified. To further explore the genetic diversity within the identified haplogroups, a median-joining haplogroup network was constructed using the mtCR haplotypes (Fig. 2). Most haplotypes were classified under haplogroup A, while 19 belonged to haplogroup B and five were assigned to haplogroup C. The haplotypes did not segregate according to sampling locations; however, the majority were grouped in haplogroup A, forming a large central network with the high-frequency haplotype Hap_8 (six samples). In contrast, the central haplotype of haplogroup B, Hap_10 (one sample), exhibited a lower frequency. Overall, the results of the Bayesian phylogenetic tree and the haplogroup network analyses were highly consistent with each other.

Figure 1.  

The Bayesian phylogenetic tree illustrating the relationship between A. latus from Central Vietnam. Posterior probabilities were used to assess the robustness of the tree. A. latus from Central Vietnam is labelled with numerical symbols at their ends, based on the haplotype order. The accession numbers on NCBI GenBank for the A. latus included in the phylogenetic analysis are provided in Suppl. material 1. Haplogroup A is denoted in light blue, haplogroup B in light green and haplogroup C in light red. Other haplogroups are included to provide a comprehensive view of all mitochondrial haplogroups. The scale bar in the tree represents the average number of substitutions per site. The posterior probability for each branch is indicated by dots, with sizes corresponding to the probability values.

Figure 2.  

The median-joining haplotype network of A. latus from Central Vietnam illustrating the relationships amongst mtCR haplotypes. Each circle denotes a unique haplotype and the size of the circle is proportional to the sample total frequency. Each branch connecting different haplotypes illustrates a number of nucleotide changes by the number of black dashes on the branches. Colours represent sample geographic origins as indicated by the legend.

Genetic diversity of A. latus in Central Vietnam

Evolutionary and historical patterns of A. latus

To investigate the evolutionary dynamics and historical patterns of A. latus in Central Vietnam, we conducted a comprehensive genetic analysis using neutrality tests, mismatch distribution and Bayesian Skyline Plot approaches across three regions: Hue, Quang Binh and Nghe An. Tajima's D values were negative for all regions, suggesting a population expansion or selective sweep (Tajima 1989). Furthermore, all regions exhibited highly significant negative Fu’s Fs values (p < 0.00001) (Table 2), reinforcing the evidence of population expansion across the studied areas (Fu 1997).

The mismatch distribution plots, based on mtCR data for the A. latus populations from Central Vietnam (Fig. 3), provide valuable information for their demographic history. The pooled data and each regional plot display a multimodal distribution, with the observed frequency (red) showing multiple peaks, particularly between 5-15 pairwise differences, alongside a secondary peak around 15-20 differences. This pattern contrasts with the expected frequency under a sudden expansion model (green), an unimodal curve peaking at higher differences (around 5-10). The divergence between observed and expected distributions, especially the extended tail towards 35 differences, suggests a complex population history that may involve stable population sizes over time or the presence of distinct subpopulations with limited gene flow (Harpending 1994). The similarity across the three regions indicates a shared demographic pattern, though variations in peak heights and tail lengths hint at localised differences in genetic structure or historical events (Schneider and Excoffier 1999).

Figure 3.  

Mismatch distribution plot, based on A. latus mtCR data, pooled data of Central Vietnam and individual sites at Hue, Quang Binh and Nghe An.

In addition, the Bayesian Skyline Plot analysis, based on the median effective population size (Ne) (Fig. 4), reveals a stable demographic history for the A. latus population over the past 50,000 years. The population experienced a slight increase by 40,000 BC, indicating a period of little expansion. From 40,000 to 15,000 BC, Ne remained relatively constant, suggesting a long phase of population stability. However, a slight decline is observed from 15,000 BC to the present. To sum up, these findings reveal a complex interplay of historical expansion, prolonged stability and recent decline in A. latus populations.

Figure 4.  

The Bayesian Skyline Plot (BSP) depicts the population dynamics of A. latus over time, spanning from 50,000 BC to the present.

The genetic structure and population dynamics of A. latus in Central Vietnam, as explored through mtDNA analysis, reveal a picture of genetic diversity and significant insights into the evolutionary history of this ecologically and economically important species. Through the mtCR markers, our study provides a comprehensive understanding of the expansion, origin and connectivity of A. latus populations along the central Vietnamese coast. The findings enhance our knowledge of the A. latus population genetics and offer critical insights for future conservation and fisheries management strategies. Specifically, our analysis of mtCR markers revealed significant patterns in genetic diversity and population connectivity.

Our study found that A. latus populations in Central Vietnam exhibit considerable genetic diversity, as reflected in high haplotype diversity across the three sampled regions: Hue, Quang Binh and Nghe An. These results are consistent with the findings of previous studies on marine species, which suggest that high levels of genetic diversity are crucial for the adaptation of populations to changing environmental conditions (Frankham et al. 2010, Liu et al. 2021). The genetic diversity observed in this study suggests that A. latus populations have been able to maintain their genetic integrity despite potential ecological and anthropogenic pressures, including habitat degradation and overfishing. For instance, such high genetic variability is particularly important in marine species, where adaptation to fluctuating coastal environments, such as variations in temperature, salinity and food availability, can determine the resilience of populations (Wang et al. 2024, Yang et al. 2024).

Genetic analysis of A. latus populations in Central Vietnam revealed little genetic differentiation amongst the three sampled regions, with pairwise Fst values ranging from -0.00101 - 0.00035 (p > 0.05), indicating low population structuring (Frankham et al. 2010). The absence of notable genetic variation amongst populations of A. latus observed in our research may be attributed to substantial gene flow occurring during their pelagic phase. This observation aligns with the life history of A. latus, characterised by an extended pelagic larval and early juvenile period, facilitating population mixing (Chang et al. 2002). Evidence of gene flow across these regions suggests that populations are not entirely isolated, likely due to the dispersal of planktonic larvae facilitated by coastal currents and the north-south ocean current in the East Sea (Doan 2022). Oceanographic factors, particularly the north-south current with velocities of 1.05–1.26 m/s along the Central Vietnam coast, play a vital role in larval transport across vast distances, maintaining population connectivity (Wang et al. 2024). Additionally, seasonal coastal currents influenced by monsoon winds enhance larval dispersal to estuarine nursery grounds, critical for population recruitment. The surface current during winter, predominantly flowing from north to south along the Vietnam coast (MRCC, Vietnam 2025), coincides with the spawning and dispersal season of yellowfin seabream larvae and juveniles (Tran et al. 2019). All over, this structure is similar to the results of the study of A. latus fish populations in western Japan by Syazni et al. (2015) and around Taiwan by Jean et al. (2000). Overall, these observations suggest a high degree of gene flow amongst A. latus populations in Central Vietnam.

Additionally, populations in Central Vietnam have very low Fst values when compared to southern China populations (Hainan, Guangdong, Fujian), ranging from -0.00015 to 0.00649 with p-values above 0.05 (Table 5), indicating no significant genetic differences. This suggests strong gene flow, likely due to environmental factors like ocean currents. Prior research indicates that A. latus spawns from September to January in the South China Sea (Wang et al. 2020). This spawning period coincides with the winter monsoon season, a critical factor for larval dispersal. This pattern of connectivity is consistent with other studies on marine species that highlight the role of ocean currents in shaping the population structure of marine organisms. For example, genetic studies on A. pacificus populations across the West Pacific suggest that ocean currents, such as the Kuroshio Current, significantly influence larval dispersal and connectivity between populations (Islam et al. 2022). The China Coastal Current has been identified as a key factor supporting larval dispersal, maintaining gene flow (Li et al. 2025). In contrast, when comparing the A. latus population in western Japan with that in Central Vietnam, the Fst index is at a moderate and significant level of 0.01783 (p < 0.05) (Table 5), reflecting that the connectivity between these two regions is somewhat weak. This weaker connectivity could be explained by the very large geographical distance between the two populations, which likely limits gene flow. Unlike the proximity and shared ocean currents facilitating connectivity with southern China, the distance to Japan introduces a barrier, reducing genetic exchange.

However, despite this connectivity driven by ocean currents, local environmental factors may also influence population differentiation. The genetic structure of A. latus also suggests that local environmental factors, including the availability of suitable estuarine and coastal habitats, may contribute to population differentiation at smaller scales. Studies of other marine species have shown that self-recruitment, where larvae are retained in their natal habitats, can also contribute to genetic differentiation between populations despite the potential for long-distance larval dispersal (Jones et al. 1999). In the case of A. latus, a shallow-water species living around rocky reefs, coral reefs, estuaries and coastal lagoons (Song et al. 2021, Tang et al. 2023), both local retention and long-distance dispersal mechanisms are at play. This dual mechanism may lead to some degree of population isolation, driven by habitat-specific conditions, such as variations in salinity and water temperature across the different coastal regions of Vietnam.

The demographic patterns indicated by the neutrality tests, including significant negative values of Fu’s Fs and Tajima’s D, along with mismatch distribution and Bayesian Skyline Plot analyses, suggest a slight historical population expansion. As a result, this expansion pattern, as observed in many marine taxa following bottleneck events or climatic shifts (Song et al. 2021), was likely driven by favourable climatic conditions at the end of the Pleistocene, when global sea levels rose, leading to the overflow of coastal areas and the creation of new habitats for marine species (Ludt and Rocha 2014, Boissin et al. 2016). These environmental changes facilitated the recovery and growth of marine populations across the Indo-Pacific (Sun et al. 2012, Ludt and Rocha 2014, Delrieu-Trottin et al. 2017, Islam et al. 2022, Wang et al. 2022, Oosting et al. 2023, Li et al. 2025). As a shallow-water species inhabiting coral reefs, estuaries and coastal lagoons, A. latus likely benefitted from this recovery, which was supported by the persistence of suitable breeding and feeding grounds in coastal and estuarine habitats, critical for maintaining population stability (Francisco et al. 2009, Sourinejad et al. 2015, Song et al. 2021, Wang et al. 2024).

The high genetic diversity and evidence of historical population expansion in A. latus in Central Vietnam suggested moderate adaptive potential to environmental changes (Song et al. 2021, Thomson et al. 2021). However, this resilience is threatened by ongoing habitat degradation, overfishing (Matsuishi 2025) and climate change impacts, which may reduce genetic diversity and population stability (Craig 2012, Von der Heyden et al. 2014). For instance, the loss of critical habitats like coral reefs, mangroves and seagrass beds underscores the need for urgent conservation measures. Specifically, Nguyen et al. (2019) reported a low resilience index (0.369) for coral reefs on Hon La Island, driven by high oil concentrations and turbidity, underscoring the need for integrated coastal management and marine protected areas (Nguyen et al. 2019). Likewise, Le (2020) found an average coral cover of only 19.8% across six sites in Central Vietnam, with widespread bleaching and disease, demanding detailed studies to guide effective protection strategies for coastal coral reef ecosystems (Le 2021). Moreover, the degradation of marine ecosystems, including the loss of 70% of mangrove forests and 40–60% of seagrass beds across Vietnam, requires robust policy enforcement and community-driven restoration initiatives to ensure long-term ecological sustainability (Pham and Khanal 2024). These findings underscore the critical need to protect key habitats, such as coral reefs, mangroves, seagrass beds and estuarine areas, which serve as essential breeding and nursery grounds for A. latus (Nagelkerken et al. 2000, Hejnowicz et al. 2015, Nordlund et al. 2018). Furthermore, the influence of ocean currents on population connectivity in this study, as evidenced by the little genetic difference pattern, highlights the need for regionally coordinated fisheries management to account for transboundary population linkages (Sills et al. 2018, Roberts et al. 2024). Therefore, integrating genetic data into management strategies, such as strengthening management of marine protected areas, based on genetic diversity hotspots (e.g. Hai Van - Son Tra, Con Co, Hon La - Hon Co, Hon Ngu - Dao Mat), will enhance the sustainability of A. latus populations in Central Vietnam and the broader Western Pacific Region.

In conclusion, effective management strategies for A. latus must account for its complex population structure and connectivity across the Western Pacific to safeguard its ecological and economic importance in the region.

To sum up, high genetic diversity and weak population differentiation in A. latus across Central Vietnam are driven by ocean currents and local retention. Historical expansion, stability and recent decline highlight the need for habitat protection and regionally coordinated fisheries management to ensure sustainability.

All authors have agreed to this acknowledgment. We extend our gratitude to the Biotechnology Laboratory and Zoology Laboratory of the Faculty of Biology, University of Education, Hue University, for kindly providing the essential equipments for this study. We also thank Le Quang Vuong and Nguyen Tuan from Vinh University, Nguyen Duc Thanh from University of Agriculture and Forestry, Hue University for their assistance in coordinating sample collection, as well as the coastal farmers Hai, Tien, Chau, Huyen, Phuong, Thiep, Quoc and Thao for their valuable help with sampling. In addition, we would like to thank the Institute of Digital Transformation and Educational Resources - Hue University for data analysis to create the BSP.

The authors sincerely thank the ministerial-level project Code: B2023-DHH-29 and the research group NCTB.DHH.2025.10 for funding this research.

Hue University

Conceptualisation: N.T., T.V.G., N.X.H.;

Data curation: N.T., H.L.T.L., N.X.H., B.V.L.;

Formal analysis: N.T., N.X.H., T.T.K.A.;

Funding acquisition: T.V.G., B.V.L.;

Investigation: N.T., T.V.G., H.L.T.L., N.X.H., B.V.L.;

Methodology: N.T., T.V.G., N.X.H.;

Writing – original draft: NT, N.X.H., T.V.G., H.L.T.L.;

Writing – review and editing: N.T., N.X.H., T.V.G., T.T.K.A.

All authors have read and approved the final manuscript