1 Introduction

Groupers belong to the family Epinephelus coioides coioides, which are common fish species in coral reefs, with 16 genera and more than 160 species. They play a very important role in maintaining the balance of coral reef ecosystems. Groupers also have high economic value due to their important position in global commercial fisheries and aquaculture (Qu et al., 2017; Yang et al., 2021; Cao et al., 2022). These fish have complex social structures and special reproduction methods, and they are distributed in tropical and subtropical oceans, which makes them very important both ecologically and economically (Chen et al., 2025).

Species of the family Epinephelus coioides coioides stand out in terms of biodiversity, and they are distributed in major marine areas around the world, including the Indo-Pacific, Atlantic, and Caribbean Seas. Studies have shown that groupers originated in the middle Eocene and then differentiated into six major evolutionary clades, each with different geographical origins and evolutionary histories (Ma et al., 2016). The Indo-Australian Archipelago and the Caribbean are the survival centers and species-rich areas of groupers, while marginal areas with less coral resources have become the source of grouper diversity. Groupers are rich in genetic diversity and there is much evidence of hybridization, which makes the biodiversity of groupers more complex (Qu et al., 2017; Chen et al., 2025).

In this study, we mainly summarize the current knowledge about the evolution of the grouper genome and analyze the factors that drive its species diversification. The study combines the latest research results in genome sequencing, phylogenetics, and population genetics to explore the genome structure and evolutionary history of groupers. We also pay special attention to the genomic characteristics and adaptive characteristics of groupers. In addition, we will also study the impact of geological events, climate change, gene flow, and ecological factors on the genetic diversity of groupers. Through this study, we hope to find out the genetic and environmental factors that affect the species formation, adaptability, and maintenance of high biodiversity of groupers. Finally, I hope this article can show you a clearer picture of the evolution of groupers and provide a reference for future research and conservation work.

2 Phylogenetic and Taxonomic Overview

2.1 Evolutionary history and taxonomic overview of groupers

Groupers live in coral reefs. They are diverse and have a long and complex taxonomic history. Molecular phylogenetic studies have revealed the relationships of groupers, indicating that they originated in the eastern Atlantic Ocean in the Middle Eocene and later gradually differentiated into six major lineages. Due to different geographical locations and times, each lineage has different evolutionary characteristics. These lineages appeared between the late Oligocene and the middle Miocene, and their differentiation speed was affected by biological and geographical factors (Ma et al., 2016). Based on the taxonomic revision of molecular data, we can know that there are 9 to 11 monophyletic genera in the family Epinephelus coioides, which corrects previous classification errors (Craig and Hastings, 2007; Ma et al., 2018).

2.2 Key genera and species: Epinephelus coioides, Mycteroperca, etc.

The most numerous and important genera in the family Epinephelus coioides are Epinephelus coioides, Mycteroperca, Cephalophoris, Plectropomus, and Variola (Craig and Hastings, 2007; Ayu et al., 2024). Among them, Epinephelus coioides has the most species, including more than 90 species, and these different fish species are distributed in tropical and subtropical waters around the world (Loh et al., 2024). Among the other genera, Mycteroperca and Plectropomus are more widely distributed and also occupy an important position in ecology. Studies in recent years have found that some genera (such as Cephalophoris and Epinephelus coioides) are not strictly monophyletic groups. For example, Anyperodon and Cromileptes were once classified in the genus Epinephelus coioides, while some species originally belonging to the genus Epinephelus coioides are now classified in the genus Mycteroperca (Figure 1) (Craig and Hastings, 2007; Amorim et al., 2021; Wang et al., 2022).

2.3 Timeline of diversification events (fossil and molecular evidence)

Through molecular phylogenetic studies, we know that groupers originated in the Middle Eocene, and their differentiation events mainly occurred between the Late Oligocene and the Middle Miocene. As a result of these differentiations, six major evolutionary branches appeared in groupers, all of which were associated with specific biogeographic regions and differentiation patterns. Through fossil and molecular evidence, it can also be found that replacement events such as ocean basin separation and regional radiation played an important role in the formation of grouper diversity (Ma et al., 2016).

2.4 Challenges in analyzing species relationships

Analyzing the species relationships of groupers is a relatively difficult task because many different species of groupers look very similar and are easily confused (Aziz et al., 2016; Ayu et al., 2024; He et al., 2024). Although molecular biological methods (especially DNA barcoding of the COI gene) have improved the accuracy of species identification, there are still difficulties and discrepancies between morphological and molecular data (Aziz et al., 2016; Loh et al., 2024). Some genera are not monophyletic groups, and the taxonomic status of closely related species requires more genetic markers and larger sample sizes for more in-depth research (Craig and Hastings, 2007; Wang et al., 2022; Loh et al., 2024).

3 Progress in Grouper Genomics

3.1 Milestones in grouper genome sequencing

Great progress has been made in grouper genomics, from the earliest preliminary assembly to the current high-quality chromosome-level genome. The genome of the yellow grouper (Epinephelus coioides awoara) has been assembled at the chromosome level, and 99.76% of the genome sequence is fixed on 24 pseudo-chromosomes, which provides a good resource for studying the population genetics, adaptive evolution and speciation of grouper (Zhang et al., 2024). In addition, the genome of the giant grouper (Epinephelus coioides lanceolatus) has also been sequenced with high precision, and the study has also discovered some key gene families, such as antimicrobial peptides, which are very important for disease resistance and aquaculture (Wang et al., 2019). These advances have laid a solid foundation for basic and applied research on groupers.

3.2 Technologies and tools used

The progress in grouper genomics has been mainly achieved through advanced sequencing technologies. Long-read sequencing platforms have played a very important role in genome assembly and complex regional analysis, which is mainly carried out through PacBio's single-molecule real-time (SMRT) sequencing technology (Wang et al., 2019; Cao et al., 2024; Zhang et al., 2024). Hi-C chromosome conformation capture technology can assemble the genome to the chromosome level, greatly improving the completeness and accuracy of researchers in the process of genome research (Zhang et al., 2024). Next-generation sequencing (NGS) combined with full-length transcriptome sequencing can better study gene expression and regulation. In the genetic study of hybrid grouper, we can better understand hybrid vigor and related genes (Cao et al., 2024).

3.3 Comparative genomics with other teleosts

With the completion of the high-quality genome of grouper and the advancement of alignment and annotation methods, comparative genomics has become more widely used. By using tools and frameworks for long-read sequencing data, comparative genomics can help us discover sample or population-specific gene sequence and structural variations, even variations in complex and repetitive regions (Wang et al., 2020; Khorsand et al., 2021). Comparing the genomes of bony fish with those of other vertebrates can help us identify conserved coding regions, non-coding regions, regulatory elements, and evolutionary dynamics, all of which help to gain a deeper understanding of the grouper genome and its diversity (Thomas et al., 2003; Armstrong et al., 2019). These comparative analyses are very important for understanding the genomic basis of adaptation, speciation, and trait evolution in groupers.

4 Genome Structure and Variation

4.1 Chromosome structure, size and gene content

The chromosome structure of groupers is well preserved, and most species have 24 chromosomes. Many grouper species have completed chromosome-level genome assemblies, such as yellow grouper (Epinephelus coioides awoara, 984.48 Mb), brown marble grouper (E. fuscoguttatus, 1 047 Mb) and giant grouper (E. lanceolatus, 1.06 Gb~1.086 Gb) (Zhou et al., 2019; Yang et al., 2021; Zhang et al., 2024). These genomes are well assembled, with scaffold N50 values generally exceeding 40 Mb, and more than 98% of the sequences are fixed on chromosomes. These species are expected to have 24 000 to 25 000 protein-coding genes, and functional annotations are also high, exceeding 90% (Yang et al., 2021; Zhang et al., 2024). Some gene families, especially those related to immunity and growth, have been expanded (Zhou et al., 2019; Wang et al., 2022).

4.2 Transposable elements and repetitive sequence content

The grouper genome contains a large number of repetitive sequences. In yellow grouper, repetitive sequences account for 41.17% of the entire genome (Zhang et al., 2024). There is currently no detailed classification of transposable elements (TE) types, but repetitive sequences are common in the grouper genome. This suggests that transposable elements and other repetitive sequences play an important role in the formation of genome structure, which can promote grouper genome evolution and species diversification (Zhou et al., 2019; Yang et al., 2021; Li et al., 2024; Zhang et al., 2024).

4.3 Structural variation: CNV, inversion and segmental duplication

Structural variation (SV) is a very common phenomenon in groupers and an important reason for the genetic differences between different grouper species. Yang et al. (2023) found 46 643 variations (SV) in their study of the genome of Shanghai-Long hybrid grouper (E. fuscoguttatus × E. lanceolatus), some of which were closely related to genes such as metabolism, cell cycle and growth. When they conducted a colinearity analysis on brown grouper, they did not find large-scale chromosome duplications, but found that its colinearity with closely related species was still high, indicating that the chromosomes were stable as a whole, but there were some local variations that may be related to adaptability (Yang et al., 2021; Yang et al., 2023). Wang et al. (2022) also observed copy number variation (CNV) and gene duplication in some other grouper species, such as potato grouper. In this grouper, the number of copies of Gh and Hsp90b1 genes is higher, which may be related to characteristics such as rapid growth and stress resistance.

4.4 Dynamic changes in mitochondrial and nuclear genomes

The mitochondrial genome of grouper is relatively conservative, and it usually contains 13 protein-coding genes, 22 tRNAs, 2 rRNAs, and a control region. Due to duplication events, new gene arrangements appear in the mitochondrial genome of some grouper species (Zhuang et al., 2013; Kundu et al., 2024). Zhuang et al. (2013) found additional tRNA genes in some grouper genera, which is a unique evolutionary event. Mitochondrial genes are usually subject to strong purifying selection, among which rRNA and tRNA genes are the most conservative, while non-coding regions and some protein-coding genes (such as ND6, ATP8) have relatively large variations (Zhuang et al., 2013; Kundu et al., 2024). In contrast, the structure of the grouper nuclear genome is more complex and more variable, including variation values (SVs) and gene family expansions, while these differences are less obvious in the mitochondrial genome (Figure 2) (Zhou et al., 2019; Yang et al., 2021; Wang et al., 2022; Yang et al., 2023; Li et al., 2024; Zhang et al., 2024).

5 Speciation Mechanisms of Groupers

5.1 Allopatric and sympatric speciation in coral reef habitats

Grouper species can form both allopatrically and sympatrically, particularly in coral reef environments in the Indo-Pacific and Tropical Atlantic + Eastern Pacific (TAEP) regions. Allopatric speciation is often caused by large-scale geological events, such as the uplift of the Isthmus of Panama and crustal movements, which created physical barriers that allowed grouper species to diverge. In contrast, sympatric speciation occurs in places like the Indo-Australian Archipelago (IAA), where species diverge in the same area, often due to differences in habitat preferences and ecological specialization. These divergences have accelerated the diversification of groupers in coral-rich areas, such as the Abu Dhabi Bay in the Indian Ocean and the Caribbean Sea. Although these places are places where species aggregate, they are not the main origins of species (Cao et al., 2014; Cao et al., 2022).

5.2 Geographic isolation and the role of ocean currents

Geographic isolation, usually caused by geological movements and sea level changes, has played a major role in the differentiation of grouper species. Taking the Isthmus of Panama as an example, its formation led to the isolation of grouper populations, thus forming allopatric species. Changes in ocean currents can also affect the dispersal of juveniles and the connection between populations, which further accelerates the regional differentiation of genetic structure. The drop in sea level during the ice age can also isolate populations, leading to lineage differentiation and population bottleneck effects. Although there is a lot of gene flow within the region, there is less migration between different regions, which further emphasizes the impact of geographic isolation in the formation of grouper species differentiation (Cao et al., 2014; Cao et al., 2022).

5.3 Hybridization and gene introgression between closely related species

Hybridization and gene introgression are important mechanisms in the evolution of groupers, and this mechanism is more important between closely related species. Studies have shown that there is extensive hybridization between different species of groupers, which makes species identification more difficult, but also promotes the formation of genetic diversity. Genetic variation introduced by past hybridization events provides the basis for rapid speciation and adaptive radiation. These processes may blur species boundaries and promote the emergence of new species by recombining existing genetic variation into new combinations (Qu et al., 2017; Marques et al., 2019).

5.4 Gametic isolation and post-zygotic barriers

Reproductive isolation in groupers is maintained by pre- and post-gametic barriers. Gametic isolation can occur for various reasons, such as differences in spawning timing, behavioral differences, or gametic incompatibility, which reduces the chance of successful fertilization between species. Post-zygotic barriers, such as sterility or low fertility in hybrid offspring, are mainly caused by genomic differences or developmental incompatibilities, which further restrict gene flow. Ecological and genetic factors, including mate choice and the need to adapt to different habitats, can influence these barriers, ultimately causing species to remain separate even if they occasionally hybridize (Rodríguez et al., 2018; Potkamp and Fransen, 2019; Cutter, 2023).

6 Selection and Adaptive Evolution

6.1 Positive selection of genes related to sex determination, vision and immune function

Analysis of the grouper genome revealed that many genes related to biological functions are affected by positive selection. In the blue-spotted grouper (Epinephelus coioides cyanopodus), some genes related to immunity, growth, reproduction and even sex determination show characteristics of positive selection, which help this grouper adapt to the complex coral reef environment and develop rapidly. In addition, the expansion of the immune gene family of grouper is higher than that of many other bony fishes, and immune function plays a vital role in grouper's adaptation to environmental pressure and maintenance of diversity (Cao et al., 2022). A similar immune gene expansion phenomenon has also been seen in the brown-spotted grouper (Epinephelus coioides fuscoguttatus), which further supports the role of immune genes in adaptive evolution (Yang et al., 2021).

6.2 Local adaptation to depth, temperature, and salinity

Groupers have significant genetic diversity and unique population structure, which is due to the racial isolation of groupers in different marine environments in history. There is a species of grouper (Epinephelus coioides coioides) that has unique genetic characteristics in waters close to the deep sea. Researchers believe that this may be due to population isolation caused by the drop in sea level during the glacial period. These phenomena show that different grouper populations can adapt to different depths, temperatures, salinity and other environments. Their ability to promote phylogenetic diversification can help them effectively cope with climate change (Cao et al., 2014; Chen et al., 2025). After the glaciers retreated, groupers expanded their populations, and this historical time also reflects their adaptation to different regional environments (Cao et al., 2014).

6.3 Detection of selective sweeps and adaptive traits

We can find some evolutionary laws of grouper from genetic research on grouper. In the blue-spotted grouper, Cao et al. (2022) found some special genes and expansions of gene families that help adapt to the environment, and they concluded that the genes of the blue-spotted grouper have undergone adaptive changes. In 2021, Yang et al. studied the genes of the brown-spotted grouper and discovered important gene regions that control growth, which are essential for the survival and artificial reproduction of grouper. These genetic data help scientists find important areas and support research on how groupers adapt to the environment and form new species.

6.4 Parallel/convergent evolution between coral reef and deep-sea lineages

The diversity of groupers is influenced by ecological and geographical factors. Studies have shown that parallel evolution and convergent evolution exist in lineages inhabiting similar environments. Rapid radiation and adaptive divergence are associated with important geological and climatic events, such as global cooling and crustal movement, which provide repeated opportunities for ecological specialization in coral reef and deep-sea environments (Qu et al., 2014; Qu et al., 2017). Similar ecological traits have repeatedly appeared in different evolutionary branches, suggesting that parallel evolution or convergent evolution has played an important role in shaping the diversity of groupers, especially in response to environmental heterogeneity and biogeographic barriers.

7 Ecological and Behavioral Drivers

7.1 Reproductive biology (hermaphroditism)

Groupers have a unique reproductive mode, especially that they are hermaphrodites, that is, they can change from female to male. This reproductive mode is related to their social structure, helping to shape the mating system and population structure, which in turn affects genetic diversity and adaptive evolution, and also promotes the formation of species and rapid changes in the genome (Cao et al., 2022). Although groupers generally have little karyotype differentiation, reproductive isolation has gradually increased over time. This suggests that reproductive biology plays an important role in hindering gene flow (Amorim et al., 2024).

7.2 Site fidelity, spawning aggregation, and larval dispersal

Groupers have strong site fidelity and spawning aggregation behaviors, which limit gene flow between populations and promote genetic differentiation. The study found that populations within the region have strong self-replenishment capabilities, while inter-regional migration is very rare, indicating that the dispersal of juveniles is limited and local spawning behavior helps maintain unique genetic populations and promotes regional diversification. These behaviors are very important for understanding the spatial distribution and evolution of grouper populations.

7.3 Trophic niche partitioning and ecological speciation

Differences in living environment, especially "different food", are the key to the emergence of new species of groupers. For example, closely related groupers live in different areas and eat different foods, so even if they live in the same sea area (such as those in Southeast Asia with many coral reefs), they will gradually become different species. Scientists have found that this change in lifestyle will prompt groupers to evolve into new species-just like they each occupy different "territories" in coral reefs (Stryjewski et al., 2017). Recent genetic studies have also shown that genes that control eating habits and survival skills are particularly susceptible to natural selection when animals differentiate. It is very likely that groupers differentiate into different species in this way (Roycroft et al., 2021; Allio et al., 2021).

7.4 Habitat specialization (e.g., coral reefs vs. rocky reefs)

Habitat specialization is a key ecological factor in grouper diversification. Studies have found that groupers originating from marginal areas with less coral resources contribute significantly to species diversity. In large coral reef biodiversity hotspots, coral reefs are the center of survival and a large number of species are concentrated (Stryjewski and Sorenson, 2017). Groupers can adapt to different reef types (such as coral reefs and rocky reefs), which is related to their genetic adaptations in immunity, growth, and reproduction, allowing them to thrive in complex environments (Cao et al., 2022). Geological and climatic events create new ecological opportunities and barriers, further promoting this diversification driven by habitat specialization.

8 Implications of Genomics for Conservation and Fishery Management

8.1 Assessment of genetic diversity and population structure

Scientists now use genetic technology to study groupers. Common methods include RAD-seq, SNP analysis, and whole genome sequencing. These technologies can help us understand the genetic differences between different grouper populations and the relationships between them. Studies have found (Jackson, 2014; Sherman et al., 2020; Weng et al., 2021) that the genetic differences between Nassau grouper and red grouper are mainly affected by two factors: one is the geographical barriers in the sea (such as deep trenches), and the other is their spawning habits. These findings are particularly important for formulating conservation measures. For example, Sherman's team used more precise SNP markers in 2020 to find that the relationship between the various populations of Nassau grouper is more complicated than previously thought. If the old method is used, these details will not be discovered at all. Recently, Begossi et al. (2022) also used a similar method to study comb groupers. Not only did they figure out the relationship between this fish and other species, but these findings can also be directly used in artificial breeding and conservation work. For example, farms can now select healthier fry based on genetic information.

8.2 Identification of evolutionarily significant units (ESUs)

Genomic data are crucial in identifying ESUs in grouper populations. The clear regional genetic differentiation between Nassau grouper and leopard grouper means that different grouper subpopulations require different management strategies. These studies also suggest that international cooperation and standardized management between genetically isolated populations are important to ensure that different evolutionary lineages are maintained (Jackson, 2014; Jackson et al., 2014).

8.3 Genomic tools for monitoring exploitation and overfishing

Molecular markers, such as mitochondrial DNA, microsatellites, and SNPs (single nucleotide polymorphisms), are increasingly being used to understand the health of grouper fisheries and to see if they are overfished. Methods such as DNA barcoding and PCR-RFLP can help us accurately distinguish between different species of fish. This is important for preventing seafood adulteration and ensuring the accuracy of fishing records (Galal-Khallaf et al., 2019; Anjali et al., 2019). These techniques can also detect whether fish populations are declining and whether genetic diversity is changing. If fish are caught too much, they can alert us earlier (Begossi et al., 2022; Galal-Khallaf et al., 2019; Anjali et al., 2019).

8.4 Stocking and breeding programs: application of genomic selection

The development of high-quality genome assembly and molecular markers has greatly facilitated the study of genomic selection in grouper stocking and breeding programs. The researchers have provided valuable resources for molecular breeding and artificial selection by studying the leopard grouper genome assembly and the growth-related genes of the brown grouper (Yang et al., 2021; Han et al., 2023). In order to ensure the genetic diversity of captive and free-range populations and maintain the long-term survival and resilience of the population, we can use SNPs and microsatellites for parentage testing (Weng et al., 2021; Yang et al., 2021).

9 Case Study: Epinephelus coioides fuscoguttatus-E. polyphekadion Complex

9.1 Overview of taxonomic controversy and hybrid zones

Many species of grouper are very similar in appearance, the most representative of which are the brown-spotted grouper (Epinephelus coioides fuscoguttatus) and the multi-spotted grouper (E. polyphekadion complex). Due to the similar appearance, large body color differences and high frequency of hybridization among different species of grouper, they are often confused in taxonomy, which also brings certain difficulties to the identification and classification of species. Molecular barcoding studies have found that there is widespread hybridization within the genus Epinephelus coioides, which requires the use of genetic tools to resolve taxonomic uncertainties, especially in areas where species overlap, so that hybrids and cryptic species can be more accurately identified (Qu et al., 2017).

9.2 Genomic evidence for incomplete gene flow and lineage sorting

Whole genome sequencing and genomic analyses such as nuclear and mitochondrial markers provide evidence for gene flow and incomplete lineage sorting in the grouper complex. High-quality genome assembly and barcoding techniques revealed significant genetic differentiation and hybridization events, indicating that gene flow still exists between E. fuscoguttatus and E. polyphekadion. Incomplete lineage sorting and gene exchange complicate species boundaries (Qu et al., 2017; Yang et al., 2021).

9.3 Ecological differentiation and reproductive isolation

Despite hybridization and gene flow, ecological differentiation still plays a role in maintaining species differences. Through genetic and genomic studies, we know that postzygotic reproductive isolation develops slowly in groupers due to similar karyotypes and the presence of many homologous regions between different grouper species. Therefore, in the E. fuscoguttatus and E. polyphekadion complexes, ecological factors have a more significant influence than strong reproductive isolation, especially in driving species diversification and maintaining different lineages (Amorim et al., 2021; Amorim et al., 2024).

9.4 Implications for species delimitation and management

The relationship between gene flow, lineages that have not been completely separated, and weak reproductive isolation is quite complex. They affect how we divide species and how we manage them. Tools like DNA barcoding and genome sequencing can help us accurately distinguish what species they are and see if there is any "hybridization" between different species. These are critical for protecting species and managing fisheries. If we can figure out the genetic relationship between these groupers and whether they are likely to hybridize, we can come up with better ways to manage them. This can protect their genetic diversity and make grouper resources last longer (Qu et al., 2017; Yang et al., 2021).

10 Future Prospects and Research Directions

Studying high-quality grouper genomes can provide a good foundation for the combination of multi-omics methods such as transcriptomics and epigenomics. The improvement and application of these methodologies can help researchers gain a deeper understanding of how groupers adapt to environmental pressures and the rapid radiation events of groupers, and also help us better understand the mechanisms of gene expression, regulatory elements, and epigenetic modifications. These studies reveal the complex mechanisms behind species diversity and ecological adaptability. Through multi-omics integration, we can better analyze the process of speciation and support resistance breeding and conservation genetics.

Population genomics plays a relatively major role in understanding how groupers respond to climate change, especially historical and ongoing climate change. Studies by multiple teams have shown that climate change and sea level fluctuations during the Pleistocene have affected grouper populations in various aspects and to varying degrees on the geographic structure, phylogenetic diversity and population history of groupers, leading to population bottleneck effects, secondary contacts and regional differentiation, etc. As climate change continues to affect the marine environment, population genomic analysis will play a long-term role in predicting the adaptive capacity of groupers, managing genetic diversity and formulating regional conservation strategies. Emerging environmental DNA (eDNA) and environmental genomics technologies are ideal tools for detecting the non-invasiveness of grouper populations, assessing biodiversity, and detecting cryptic or hybrid species. These methods can complement the shortcomings of traditional barcoding and genomics technologies, provide real-time data on species distribution, genetic diversity, and hybridization events, and have far-reaching impacts on the effective management and conservation of groupers.

Groupers are widely distributed in many oceans around the world and have a complex biogeographic history. They show diverse distribution patterns in different oceans. Collaborative research across marine biogeographic regions is an important and urgent task for grouper research. Through multi-team collaboration, combining genomic, ecological and biogeographic data from different oceans (such as the Indo-Australian Archipelago, the Caribbean Sea, etc.) for comparative studies can help us reveal the drivers of grouper species diversification and resolve some taxonomic disputes. Collaborative research can also help develop a unified conservation and management framework that takes into account differences in evolutionary history and genetic structure in different oceans.

Acknowledgments

We would like to thank Zhao X.Y. continuous support throughout the development of this study.

Conflict of Interest Disclosure

The authors affirm that this research was conducted without any commercial or financial relationships that could be construed as a potential conflict of interest.

References

Allio R., Nabholz B., Wanke S., Chomicki G., Pérez-Escobar Ó., Cotton A., Clamens A., Kergoat G., Sperling F., and Condamine F., 2021, Genome-wide macroevolutionary signatures of key innovations in butterflies colonizing new host plants, Nature Communications, 12(1): 354.

https://doi.org/10.1038/s41467-020-20507-3

Amorim K.D.J., Costa G.W.W.F., Cioffi M.B., Tanomtong A., Bertollo L.A.C., and Molina W.F., 2021, A new view on the scenario of karyotypic stasis in Epinephelidae fish: cytogenetic historical and biogeographic approaches, Genetics and Molecular Biology, 44: e20210122.

https://doi.org/10.1590/1678-4685-GMB-2021-0122

Amorim K., Costa G., Motta-Neto C., Soares R., Borges A., Benetti D., Cioffi M., Bertollo L., Tanomtong A., and Molina W., 2024, Karyotypic changes and diversification time in Epinephelidae groupers (Perciformes), implications on reproductive isolation, Anais da Academia Brasileira de Ciencias, 96(1): e20221011.

https://doi.org/10.1590/0001-3765202420221011

Anjali K., Mandal A., Gunalan B., Ruban L., Anandajothi E., Thineshsanthar D., Manojkumar T., and Kandan S., 2019, Identification of six grouper species under the genus Epinephelus (Bloch 1793) from Indian waters using PCR-RFLP of cytochrome c oxidase I (COI) gene fragment, Food Control, 101: 39-44.

https://doi.org/10.1016/J.FOODCONT.2019.02.024

Armstrong J., Fiddes I., Diekhans M., and Paten B., 2019, Whole-genome alignment and comparative annotation, Annual Review of Animal Biosciences, 7: 41-64.

https://doi.org/10.3410/f.734326805.793570658

Ayu I.P., Mashar A., Wardiatno Y., Butet N.A., Mukhsin L., Sani I., Irianda N., Madduppa H., Gelis E., Lane C., Borbee E., and Subhan B., 2024, DNA barcoding and phylogenetic analysis of commercially important groupers (Serranidae) in raja ampat using gene marker Cytochrome c Oxidase I (COI), Ilmu Kelautan: Indonesian Journal of Marine Sciences, 29(3): 321-328.

https://doi.org/10.14710/ik.ijms.29.3.321-328

Aziz N., Esa Y., and Arshad A., 2016, DNA barcoding and phylogenetic analysis of Malaysian groupers (Subfamily: Epinephelinae) using mitochondrial Cytochrome c oxidase I (COI) gene, Journal of Environmental Biology, 37(4): 725-733.

Begossi A., Salivonchyk S., Glamuzina B., Alves-Pereira A., Batista C., and Priolli R., 2022, Filling gaps in the knowledge of grouper especially Comb grouper (Mycteroperca acutirostris) (2013-2020), copacabana fishery Rio de Janeiro Brazil, Ambiente e Agua, 17: e2774.

https://doi.org/10.4136/ambi-agua.2774

Bernard A.M., Johnston M.W., Pérez-Portela R., Oleksiak M.F., Coleman F.C., and Shivji M.S., 2019, Genetic and biophysical modelling evidence of generational connectivity in the intensively exploited western North Atlantic red grouper (Epinephelus morio), ICES Journal of Marine Science, 77(1): 359-370.

https://doi.org/10.1093/icesjms/fsz201

Cao L., Ma J., Lu Y., Chen P., Hou X., Yang N., and Huang H., 2024, Combining full-length transcriptome sequencing and next generation sequencing to provide insight into the growth superiority of the hybrid grouper (Cromileptes altivelas (♀) × Epinephelus lanceolatus (♂)), PLoS ONE, 19(10): e0308802.

https://doi.org/10.1371/journal.pone.0308802

Cao X., Zhang J., Deng S., and Ding S., 2022, Chromosome-level genome assembly of the speckled blue grouper (Epinephelus cyanopodus) provides insight into its adaptive evolution, Biology, 11(12): 1810.

https://doi.org/10.3390/biology11121810

Chen Y., Luo Z., Zhang Z., Luo Z., Ren M., He X., Lin H., and Yan Y., 2025, Genetic pattern and demographic history of orange‐spotted grouper (Epinephelus coioides) in the South China Sea by the influence of pleistocene climatic oscillations, Ecology and Evolution, 15(2): e70967.

https://doi.org/10.1002/ece3.70967

Craig M., and Hastings P., 2007, A molecular phylogeny of the groupers of the subfamily Epinephelinae (Serranidae) with a revised classification of the Epinephelini, Ichthyological Researchm, 54: 1-17.

https://doi.org/10.1007/s10228-006-0367-x

Cutter A., 2023, Speciation and development, Evolution and Development, 25: 289-327.

https://doi.org/10.1111/ede.12454

Galal-Khallaf A., Osman A., El-Ganainy A., Farrag M., Mohammed-AbdAllah E., Moustafa M., and Mohammed-Geba K., 2019, Mitochondrial genetic markers for authentication of major Red Sea grouper species (Perciformes: Serranidae) in Egypt: a tool for enhancing fisheries management and species conservation, Gene, 689: 235-245.

https://doi.org/10.1016/j.gene.2018.12.021

Han W., Wu S., Ding H., Wang M., Wang M., Bao Z., Wang B., and Hu J., 2023, Improved chromosomal-level genome assembly and re-annotation of leopard coral grouper, Scientific Data, 10(1): 156.

https://doi.org/10.1038/s41597-023-02051-z

He H., Gao Z., Hu Z., Cai L., Huang Y., Zhou M., and Liang R., 2024, Comparative characterization and phylogenetic analysis of complete mitogenome of three taxonomic confused groupers and the insight to the novel gene tandem duplication in Epinephelus, Frontiers in Marine Science, 11: 1450003.

https://doi.org/10.3389/fmars.2024.1450003

Jackson A., 2014, Conservation genetics of commercially exploited fishes with case studies on leopard and nassau grouper, University of California, Santa Cruz, 2014.

Jackson A.M., Semmens B.X., De Mitcheson S., Nemeth R., Heppell S., Bush P., Aguilar-Perera A., Claydon J., Calosso M., Sealey K., Schärer M., and Bernardi G., 2014, Population structure and phylogeography in nassau grouper (Epinephelus striatus) a mass-aggregating marine fish, PLoS ONE, 9(5): e97508.

https://doi.org/10.1371/journal.pone.0097508

Khorsand P., Denti L., Bonizzoni P., Chikhi R., and Hormozdiari F., 2021, Comparative genome analysis using sample-specific string detection in accurate long reads, Bioinformatics Advances, 1(1): vbab005.

https://doi.org/10.1101/2021.03.23.436571

Kundu S., Kang H.E., Kim A.R., Lee S.R., Kim E.B., Amin M.H.F., Andriyono S., Kim H.W., and Kang K., 2024, Mitogenomic characterization and phylogenetic placement of african hind Cephalopholis taeniops: shedding light on the evolution of groupers (Serranidae: Epinephelinae), International Journal of Molecular Sciences, 25(3): 1822.

https://doi.org/10.3390/ijms25031822

Li H., Liu Y., Mao M., and Mao Y., 2024, Chromosome-level genome assembly and annotation of the camouflage grouper (Epinephelus polyphekadion), Scientific Data, 11(1): 1353.

https://doi.org/10.1038/s41597-024-04212-0

Loh K.H., Poong S.W., Du J.L., Ong J., Zheng X., Li Y., and Hu W., 2024, First record of the blue-and-yellow grouper Epinephelus flavocaeruleus (Lacepède 1802) (Perciformes: Epinephelidae) from the borneo waters malaysia, Zootaxa, 5550(1): 133-144.

https://doi.org/10.11646/zootaxa.5550.1.14

Ma K., Craig M., Choat J., and Van Herwerden L., 2016, The historical biogeography of groupers: Clade diversification patterns and processes, Molecular Phylogenetics and Evolution, 100: 21-30.

https://doi.org/10.1016/j.ympev.2016.02.012

Ma K., and Craig M., 2018, An inconvenient monophyly: an update on the taxonomy of the groupers (Epinephelidae), Copeia, 106: 443-456.

https://doi.org/10.1643/CI-18-055

Marin J., Achaz G., Crombach A., and Lambert A., 2020, The genomic view of diversification, Journal of Evolutionary Biology, 33(10): 1387-1404.

https://doi.org/10.1111/jeb.13677

Marques D., Meier J., and Seehausen O., 2019, A combinatorial view on speciation and adaptive radiation, Trends in Ecology and Evolution, 34(6): 531-544.

https://doi.org/10.1016/j.tree.2019.02.008

Potkamp G., and Fransen C.H.J.M., 2019, Speciation with gene flow in marine systems, Contributions to Zoology, 88(2): 133-172.

https://doi.org/10.1163/18759866-20191344

Qu M., Tang W., Liu Q., Wang D., and Ding S., 2017, Genetic diversity within grouper species and a method for interspecific hybrid identification using DNA barcoding and RYR3 marker, Molecular Phylogenetics and Evolution, 121: 46-51.

https://doi.org/10.1016/j.ympev.2017.12.031

Rodríguez R., Hauber R., Scordato M., Symes E., Balakrishnan L., Zonana C., David M., Kopp M., Servedio M., Mendelson T., Safran R., Rodríguez R., Hauber M., Scordato E., Symes L., Balakrishnan C., Zonana D., and Doorn S., 2018, Mechanisms of assortative mating in speciation with gene flow: connecting theory and empirical research, The American Naturalist, 191: 1-20.

https://doi.org/10.1086/694889

Roycroft E., Achmadi A., Callahan C.M., Esselstyn J.A., Good J.M., Moussalli A., and Rowe K.C., 2021, Molecular evolution of ecological specialisation: genomic insights from the diversification of murine rodents, Genome Biology and Evolution, 13(7): evab103.

https://doi.org/10.1093/gbe/evab103

Sherman K.D., Paris J.R., King R.A., Moore K.A., Dahlgren C.P., Knowles L.C., Stump K., Tyler C.R., and Stevens J., 2020, RAD-seq analysis and in situ monitoring of nassau grouper reveal fine-scale population structure and origins of aggregating fish, Frontiers in Marine Science, 7: 157.

https://doi.org/10.3389/fmars.2020.00157

Stryjewski K.F., and Sorenson M.D., 2017, Mosaic genome evolution in a recent and rapid avian radiation, Nature Ecology and Evolution, 1: 1912-1922.

https://doi.org/10.1038/s41559-017-0364-7

Thomas J., Thomas J., Touchman J., Blakesley R., Bouffard G., Beckstrom-Sternberg S., Margulies E., Blanchette M., Siepel A., Thomas P., and Green E., 2003, Comparative analyses of multi-species sequences from targeted genomic regions, Nature, 424: 788-793.

https://doi.org/10.1038/nature01858

Wang C., Ye P., Liu M., Zhang Y., Feng H., Liu J., Zhou H., Wang J., and Chen X., 2022, Comparative analysis of four complete mitochondrial genomes of epinephelidae (Perciformes), Genes, 13(4): 660.

Wang D., Chen X., Zhang X., Li J., Yi Y., Bian C., Shi Q., Lin H., Li S., Zhang Y., and You X., 2019, Whole genome sequencing of the giant grouper (Epinephelus lanceolatus) and high-throughput screening of putative antimicrobial peptide genes, Marine Drugs, 17(9): 503.

https://doi.org/10.3390/md17090503

Wang Y., Chen Q., Deng C., Zheng Y., and Sun F., 2020, KmerGO: a tool to identify group-specific sequences with k-mers, Frontiers in Microbiology, 11: 2067.

https://doi.org/10.3389/fmicb.2020.02067

Weng Z., Yang Y., Wang X., Wu L., Hua S., Zhang H., and Meng Z., 2021, Parentage analysis in giant grouper (Epinephelus lanceolatus) using microsatellite and SNP markers from genotyping-by-sequencing data, Genes, 12(7): 1042.

https://doi.org/10.3390/genes12071042

Yang Y., Wang T., Chen J., Wu L., Wu X., Zhang W., Luo J., Xia J., Meng Z., and Liu X., 2021, Whole‐genome sequencing of brown‐marbled grouper (Epinephelus fuscoguttatus) provides insights into adaptive evolution and growth differences, Molecular Ecology Resources, 22: 711-723.

https://doi.org/10.1111/1755-0998.13494

Yang Y., Zeng L., Wang T., Wu L., Wu X., Xia J., Meng Z., and Liu X., 2023, Assembly of genome and resequencing provide insights into genetic differentiation between parents of Hulong hybrid grouper (Epinephelus fuscoguttatus ♀ × E. lanceolatus ♂), International Journal of Molecular Sciences, 24(15): 12007.

https://doi.org/10.3390/ijms241512007

Zhang W., Yang Y., Hua S., Ruan Q., Li D., Wang L., Wang X., Wen X., Liu X., and Meng Z., 2024, Chromosome-level genome assembly and annotation of the yellow grouper Epinephelus awoara, Scientific Data, 11(1): 151.

https://doi.org/10.1038/s41597-024-02989-8

Zhou Q., Gao H., Zhang Y., Fan G., Xu H., Zhai J., Xu W., Chen Z., Zhang H., Liu S., Niu Y., Li W., Li W., Lin H., and Chen S., 2019, A chromosome‐level genome assembly of the giant grouper (Epinephelus lanceolatus) provides insights into its innate immunity and rapid growth, Molecular Ecology Resources, 19: 1322-1332.

https://doi.org/10.1111/1755-0998.13048

Zhou Q., Lu S., Liu Y., Zhou B., and Chen S., 2023, Development of a 20 K SNP array for the leopard coral grouper Plectropomus leopardus, Aquaculture, 578: 740079.

https://doi.org/10.1016/j.aquaculture.2023.740079

Zhuang X., Qu M., Zhang X., and Ding S., 2013, A comprehensive description and evolutionary analysis of 22 grouper (Perciformes Epinephelidae) mitochondrial genomes with emphasis on two novel genome organizations, PLoS One, 8(8): e73561.

https://doi.org/10.1371/journal.pone.0073561