International Journal of Marine Science, 2025, Vol.15, No.2, 53-64 http://www.aquapublisher.com/index.php/ijms 60 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. polyphekadionComplex 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
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