International Journal of Marine Science, 2025, Vol.15, No.3, 130-143 http://www.aquapublisher.com/index.php/ijms 130 Research Report Open Access Reconstructing the Phylogenetic Relationships of Scomberomorus spp.: Evolutionary History from Whole-Genome Data Liting Wang1 , Liang Chen2 1 Hainan Institute of Biotechnology, Haikou, 570206, Hainan, China 2 Center for Tropical Marine Fisheries Research, Hainan Institute of Tropical Agricultural Resouces, Sanya, 572025, Hainan, China Corresponding author: liting.wang@hitar.org International Journal of Marine Science, 2025, Vol.15, No.3, doi: 10.5376/ijms.2025.15.0012 Received: 20 Mar., 2025 Accepted: 22 Apr., 2025 Published: 25 May, 2025 Copyright © 2025 Wang and Chen, This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Wang L.T., and Chen L., 2025, Reconstructing the phylogenetic relationships of Scomberomorus spp.: evolutionary history from whole-genome data, International Journal of Marine Science, 15(3): 130-143 (doi: 10.5376/ijms.2025.15.0012) Abstract The genus Scomberomorus (mackerels) includes several important marine fish species of high economic value in global fisheries and aquaculture, particularly across Asia. However, due to the large number of species and their morphological similarity, traditional taxonomy has been ambiguous, hindering efforts in genetic improvement and resource conservation. In recent years, with the advancement of high-throughput sequencing technologies, phylogenetic studies have entered the "whole-genome era." This paper provides a comprehensive review of the latest developments in reconstructing the phylogeny of Scomberomorus, highlighting the application of whole-genome data in species classification, lineage delimitation, speciation mechanisms, and evolutionary timescales. Case studies on farmed populations in Asia are also discussed, evaluating the genetic structure of hatchery and released stocks relative to wild lineages, and proposing lineage-based population optimization strategies. Further analysis indicates that phylogenetic research contributes not only to the identification of genetic resources and resistance traits but also offers scientific support for molecular breeding, broodstock selection, and genetic improvement. The paper concludes by recommending expanded global sampling, multi-omics integration, and the application of phylogenetic findings in aquaculture management, aiming to bridge foundational evolutionary research with practical breeding applications. Keywords Scomberomorus; Phylogeny; Whole-genome data; Genetic structure; Aquaculture breeding 1 Introduction Scomberomorus is a species-rich group of fish in the Scombridae family, which can be found in tropical and temperate waters around the world. Most of them are fast-swimming and predatory, occupying a high position in the marine food chain and are considered key species to maintain the balance of coastal ecosystems (Andersson et al., 2024). There are currently about 18 species in this genus that are generally recognized. Although there are slight differences in morphology between different species, they are generally similar (Jeena et al., 2022). Due to its tender meat and rich in high-quality fatty acids such as DHA and EPA, Scomberomorus has long been in high demand in the market and has a high price (Gao et al., 2024). However, the species classification of Scomberomorus has always been confusing. Traditional classification methods mainly rely on appearance, but the members of this genus are too similar in appearance and are easily affected by the marine environment and mutate, so it is often difficult to distinguish which category they belong to (Sun et al., 2022). Later, the application of molecular technology, such as the detection of mitochondrial genes such as COI and Cytb, made species identification more accurate (Yang et al., 2023). However, these mitochondrial genes can only reflect maternal genetic information, and they evolve rapidly, sometimes with deviations, and may not accurately reflect the true system relationship (Zhang, 2023). In recent years, phylogenetic genomics has gradually emerged, bringing new solutions to this type of classification problem. Compared with the traditional method of only looking at one or two gene fragments, the study of integrating whole genome information can use tens of thousands of nuclear gene sites to provide higher-resolution pedigree results (Oliveira et al., 2021). For non-model marine fish such as Spanish mackerel, whole genome
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