DNA Barcoding Reveals Species Diversity and Cryptic Lineages of Commercially Important Carangidae in Aceh Waters, Indonesia

The Carangidae family, commonly referred to in Indonesia as Ikan Kuwe or Ikan Rambue, includes a variety of pelagic fish species that hold substantial economic significance, particularly in regions such as Aceh. Based on data from the FAO (2020), Indonesia’s total Carangidae catch amounted to approximately 1,034,529.384 tons. In Aceh Province alone, the record of the Ministry of Marine Affairs and Fisheries catch was 48,041.15 tons, generating a production value of IDR 1,120,702,238,000. Taxonomically, Carangidae consists of four subfamilies, 30 genera, and 147 identified species, and is widely distributed in tropical and subtropical marine environments [1]. While most species dwell in waters shallower than 20 meters, some can be found at depths reaching 100 meters [2]. Distinctive morphological traits of this family include the presence of two separate dorsal fins, a lateral line that curves near the head and runs straight toward the tail, and coarse, enlarged scales around the caudal peduncle [3]. Members of the Carangidae family exhibit a broad size range—from 16 cm up to 250 cm—and display diverse body forms, including elongated, fusiform (torpedo-like), and laterally compressed shapes [4]. Various species are known by common names such as jacks, pilotfish, trevallies, pompanos, amberjacks, kingfish, scads, rainbow runners, and queenfish [3, 5].

Identifying species within the Carangidae family presents significant challenges due to their highly similar morphometric and meristic traits, along with overlapping body shapes, sizes, and coloration patterns [3, 6]. Furthermore, many Carangidae species undergo notable changes in morphology and pigmentation throughout different stages of their development, increasing the risk of taxonomic misidentification [5]. One prominent example is the giant trevally (Caranx ignobilis), which is often mistaken for other species due to its ontogenetic variations. Juvenile C. ignobilis typically displays a silvery yellow to silvery brown coloration, whereas adults exhibit a silvery white underside with a dorsal side ranging from silvery olive to blue-green. The coloration of this species may also vary—shifting to white or yellow—based on environmental factors [7, 8].

Accurate species identification, particularly for fish recorded at fish landing sites (Tempat Pendaratan Ikan, TPI), is crucial for the sustainable management of capture fisheries [9]. In many leading fishing nations, including Indonesia, catch data are frequently recorded using vernacular or local names rather than standardized scientific nomenclature. For example, Carangidae species are often documented under various regional names such as Cipa-Cipa, Kuwe Abu-Abu, Totol Kuning, Kuwe Bibir Tebal, and Kuwe Pectoral, rather than by their taxonomic names (http://nelpin.kkp.go.id/). This practice complicates accurate stock assessments and biodiversity monitoring. Consequently, molecular identification techniques—such as DNA barcoding—have become indispensable for clarifying species-level classifications and addressing these inconsistencies.

DNA barcoding, first introduced by Hebert et al. [10], employs the mitochondrial cytochrome c oxidase subunit I (COI) gene as a universal marker for species identification across a broad range of organisms. This molecular technique has gained widespread acceptance for identifying marine fish species, including those belonging to the Carangidae family. Numerous studies have utilized DNA barcoding to delineate Carangidae species in various geographic regions. For example, Mat Jaafar [2] successfully barcoded 36 Carangidae species in the Indo-Malaya Archipelago. In the Philippines, Templonuevo et al. [11] applied the method to seven species found in Palawan. Along Vietnam’s coastline, Thu et al. [12] identified 21 species spanning 16 genera within the Carangidae family. Similarly, Ahmed et al. [13] recorded 185 marine fish species in Bangladesh, including 12 Carangidae species. In Malaysia, Nur et al. [14] focused on 13 economically important Carangidae species. Despite these regional advancements, DNA barcoding studies specific to Indonesian Carangidae are still relatively scarce. One such effort by Andriyono et al. [5] involved the identification of five Carangidae species collected from traditional fish markets in Java and Bali.

In addition to aiding species identification, DNA barcoding has significantly contributed to the detection of cryptic species within the Carangidae family across various regions. For instance, Mat Jaafar et al. [6] uncovered cryptic diversity among species such as Atule mate, Selar crumenophthalmus, and Seriola nigrofasciata in the Indo-Malaya Islands. Similarly, a study by Nur et al. [14] demonstrated substantial intraspecific genetic divergence in Carangoides coeruleopinnatus and C. gymnostethus from Malaysian waters, suggesting the possible existence of cryptic species within these taxa.

To date, comprehensive research on Carangidae species in the Aceh region remains limited. For instance, Batubara et al. [15] documented three Carangidae species from Simeulue Island, while Dekar et al. [16] reported the presence of Carangoides malabaricus, Caranx sexfasciatus, and Caranx crysos in the Aceh River, Aceh Besar. In another study, Zulfahmi et al. [17] identified six species belonging to the Carangidae family in the coastal waters of Sabang, Aceh. However, none of these investigations utilized DNA barcoding techniques for species identification, and the lack of such reliable molecular tools has limited accurate stock assessment and biodiversity monitoring in this economically important region. Instead, they relied solely on morphological traits, which may lead to misidentification due to the high degree of similarity among Carangidae species.

Therefore, the present study aims to develop the first comprehensive COI sequence reference library for Carangidae species in Aceh and to identify potential cryptic species diversity within the collected specimens. This molecular database will serve as a foundational resource for improving species identification accuracy and will support more effective fisheries management strategies, both regionally in Aceh and nationally across Indonesia.

Table 1. List of commercially important Carangidae species identified in this study, their sampling locations, sample sizes, and GenBank accession numbers from Aceh, Indonesia

Table 4. COI gene pairwise comparisons based on mean K2P distances (%) between Carangidae species and within species

This study represents the first comprehensive molecular identification of Carangidae species in the Aceh region, utilizing DNA barcoding based on the mitochondrial cytochrome c oxidase subunit I (COI) gene. A total of 20 species were successfully identified from multiple fish landing sites across Aceh. The genus Caranx was the most frequently represented, accounting for approximately 35% of the identified specimens, followed by Atropus, which comprised 15% of the total Carangidae samples (Figure 4). The number of species reported in this study is comparable with the study by Andriyono et al. [5], who barcoded 20 Carangidae species from traditional fish markets in Java and Bali, Indonesia. In addition, the number of species reported in this study is higher than in the study by Templonuevo et al. [11], who barcoded seven species 7 species of carangids from Cuyo, Palawan, Philippines, and Ramadhaniaty et al. [25], who barcoded three Carangidae species from Nias Islands, Indonesia. However, the number of reported species is lower compared to studies by Mat Jaafar et al. [6] and Thu et al. [12], who barcoded 36 and 21 species of Carangidae from Malaysia and Vietnam, respectively.

The genetic distance patterns and barcode gap observed in this study are consistent with previous barcoding efforts in the Indo-Malay region. Mat Jaafar et al. [6] and Nur et al. [14] reported similar divergence thresholds for Carangidae in Malaysia, while Thu et al. [12] recorded comparable inter- and intraspecific divergences along the Vietnamese coast. This concordance underscores the robustness of COI-based barcoding as a standardized method for species discrimination across geographic boundaries. In addition, the findings of the genetic distance and phylogenetic analyses suggest a close evolutionary relationship between Caranx melampygus and Caranx papuensis, as indicated by their low genetic divergence (2.05%). A similarly close relationship was observed between Platycaranx malabaricus and Platycaranx talamparoides (2.18%), supporting their close taxonomic grouping. Both Caranx papuensis and Caranx melampygus exhibited a similar spotted body, but Caranx melampygus has bright blue second dorsal, anal, and caudal fins [3].

Interestingly, the study also identified a Caranx specimen that could not be assigned to a known species, suggesting the potential presence of a cryptic or unrecorded species in Aceh waters. This aligns with earlier reports of cryptic diversity within the Carangidae, such as those reported by Mat Jaafar et al. [6], who uncovered hidden lineages within Atule mate and Selar crumenophthalmus in the Indo-Malaya region. Such findings highlight the limitations of relying solely on morphology for species identification, especially in taxonomically complex groups like Carangidae, which often exhibit overlapping phenotypic traits and ontogenetic shifts in coloration and morphology.

The establishment of a COI sequence reference library for Carangidae in Aceh holds significant implications for fisheries management. Accurate species identification is critical for monitoring fishery resources, especially in regions like Indonesia, where catch records are often reported under local or generic names (e.g., "Ikan Kuwe"). Misidentification can result in flawed stock assessments, inappropriate management strategies, and potential overexploitation of commercially valuable species. By providing molecular-level species resolution, this study offers a foundation for improving the accuracy of fish landing data and supporting evidence-based conservation policies.

Despite its contributions, this study has some limitations. The number of specimens per species was constrained by availability at landing sites, and sampling was limited to a single collection period. Future research should involve broader temporal and spatial sampling to capture seasonal variation and potential population structure. Moreover, while the COI gene is highly effective for initial species identification, integrating nuclear markers or genome-wide approaches such as RAD-seq or eDNA could provide deeper insights into population connectivity, hybridization events, and phylogeographic patterns.

In conclusion, this study demonstrates the power of DNA barcoding in revealing species diversity and resolving taxonomic ambiguities in Aceh's Carangidae. The genetic baseline provided here not only enhances our understanding of local marine biodiversity but also serves as a critical tool for sustainable fisheries management and biodiversity conservation in Indonesia’s coastal ecosystems.