DNA Barcoding Is a Useful Tool for the Identification of the Family Scaridae in Hainan

Liu, Bo; Yao, Yan; Zhang, Nan; Guo, Hua-Yang; Liu, Bao-Suo; Yang, Jingwen; Zhu, Ke-Cheng; Zhang, Dianchang

doi:10.3390/jmse10121915

Cited by 4 publications

(1 citation statement)

References 43 publications

(49 reference statements)

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“…Meanwhile, Scarus sp. was not identified at the species level due to the cryptic morphological nature of the species (Liu et al 2022). Moreover, the new Indo-pacific atherinomorine genus Doboatherina (D. magnidentata) was found in the area (Sasaki and Kimura 2019).…”

Section: Fish Visual Censusmentioning

confidence: 99%

Environmental DNA (eDNA) metabarcoding and fish visual census reveals the first record of Doboatherina magnidentata in the Philippines

BAUTISTA,

MANUBAG,

SUMAYA

et al. 2023

Biodiversitas

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Abstract. Bautista JA, Manubag JJ, Sumaya NH, Martinez JG, Tabugo SR. 2023. Environmental DNA (eDNA) metabarcoding and fish visual census reveals the first record of Doboatherina magnidentatain the Philippines. Biodiversitas 24: 3063-3072. Biodiversity monitoring is the cornerstone for conserving marine fish species. However, classical methods, like the Fish Visual Census (FVC), are often limited due to sampling difficulties, the occurrence of rare and cryptic organisms, and reliance on a taxonomic expert for species identification. Recently, environmental DNA (eDNA) metabarcoding has been suggested as a non-invasive, powerful tool for biomonitoring. This study evaluates the eDNA approach as complementary tool for the FVC data in species detection and identification of important marine fishes from the marine sanctuary of Dalipuga, Iligan City, Philippines. The findings obtained through the eDNA approach provide insights into identifying significant fish species. Notably, the presence of the Hippocampus kuda Bleeker, 1852 (yellow seahorse), categorized as a vulnerable and threatened species, was detected. Additionally, the study identified Herklotsichthys quadrimaculatus Rüppell, 1837 (bluestripe herring), a native species to the Philippines that may pose potential risks to humans and the ecological balance. Furthermore, two demersal fish species, namely Large-scale whiting (Sillaginops macrolepis Bleeker, 1858) and Large-scale mullet (Planiliza macrolepis Smith, 1846), were also detected. The eDNA approach also delineated the morphologically cryptic fishes from Scaridae (parrotfishes) and Mugilidae (mullet fish) taxa to the species level. The highlight of this study was the detectionof the new Indo-pacific atherinomorine fish species Doboatherina magnidentata, which to the best of our knowledge, was the first record in the Philippine marine waters. Despite the efficiency of the eDNA metabarcoding in fish species detection and identification, the viability of eDNA in the marine environment and biases of the primer limit this method. Thus, the classical method must complement the molecular approach for better taxonomic resolution and community analysis. Future studies were also recommended to use a multigene eDNA approach to improve taxonomic sensitivity and reduce primer biases.

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Section: Fish Visual Censusmentioning

confidence: 99%

Environmental DNA (eDNA) metabarcoding and fish visual census reveals the first record of Doboatherina magnidentata in the Philippines

BAUTISTA,

MANUBAG,

SUMAYA

et al. 2023

Biodiversitas

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A molecular approach to identify parrotfish (Sparisoma) species during early ontogeny

Morales‐Pulido,

Galindo‐Sánchez,

Jiménez‐Rosenberg

et al. 2024

Journal of Fish Biology

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Sparisoma species (parrotfish) comprise an important functional group contributing to coral‐reef resilience. The morphological diagnostic characteristics for species identification are clearly described for adult forms but not for the early stages. Consequently, many taxonomical listings of Sparisoma larvae are restricted to the genus level. The aims of this study are to determine whether the morphological and molecular identification techniques are useful to assign the species taxonomic level to Sparisoma larvae occurring in the Gulf of Mexico and whether there is a set of diagnostic features that could be used to discriminate between species in larvae of different developmental stages. Morphological assignment of Sparisoma was performed based on morphological and meristic features for 30 larvae collected in the Gulf of Mexico from late August to mid‐September 2015. To corroborate and complement the morphological assignments, molecular identification was carried out using DNA sequences from regions of two mitochondrial genes, mitochondrial cytochrome oxidase I (mtDNA COI) and mitochondrial 16S rRNA (mtDNA 16S rRNA). COI and 16S gene trees for Sparisoma and related fish taxa were constructed using sequences available in the NCBI (National Center for Biotechnology Information) GenBank and BOLD (Barcode of Life Data) databases. Two morphotypes were identified based on morphology, but no diagnostic characteristics for species discrimination were found. Molecular identification, in contrast, successfully discriminated four early development stages of Sparisoma atomarium, three stages of Sparisoma radians, and two stages of Sparisoma chrysopterum and Sparisoma aurofrenatum, therefore demonstrating the successful and necessary application of molecular taxonomic approaches for species‐level identifications of Sparisoma larvae.

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MOLECULAR APPROACH FOR VALIDATION OF Lutjanus lutjanus AND Lutjanus vitta FROM TERENGGANU WATERS

RONHAKEM,

MOHD NASIR,

ARIFFIN

2024

UMT JUR

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The Snapper is a fish that belongs to the family Lutjanidae and the order Perciformes. It can be discovered in tropical and subtropical mangrove habitats and reefs from depths ranging from 1 m to 500 m. Lutjanus lutjanus and Lutjanus vitta are two snappers found inhibiting Malaysia’s coastal waters, including Terengganu. A total of 100 Lutjanid samples with the admixture of varieties of freshness grade were collected from 11 sampling sites that consist of landing ports and fish markets. Note that external morphological examination based on the body stripes’ colour led to the identification of 30 samples of L. lutjanus and 30 samples of L. vitta. The samples were first identified via morphometric and meristic characterisation, with 39 morphological characters measured, and seven meristic characters were counted. 50 samples were successfully identified as L. lutjanus (n = 25) and L. vitta (n = 25) via morphometric and meristic identification. However, five samples of L. lutjanus with soft dorsal fin counts and five samples of L. vitta with the number of gill rakers did not follow the range stated by the previous study. These 10 samples were further analysed using molecular identification utilising the CO1 gene. Consequently, the constructed phylogenetic tree using the Neighbour Joining method with the Kimura-2 Parameter (K2P) model indicates that both species were divided into clades. Furthermore, the molecular approach indicated five samples were validated as L. Lutjanus while another five samples were L. vitta, with a 99% identical percentage. For future research, it is recommended to use fresh samples, increase the number of samples from other states, and continue to validate the identity via DNA barcoding using the CO1 gene.

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DNA Barcoding Is a Useful Tool for the Identification of the Family Scaridae in Hainan

Cited by 4 publications

References 43 publications

Environmental DNA (eDNA) metabarcoding and fish visual census reveals the first record of Doboatherina magnidentata in the Philippines

Environmental DNA (eDNA) metabarcoding and fish visual census reveals the first record of Doboatherina magnidentata in the Philippines

A molecular approach to identify parrotfish (Sparisoma) species during early ontogeny

MOLECULAR APPROACH FOR VALIDATION OF Lutjanus lutjanus AND Lutjanus vitta FROM TERENGGANU WATERS

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