Zoological Studies

Vol. 58, 2019

(update: 2019.08.23)

Utilization of DNA Barcodes for the Identification of Larval Fishes in Tropical Estuarine Waters (Malacca Straits, Malaysia)

Cecilia Chu1, Kar Hoe Loh1, Ching Ching Ng2, Ai Lin Ooi3, Yoshinobu Konishi4, Shih-Pin Huang5, and Ving Ching Chong2,*


1Institute of Ocean and Earth Sciences, University of Malaya, Kuala Lumpur, Malaysia. E-mail: cecilia@siswa.um.edu.my, khloh@um.edu.my
2Institute of Biological Science, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia. *Correspondence: E-mail: chong@um.edu.my. E-mail: ccng@um.edu.my (Ng)
3Department of Agricultural and Food Science, Faculty of Science, University Tunku Abdul Rahman, Kampar, Perak. E-mail: ooial@utar.edu.my
4Seikai National Fisheries Research Institute, Nagasaki, Japan. E-mail: ykoni21080@gmail.com
5Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan. E-mail: huangshihpin@gmail.com

Received 3 April 2019 / Accepted 18 August 2019
Communicated by Benny K.K. Chan

Larval descriptions of tropical marine and coastal fishes are very few, and the taxonomic problem is further exacerbated by the high diversity of fish species in these waters. Nonetheless, accurate larval identification is crucial in ecological and early life history studies of larval fishes for the purpose of fishery management and habitat protection. The present study aimed to evaluate the usefulness of DNA barcodes to support larval fish identification since conventional dichotomous keys based on morphological traits are not efficient due to the lack of larval traits and the rapid morphological changes during ontogeny. The molecular analysis uncovered a total of 48 taxa (21 families) from the larval samples collected from Klang Strait waters encompassing both spawning and nursery grounds of marine and estuarine fishes. Thirty-two (67%) of the larval taxa were matched at the species level, whereas two taxa (4%) were identified at the genus, and 14 taxa (29%) identified at family level. The relatively low rate of species-level identification is not necessarily due to the DNA barcoding method per se, but a general lack of reference sequences for speciose and non-commercial fish families such as Gobiidae, Blenniidae, and Callionymidae. Larval morphology remains important in species diagnosis when molecular matches are ambiguous. The lower ethanol percentage at 50% for larva preservation is also useful to keep the body of larvae intact for morphological identification, and to preserve DNA for subsequent molecular analysis. The 10% Chelex resin used for extracting DNA is also cost-effective for long term monitoring of larval fishes. Hence, future studies on larval fish ecology in the mangrove ecosystem are expected to progress further by using the DNA barcoding method since species-level identification of estuarine larval fishes is successful and made easier.

Key words: Molecular identification, Morphology, Fish larvae, Coastal fishes, Mangrove-associated.

Citation: Chu C, Loh KH, Ng CC, Ooi AL, Konishi Y, Huang SP, Chong VC. 2019. Utilization of DNA barcodes for the identification of larval fishes in tropical estuarine waters (Malacca Straits, Malaysia). Zool Stud 58:0dd. doi:-.

Supplementary Materials: Table S1 | Table S2 | Fig. S1 | Fig. S2 | Fig. S3 | Fig. S4 | Fig. S5 | Fig. S6