Zoological Studies

Vol. 58, 2019

(update: 2019.08.23; 10.18)

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 (Chu); khloh@um.edu.my (Loh)
2Institute of Biological Sciences, 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, Universiti 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 this taxonomic problem is further exacerbated by the high diversity of fish species in these waters. Nonetheless, accurate larval identification in ecological and early life history studies of larval fishes is crucial for 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. Our molecular analysis uncovered a total of 48 taxa (21 families) from the larval samples collected from the Klang Strait waters encompassing both spawning and nursery grounds of marine and estuarine fishes. Thirty-two (67%) of the larval taxa were identified at the species level, two taxa (4%) at the genus level, and 14 taxa (29%) 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 diagnoses when molecular matches are ambiguous. A lower ethanol percentage (50%) for larva preservation is also useful to keep the body of larvae intact for morphological identification, and to preserve DNA for subsequent molecular analyses. The 10% Chelex resin used to extract DNA is also cost-effective for long term monitoring of larval fishes. Hence, the DNA barcoding method is an effective and easy way to aid the identification of estuarine larval fishes at the species level.

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 58:30. doi:10.6620/ZS.2019.58-30.

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