DNA barcoding of fish larvae reveals uncharacterised biodiversity in tropical peat swamps of New Guinea, Indonesia
Arif Wibowo A E , Niklas Wahlberg B D and Anti Vasemägi B C
+ Author Affiliations
- Author Affiliations
A Research Institute for Inland Fisheries, Agency for Marine and Fisheries Research, Ministry of Marine Affairs and Fisheries, Jalan Beringin 08 Mariana, Palembang, 30763, South Sumatera, Indonesia.
B Department of Biology, University of Turku, Pharmacity Itäinen Pitkäkatu 4, FI-20014 Turku, Finland.
C Department of Aquaculture, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Kreutzwaldi 1, EE-51014 Tartu, Estonia.
D Department of Biology, Lund University, Sölvegatan 35, SE-223 62 Lund, Sweden.
E Corresponding author. Email: wibowo@daad-alumni.de
Marine and Freshwater Research 68(6) 1079-1087 https://doi.org/10.1071/MF16078
Submitted: 14 March 2016 Accepted: 5 August 2016 Published: 13 September 2016
Abstract
The Indonesian archipelago, Borneo, Sumatra and West New Guinea (Papua), hosts half of the world’s known tropical peat swamps, which support a significant proportion of the estimated biodiversity on Earth. However, several species groups that inhabit peat swamp environments remain poorly characterised and their biology, particularly during early life stages, is not well understood. In the present study we characterised larval and juvenile fish biodiversity, as well as spatial and temporal variability, in a pristine peat swamp environment of the River Kumbe in West New Guinea, Indonesia, based on analysis of the mitochondrial cytochrome-c oxidase subunit 1 (COI) sequence (501 bp). Altogether, 10 fish species were detected in the peat swamp habitat during the larval and juvenile stages, whereas 13 additional species were caught at older stages. Twelve species were detected only in a single site, whereas some species, such as the Western archerfish (Toxotes oligolepis) and Lorentz’s grunter (Pingalla lorentzi), were observed in all sampling sites. The occurrence of fish larvae also varied temporally for several species. In contrast with many earlier DNA barcoding studies in fish, we were not able to determine the species identity for a large proportion of sequenced larvae (68%) because of the lack of corresponding COI sequences in the reference dataset. Unidentified sequences clustered into five separate monophyletic clades. Based on genetic divergences, the putative taxonomic origin for the five morphotypes are Atherinidae, Osteoglossidae, Terapontidae and Gobiidae.
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