Eastern little tuna or kawakawa (Euthynnus affinis) is one of the commercially important tunas
in the Philippines and in the Southeast Asian region. Therefore, its sustainability needs to be
ensured by effective management. Unfortunately, knowledge on the stock structure of this
migratory species in the region, needed for management, is unclear. Here, we studied its genetic
population structure using a 300 bp mitochondrial DNA control region (D-loop) marker. Thirtyfive
samples collected in five areas around the Philippines (Aparri, Palawan, Cagayan de Oro,
Tawi-Tawi, and Davao) and thirteen from Peninsular Malaysia (Pangkor Island, Penang) were
sequenced and analyzed. Forty five haplotype sequences were homologous (99%) to each other
while three (all from Malaysia) were divergent (80%) sequences indicating misidentification.
Haplotype distribution, low overall FST value and non-concordant phylogeographic grouping
of the haplotypes indicated that eastern little tuna is panmixing in Southeast Asia.
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