Estimating Crustacean Species Utilize Segara Anakan Estuary Cilacap, Indonesia as Nursery Ground through DNA Barcoding

Elly Tuti Winarni, Kusbiyanto, Agus Nuryanto


Estimating crustaceans that utilized Segara Anakan Cilacap, Central Java, Indonesia, is constrained by larvae identification difficulties because of the lack of identification key and limited morphological characteristics of the larva. Species-level identification of crustacean larvae can be conducted using DNA barcoding using cytochrome c oxidase 1 (COI). This study aimed to disentangle crustacean larvae diversity in the central areas of Segara Anakan Cilacap, Central Java, Indonesia. The COI gene was processed in Genetika Science Indonesia and 1st BASE Asia Malaysia for species barcoding. The sequences were edited and aligned manually in the bio edit package. Homology and sequence divergences were obtained for similarity tests using a basic local alignment search tool to the reference sequences in the database. The genetic threshold for species delineation was 5% divergence or 95% homology. We reconstructed the phylogenetic tree by applying maximum likelihood and neighbor-joining algorithms based Kimura 2-parameter substitution model in the MEGAX software. Eleven crustacean larvae were successfully barcoded and delineated into eleven species. Eight of eleven morphotypes were convincingly identified at a species level due to low divergence from the reference species. The three remaining morphotypes could be assigned only to the genus level because of high genetic divergence. Their monophyly determined their morphotypes' assignment to specified taxa in the phylogenetic tree.  The COI gene is a good marker for species delineation of crustacean larvae. Eleven freshwater, brackish water, and marine water crustacean use central areas of the Segara Anakan estuary as a nursery ground. This study is the first report about crustacean larvae diversity in the central regions of Segara Anakan Cilacap, Central Java, Indonesia. The data implied that Segara Anakan is an essential source of recruit for the surrounding ecosystem and a high priority for conservation.


Keywords: barcoding, homology, larvae, nursery, threshold.

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