The genetic relationships and indo-pacific connectivity of whale sharks (Rhincodon typus) with particular reference to mitochondrial COI gene sequences from Cendrawasih bay, Papua, Indonesia

Cenderawasih Bay, in the Birdhead Seascape of Papua, is a favorable habitat for whale sharks (Rhincodon typus). They are frequently sited in this large open Bay but little is known about their genetic characteristics and their connection to whale shark populations in other parts of the world. The study reported in this paper was conducted to characterize the nucleotide sequences of the COI gene fragment in whale sharks from Cenderawasih Bay, and to compare these with sequences held in GeneBank for the COI gene fragment obtained from 27 whale sharks sampled around the Indian and Pacific Oceans. A total of 28 meat samples of whale shark in the Bay were collected by a biopsy punch attached to a pole spear. The DNA of the meat samples was extracted to obtain whole genomes which were then amplified and sequenced to identify nucleotides of the COI gene fragments of the mitochondrial DNA. The size determined for the COI gene fragment from all Cenderawasih Bay samples was 669 bp, consisting of A = 26.5, T/U = 30.5, C = 28.3, dan G = 14.7. In total, there were 41 cutting sites obtained for each of the 28 sequences, ranging in length from 5 to 7 bp. One COI single nucleotide polymorphism and two haplotypes were identified within the Cenderawasih Bay population. A single site substitution change from T to C was observed for both haplotypes. Overall, the haplotype diversity (Hd= 0.137) and nucleotide diversity (�=0.0002) were relatively low. Differences were detected in the nucleotide composition, number and arrangement in the COI sequences obtained from Cenderawasih Bay compared with the other IndoPacific COI gene fragment sequences deposited in GenBank. This study makes a contribution to our understanding of the molecular systematics, phylogeography, genetic differentiation and conservation genetics of the whale shark (R. typus). © 2020 Elsevier B.V., All rights reserved.