Close genetic relatedness of whale sharks, Rhincodon typus in the Indo-Pacific region

The whale shark is a key species in the bay, with a rich marine life, including at least 500 species of fish, more than 1,000 species of invertebrates, and a variety of turtles and marine mammals. The genetic diversity of whale sharks in Cenderawasih Bay was evaluated using mitochondrial DNA. Tissue samples were collected from 31 whale sharks in November 2012, April 2013, and June 2013. The samples were preserved in 96% ethanol and stored at 4°C in the laboratory until DNA extraction. The mitochondrial DNA was extracted using Chelex 5-10% and amplified using the Hot start and Gold program with the modified protocol of Barber & Erdmann (2000) and the primer FISH-BCH and FISH-BCL. The amplified products were visualized by electrophoresis with agarose gel 1% and purified using Shrimp Alkaline Phosphatase and Exonuclease. The COI mtDNA was sequenced using Big Dye chemistry and purified using isopropanol precipitation. The sequence data was edited using the automatic sequencer ABI 377 and Mega5. The nucleotide composition of the COI gene was analyzed using Mega5, with a similarity percentage of 22.27% for C, 32.28% for T, 29.64% for A, and 15.83% for G. The genetic diversity of whale sharks in Cenderawasih Bay was found to be low, with a haplotype diversity of 0.1871 and a nucleotide diversity of 0.00244. The genetic lineage estimation was 0.00004 for St, 0.00659 for GammaSt, and 14.82 for Nm. The mismatch distribution was not significantly different between observation and expectation. The genetic diversity and relatedness of whale sharks in Cenderawasih Bay were compared with those of whale sharks in other regions, including the Indian Ocean and Western Pacific Ocean. The neighbor-joining tree for individual whale sharks from Cenderawasih Bay and other regions showed that the whale sharks in Cenderawasih Bay were closely related to each other and to whale sharks in other regions. The genetic diversity of whale sharks in Cenderawasih Bay was similar to that reported in other studies, indicating a low genetic diversity. The genetic diversity of whale sharks in other nearby areas was also low, indicating a degree of connection within the regional group. However, the genetic diversity of whale sharks in the Atlantic Ocean was higher than that in Cenderawasih Bay. The distribution of haplotypes among whale sharks in Cenderawasih Bay and nearby areas in the Indian Ocean and Western Pacific Ocean indicated a low genetic diversity. The genetic diversity of whale sharks in Cenderawasih Bay was similar to that reported in other studies, indicating a low genetic diversity. The genetic diversity of whale sharks in other nearby areas was also low, indicating a degree of connection within the regional group. The neighbor-joining tree for individual whale sharks from Cenderawasih Bay and other regions showed that the whale sharks in C