Population Genetics of Whale Shark (Rhincodon typus) in Qatar.

Abstract

The whale shark (Rhincodon typus), the largest extant fish, listed as endangered on the IUCN Red list, forms one of its most significant feeding aggregations around the Al Shaheen oil field in Qatar. Despite its ecological importance, limited information exists on the genetic diversity and population structure of these aggregations in Qatar. This study used mitochondrial DNA (mtDNA) markers to assess the genetic diversity, population structure, and connectivity of whale sharks in Qatari waters with global populations. A total of 108 tissue samples were collected during the aggregation seasons of 2023–2024, which yielding 88 high-quality sequences. The net sequence length obtained for the consensus sequences was 1,303 bp after cleaning, trimming, and alignment. Analysis revealed high haplotype diversity (Hd = 0.977) and nucleotide diversity (π = 0.288), with 68 distinct haplotypes, higher than previously reported in the region. Phylogenetic analyses revealed five unique lineages, with strong genetic connectivity across several geographic regions worldwide. Also, one unique lineage, though not drastically different from other clades, was found which was not represented in the global database. This genetic divergence may result from mutations, varying environmental pressures, or distinct evolutionary histories. Alternatively, this clad could arise from the fact that the incomplete global database of whale shark sequences, with poor representation from certain regions. Overall, our findings support the hypothesis of a broadly connected Indo-Pacific population and emphasize Qatar’s role as a key genetic reservoir. Continued genetic monitoring using broader regions is recommended to support conservation of this endangered species. The study also highlights the significance of Qatar’s habitats and conservation initiatives in supporting the long-term survival of the whale shark’s global populations, as aggregations in Qatar represent a large population converging from diverse geographic regions and genetic lineages.