Population genetic structure of Earth's largest fish, the whale shark (Rhincodon typus)

Abstract

Large pelagic vertebrates pose special conservation challenges because their movements generally exceed the boundaries of any single jurisdiction. To assess the population structure of whale sharks (Rhincodon typus), we sequenced complete mitochondrial DNA control regions from individuals collected across a global distribution. We observed 51 single site polymorphisms and 8 regions with indels comprising 44 haplotypes in 70 individuals, with high haplotype (h = 0.974 +/- 0.008) and nucleotide diversity (pi = 0.011 +/- 0.006). The control region has the largest length variation yet reported for an elasmobranch (1143-1332 bp). Phylogenetic analyses reveal no geographical clustering of lineages and the most common haplotype was distributed globally. The absence of population structure across the Indian and Pacific basins indicates that oceanic expanses and land barriers in Southeast Asia are not impediments to whale shark dispersal. We did, however, find significant haplotype frequency differences (AMOVA, Phi(ST) = 0.107, P < 0.001) principally between the Atlantic and Indo-Pacific populations. In contrast to other recent surveys of globally distributed sharks, we find much less population subdivision and no evidence for cryptic evolutionary partitions. Discovery of the mating and pupping areas of whale sharks is key to further population genetic studies. The global pattern of shared haplotypes in whale sharks provides a compelling argument for development of broad international approaches for management and conservation of Earth's largest fish.

Phylogeographic mitogenomics of Atlantic codGadus morhua: Variation in and among trans‐Atlantic, trans‐Laurentian, Northern cod, and landlocked fjord populations

“…Unlike terrestrial and freshwater species that frequently exhibit strong population genetic structure from barriers to gene flow such as rivers, waterfalls, mountains, and deserts, marine species typically experience fewer and less formidable physical obstacles. While some species are restricted by habitat requirements or feeding habits (e.g., tropical reef fishes) and show clear population genetic structure (Shulman & Bermingham, 1995), pelagic species often have wide distributions, large population sizes, high fecundity, and extensive gene flow (Palumbi, 1992), and tend to display weak population structure in the absence of natal philopatry (Carr, Duggan, Stenson, & Marshall, 2015; Castro et al., 2007; Vis, Carr, Bowering, & Davidson, 1997; Ward, 1995). …”

Population genetics of Australian white sharks reveals fine-scale spatial structure, transoceanic dispersal events and low effective population sizes

“…However, genetic analysis contradicts assumptions of panmixia in some species, e.g. narrow-barred Spanish mackerel Scomberomorus commerson (Sulaiman & Ovenden 2010), Atlantic bluefin tuna Thunnus thynnus (Boustany et al 2008, Riccioni et al 2010) and whale shark Rhincodon typus (Castro et al 2007). Some marine species range widely to feed; during this phase, individuals of the same species will be admixed, spatial genetic population subdivision will be minimal and gene flow will be assumed to be high.…”

Population genetics of cobia (Rachycentron canadum) in the Gulf of Thailand and Andaman Sea: fisheries management implications

“…Cobia is well known for hitchhiking on large marine animals and migrating to long distances on its own (Shaffer and Nakamura 1989). Population genetic studies on whale sharks, a frequently observed hitchhiking host of cobia, have shown that whale shark migrations can cover vast distances (as much as 13,000 km) and that their population shows no marked structure between the Indian and Pacific Oceans (Castro et al 2007;Schmidt et al 2009). This behavior of cobia therefore has the potential to increase its migration range to include geographic regions separated by vast distances.…”