Research efforts on whale sharks have so far been limited to sub-adult males which make-up the vast majority of aggregations around the world. The movements of mature sharks, their reproductive techniques and key habitats remain poorly understood, whilst details of this demographic group are the most important to mitigate current threats. This quandary qualifies the use of indirect analyses such as genetic inference to characterise cryptic life-stages of the species. Tissue samples will be collected from free-swimming whale sharks from locations around the WIO with past biopsy efforts providing additional tissue from every tropical ocean. Photographic identification, approximate visual size and gender information will be recorded for each individual. Microsatellite markers will be extracted from the samples using species-specific primers from previous studies. Additional open access sequences will be obtained via GenBank for appropriate locations. Software packages simulating modes of inheritance such as GERUD will be used to reconstruct parental genotypes. This is an outline of potential results of the study. Parental genotype reconstruction can provide information on: 1) Number of parents per litter – maternal genotypes will be reconstructed first as the likelihood of sampling littermates is higher than sampling offspring from different females who happened to mate with the same male. Paternal genotypes can be determined once the maternal genotypes are removed from the progeny sequences. 2) Juvenile recruitment – survival rate of individuals per litter, considering however that juvenile female whale sharks are underrepresented in the majority of sampling areas. Incomplete reconstruction of a parental genotype suggests incomplete offspring sampling. 3) Reproductive mode – i.e. monoor polyandry, demonstrated by single or multiple male genotypes per litter (respectively), which may confirm or refute the single only other demonstration of reproductive mechanism, monandry, in the species. 4) Breeding site fidelity – common and complete parental genotypes of either or both parents within an aggregation or in associated areas (assuming monandry) suggests that whale sharks return to or remain in a common area to pup whereas multiple incomplete genotypes may suggest random dispersal from any given pupping site. The reproductive patterns of mature sharks, as inferred by these analyses, will define whale shark movements within their circumglobal range and may highlight important habitats such as breeding or pupping grounds. Resources for protecting the species will be limited and so must target these groups and areas to be most effective at mitigating threats and conserving the species.


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