Abstract
The whale shark Rhincodon typus is found throughout the world's tropical and warm‐temperate ocean basins. Despite their broad physical distribution, research on the species has been concentrated at a few aggregation sites. Comparing DNA sequences from sharks at different sites can provide a demographically neutral understanding of the whale shark's global ecology. Here, we created genetic profiles for 84 whale sharks from the Saudi Arabian Red Sea and 72 individuals from the coast of Tanzania using a combination of microsatellite and mitochondrial sequences. These two sites, separated by approximately 4500 km (shortest over‐water distance), exhibit markedly different population demographics and behavioral ecologies. Eleven microsatellite DNA markers revealed that the two aggregation sites have similar levels of allelic richness and appear to be derived from the same source population. We sequenced the mitochondrial control region to produce multiple global haplotype networks (based on different alignment methodologies) that were broadly similar to each other in terms of population structure but suggested different demographic histories. Data from both microsatellite and mitochondrial markers demonstrated the stability of genetic diversity within the Saudi Arabian aggregation site throughout the sampling period. These results contrast previously measured declines in diversity at Ningaloo Reef, Western Australia. Mapping the geographic distribution of whale shark lineages provides insight into the species’ connectivity and can be used to direct management efforts at both local and global scales. Similarly, understanding historical fluctuations in whale shark abundance provides a baseline by which to assess current trends. Continued development of new sequencing methods and the incorporation of genomic data could lead to considerable advances in the scientific understanding of whale shark population ecology and corresponding improvements to conservation policy.
Highlights
The whale shark, Rhincodon typus Smith 1828, has often been described as an enigmatic species (Rowat & Brooks, 2012)
In Arlequin v3.5 (Excoffier & Lischer, 2010), each sampling site was treated as a population and genetic structure was tested with analysis of molecular variance (Nei & Jin, 1989) with 10,000 permutations, using the T92+G substitution model (Tamura, 1992) with a gamma shape parameter of 0.48 (Appendix S1: SI 4)
This study provides the first mitochondrial and microsatellite sequences from the Mafia Island aggregation site in Tanzania and nearly quadruples the sample size from the Shib Habil aggregation site in the Saudi Arabian Red Sea
Summary
The whale shark, Rhincodon typus Smith 1828, has often been described as an enigmatic species (Rowat & Brooks, 2012). Most whale shark population and movement ecology studies are based on photo-identification (Araujo et al, 2014; Cochran et al, 2016; McKinney et al, 2017; Norman, Holmberg, et al, 2017; Robinson et al, 2016; Rohner et al, 2015) and/or telemetry (Berumen et al, 2014; Cagua et al, 2015; Cochran et al, 2019; Hueter et al, 2013; Norman, Whitty, et al, 2017; Robinson et al, 2016) While these methods have been successfully used to describe local population structure and to track movements within, between, and away from aggregation sites, they are limited by their focus on known aggregations (Sequeira et al, 2012). These networks map the genetic similarity of sampled sharks based on mitochondrial sequences and can be used to identify geographic patterns in the molecular data
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