Pieces in a global puzzle: Population genetics at two whale shark aggregations in the western Indian Ocean

• Published in: Ecology and evolution Vol. 12; no. 1; pp. e8492 - n/a
• Main Authors: Hardenstine, Royale S., He, Song, Cochran, Jesse E. M., Braun, Camrin D., Cagua, Edgar Fernando, Pierce, Simon J., Prebble, Clare E. M., Rohner, Christoph A., Saenz‐Angudelo, Pablo, Sinclair‐Taylor, Tane H., Skomal, Gregory B., Thorrold, Simon R., Watts, Alexandra M., Zakroff, Casey J., Berumen, Michael L.
• Format: Journal Article
• Language: English
• Published: England John Wiley & Sons, Inc 01.01.2022; John Wiley and Sons Inc; Wiley
• Subjects: Agglomeration; Aquatic mammals; Demographics; Demography; Deoxyribonucleic acid; DNA; Ecology; Environmental policy; Ethanol; Fish populations; Gene mapping; Gene sequencing; Genetic diversity; Genetics; Geographical distribution; global population structure; Haplotypes; Identification; Markers; microsatellites; Mitochondria; mtDNA; Nucleotide sequence; Ocean basins; Population ecology; Population Genetics; Population structure; Rhincodon typus; Sharks; Software; Telemetry; Saudi Arabia; Indian Ocean; Mafia Island; Tanzania; Red Sea; Australia; Western Australia Australia; microsatellites; genetic diversity; global population structure; Rhincodon typus; mtDNA
• ISSN: 2045-7758; 2045-7758
• DOI: 10.1002/ece3.8492

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. This study adds samples from whale sharks in two understudied regions, describes new microsatellite markers, proposes an incremental improvement to mitochondrial analysis, and provides a point of comparison to previous results from other aggregations. We include the first genetic sequences for whale sharks from the Mafia Island, Tanzania aggregation, and nearly quadruple those available from the Saudi Arabian Red Sea. These sequences were analyzed alongside 699 publicly available sequences from other aggregations. Our results demonstrate that our two study aggregations are derived from the same source population, despite strong ecological differences shown in previous work.