Appendix S1. Photo-ID sampling methods Describes photo-ID data collection for each aggregation site from The ecological connectivity of whale shark aggregations in the Indian Ocean: a photo-identification approach

Genetic and modelling studies suggest that seasonal aggregations of whale sharks (<i>Rhincodon typus</i>) at coastal sites in the tropics may be linked by migration. Here, we used photo-identification data collected by both citizen scientists and researchers to assess the connectedness of five whale shark aggregation sites across the entire Indian Ocean at timescales of up to a decade. We used the semi-automated programme I<sup>3</sup>S (Individual Interactive Identification System) to compare photographs of the unique natural marking patterns of individual whale sharks collected from aggregations at Mozambique, the Seychelles, the Maldives, Christmas Island (Australia) and Ningaloo Reef (Australia). From a total of 6519 photos, we found no evidence of connectivity of whale shark aggregations at ocean-basin scales within the time frame of the study and evidence for only limited connectivity at regional (100-1000km) scales. A male whale shark photographed in January 2010 at Mozambique was resighted eight months later in the Seychelles and was the only one of 1724 individuals in the database to be photographed at more than one site. On average, 35% of individuals were re-sighted at the same site in more than one year. A Monte Carlo simulation study showed that the power of this photo-ID approach to document patterns of emigration and immigration was strongly dependent on both the number of individuals identified in aggregations and the size of resident populations.