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Background Off Mafia Island, Tanzania, whale sharks are seen in a small bay that also boasts one of the country's largest coastal fisheries. We set out to determine the population structure of whale sharks here, examine their feeding behaviour and residency, and investigate the interaction between the sharks and fishers. Approach We conducted 261 boat-based surveys at Mafia Island between Oct 2012 and Dec 2015, recording all whale shark sightings as well as counting the numbers of tourist and fishing boats in the survey area during each trip. We estimated shark size visually and with laser photogrammetry and recorded sex, scars and behaviour of each shark. To examine residency, we deployed 67 acoustic tags on whale sharks and 19 receiver stations within the bay, and analysed recapture probability (both visual- and acoustic-based) with generalised additive mixing models. To investigate feeding plankton biomass and community structure, we collected 20 plankton samples when whale sharks were feeding and 202 background samples for comparison. We interviewed fishers and they recorded their fishing locations using a GPS. Results We identified 129 different whale sharks at Mafia Island, 54% of which were resighted in two or more years. Tagged sharks were acoustically detected throughout the year even though sightings were largely limited to Oct-Mar. Sharks ranged in total length from 2.5–9.7 m, were mostly male (87%), and were usually seen feeding (75%) at or near the surface. Dense patches (25 mg m–3) of large sergestids Lucifer hanseni prompted feeding, while background plankton tows were dominated by small copepods (2.5 mg m–3). Small and medium-sized planktivorous fishes also fed on the same patches of sergestids, often together with whale sharks. These smaller species were the main target of the local fishers. Fishing boats operated in the survey area on 90% of the time, but also made catches further afield. Fishers reported a conflict between whale sharks and their fishing operations on 36% of the time, although sharks were usually released from the nets without injury. A mean of 2.6 tourist boats per day searched the same survey area for whale sharks. Conclusions This small, resident group of whale sharks is routinely exposed to tourists, boat traffic and high fishing pressure. Whale sharks are commonly encircled in fishing nets and released, but scars indicate that they do occasionally get injured during this process. Mortalities are rare, based on interviews with fishers and long-term observers. Whale sharks at Mafia Island are unusually resident and face clear local threats. No defined management measures are currently in place, but we present some potential strategies for mitigating threats to whale sharks here.

Background A recent global study of whale shark population genetics has allowed for better understanding of genetic connections between aggregations in both the Indo-Pacific and Atlantic. This overview included an aggregation found within the Red Sea near Al Lith, Saudi Arabia, however the Mafia Island, Tanzania, aggregation was not part of the study. The ecological behavior of these aggregations differs with the Saudi Arabian individuals showing strong seasonality, while acoustic telemetry data revealed cryptic residency at Mafia Island. Approach Genetic analysis using 11 microsatellite markers was performed on whale sharks from both locations. A combination of primers sourced from previous studies and newly designed primers were used to compare both aggregations and the individuals within. The Red Sea population was compared between 5 seasons spanning 6 years from 2010–2015. The Tanzanian population was compared for 2 field seasons from 2012–2014. Temporal genetic diversity was examined using allelic richness on only the Saudi Arabian individuals due to a short sampling period in Tanzania. Kinship for both aggregations was tested using COLONY and KINALYZER. Results Over a 6 year period, genetic diversity in the Red Sea showed no significant change. Contrasting to other whale shark aggregations, allelic richness in the Red Sea shows no sign of reduction. Kinship analysis using COLONY found two potential sibling pairs in Tanzania. One pair had a high probability (.993) of being a full sibling dyad while the other had a lower probability (.357). There were no sibling pairs identified in the Red Sea. Conclusions The lack of significant change of genetic diversity in Al Lith, Saudi Arabia, differs from a trend at Ningaloo Reef, Australia that showed a decrease in genetic diversity. Although these differences could be driven by location, this should encourage further long term genetic sampling at aggregations to better understand whale shark population trends. The potential of sibling pairs being found within one aggregation warrants further investigation into kinship within and between aggregations throughout the Indo-Pacific.