Masters by research
College of Science and Engineering
Masters by research
College of Science and Engineering
Sharks in time: exploring the effects of time on sharks and implications for sampling methods.
Martina is an international student, currently enrolled in a Master by Research program at James Cook University. After graduating from a scientific-focus high school in Italy, she joined a volunteer project in Fiji for 6 months, working on shark conservation and monitoring, habitat restoration and community engagement. Martina then enrolled in a science degree, majoring in Marine Biology at James Cook University. During her undergraduate degree, she volunteered and worked on research projects at JCU and abroad, in different fields. She worked as a dive guide of the Great Barrier Reef and as a volunteer in ornamental fish husbandry and in behavioural studies of fish embryos. While studying abroad in Scotland, Martina learned honours-level statistical skills, working on modelling, sampling design and surveying techniques for temperate/semi-polar marine and terrestrial ecosystems. Such knowledge was further developed during a two-week field trip to South Africa with an Italian research team, investigating the predatory behaviour of great white sharks. While in South Africa Martina learned several new field techniques for shark research, such as photographic identification, behavioural observation, tissue sampling, and traditional shark tagging. During her last semester of university, Martina volunteered on Orpheus Island for coral genetics studies and worked in the Global Fin Print Project in the Fish and Fisheries Lab. (with dr. Colin Simpendorfer and dr. Andrew Chin). In past two years, Martina worked as a dive instructor and a dive leader on the Crown of Thorns (COTs) Control program. Working for the COTs Control Program, she planned dives strategically to tackle priority zones for culling, leading a team of four to eight divers through the planned zones. This job helped her gain important leadership skills, people management skills, teamwork, problem-solving and critical thinking, which were applied every day to investigating COTs distribution and best practices to reach culling targets. While based on land, Martina worked as a volunteer in the Fish and Fisheries Lab. and in the Rummer Lab. with the physio-shark project. Working with dr. Andrew Chin and dr. Jodie Rummer, Martina learned valuable research skills, fieldwork and practical laboratory and epaulette shark’s husbandry. Since enrolling in an MPhil degree, Martina’s research focuses on elasmobranchs conservation adopting new technologies such as artificial intelligence and remotely operated underwater vehicles, to improve field sampling for shark research.
Sharks in time: exploring the effects of time on sharks and implications for sampling methods.
2021 to 2023
This project will examine the effects of time on aspects of shark morphology and behaviour, and the implications of these variations for shark sampling methods and the interpretation of the data they provide. By looking at four examples of sampling methods, this study will examine how time affects the data collected.
The first technique examined in this study is a popular non-invasive sampling technique: photographic identification. Although proven to be successful for certain species (Sherman et al., 2018) the unique natural markings used to identify individuals might not persist through time. The need to verify the consistency of markings over time has been previously raised (Sherman et al., 2018). With an applied case study on Hemyscillium oceallatum, this study will evaluate the viability of photo-ID for long-term sampling of elasmobranchs.
Another technique commonly used in shark science for behavioural and abundance data is Underwater Visual Surveys (UVS), often performed on scuba. This type of sampling is often limited to short periods of time and good weather conditions, which could result in misrepresentative or highly selective data. Indeed, shark and ray populations can remarkably change in different seasons even in tropical regions where temperature has limited fluctuations, and across different years. This project further examines the effect of time on data collected through UVS, looking at changes of species and population composition on the Great Barrier Reef. Finally, elasmobranch research is mostly relying on daytime sampling, and shark researchers have been questioning whether current knowledge truly represents elasmobranch’s abundance and behaviour. This project will provide an insight on the effect of time-of-the-day (day vs night surveys) on data collected, comparing daytime surveys with night time surveys using remotely operated underwater vehicles (ROV), with daytime comparative data collected using UVS.
Shark research is inherently limited by temporal constraints. Often, study sites are accessible only in good weather conditions, or for a limited window of time due to financial and logistic constraints. Some species of sharks can only be studied during periods of aggregation, tags for telemetry studies can track the sharks for a limited number of years, and researchers are restricted to daylight hours to perform underwater activities such as diving. For this reason, data collected from traditional field methods may only represent abundance and behaviour at very specific times, and the effects of these limitations are not well understood. This project will examine how time affects shark morphology and behaviour, and how variations could affect the accuracy of shark sampling methods and the interpretation of the data they provide. By looking at four examples of sampling methods for shark research, this study will examine how time affects the data collected.
An increasingly popular and minimally invasive technique for sharks and rays research is photographic identification, but few studies have validated the assumptions behind this technique (Meenakshisundaram et al., 2021). Indeed, photo-ID relies on the persistence of distinctive, natural patterns through time, to be able to identify the same individual in consecutive years (Pierce et al., 2019). Nevertheless, while well studied, long-lived species such as whale sharks and manta rays shown persistent individual markings (Marshall et al., 2012) researchers have raised the need to validate the long-term persistence and consistency of the individual markings used for other species (Sherman et al., 2018). With the help of artificial intelligence technologies, this project will quantify how unique spot patterns can identify different individuals of Hemiscyllium ocellatum and examine the change of their patterns through time. Results from this study will help validate photo-ID as a method for collecting accurate long-term population data.
Another issue to consider is how the timing of a survey may influence the data collected. A widely applied field technique in shark research is Underwater Visual Surveys (UVS). However, these studies tend to report data from periodic visits in many causes study site visits are only visited once per year (Robbins et al., 2006; Stevenson et al., 2007; Sandin et al., 2008). There are few data available to assess whether the local abundance of sharks detected by UVS varies across a year, and thus, how the timing of an annual survey could bias the data collected. This study will use two years of fine-temporal scale UVS data to explore how local shark abundance at fixed sites on the Great Barrier Reef (GBR) changes over different seasons. Additionally, some species of reef sharks have been shown to be in sharp decline in the Great Barrier Reef (Heupel et al., 2009; Robbins et al., 2006) and the need for long-term continuous records of shark populations has been raised by managers to see if declines have stabilised since management interven6ions were introduced (Great Barrier Reef Outlook Report, 2019). This project will provide an assessment of the composition and relative abundance of shark populations in the GBR, comparing UVS data collected in 2020 and 2021 with 10-years old data. Results will provide an insight into the importance of temporal knowledge gaps in elasmobranch research.
Finally, field sampling for behavioural and abundance studies on elasmobranchs is usually performed during the day, with limited data collected during crepuscular and nocturnal hours. For this reason, our current knowledge of sharks and rays might be biased and misrepresentative (Hammershlag et al., 2017). Using new technologies, such as remotely operated underwater vehicles (ROVs), this project will examine the potential to use ROVs to sample elasmobranch species, evaluating the effect of time of the day (diurnal vs nocturnal) on the data collected.
AIM 1: Understanding how time can affect accuracy of photographic ID studies. A case study for Hemiscyllium oceallatum photo-ID with applied artificial intelligence technology.
- Past and current pictures of captive and wild Epaulette sharks (Hemiscyllium oceallatum) have been collected, edited, and masked ensuring the best quality for software processing. Pictures have been arranged in folders according to time, in a way that the same shark will have different folders containing pictures form consecutive times.
- With the help of a co-investigator, an artificial intelligence has been trained to recognise individual sharks based on distinctive spot-patterns characteristic of this species but unique to the individual shark.
- the artificial intelligence is trained to evaluate the baseline accuracy (50% and above accuracy is considered adequate for this study)
- Once baseline accuracy has been evaluated, the artificial intelligence will help finding whether small changes in the spot-patterns of individual sharks occur.
- This method can be used to validate photo-ID methodologies ofr different shark speices.
AIM 2: using UVS sighting data to understand how different time of the year can affect shark and ray populations composition.
At this stage, preliminary data have been collected during culling dives by the COTs Control Program divers. Such data include species, size, sex, evident mating scars, time of the day, reef ID, and zone, and all data have been standardised by effort (e.g., CPUE). These data allow cross-layered analyses, recording sharks and rays across seasons, reef aspects (North, South, East, West), reef habitat (crest, flat, lagoon, slope, base), and reef zonation (green, blue, yellow). Culling dives are methodically performed every day, 4 times per day, across target reefs, which are divided in zones approximately rectangular and 500-700 meters long and placed as a grid on the reef map. During culling dives, divers are spread in a line of 8 people, 2.5m apart from each other and progressing along the zone. Data on sharks and rays are recorded at the end of each dive, associated with the zone targeted and the time of the day. This method resembles Underwater Visual Census methodology. Predicted results will show changes across different times of the year in population composition (male vs female, juvenile vs adults within the same species) and/or species composition. Such changes are likely correlated to changes in water temperature, and other abiotic factors.
AIM 3: using UVS sighting data to evaluate how the structures of shark and ray populations have changed through time, addressing the impact of temporal knowledge gaps for conservation.
At this stage, preliminary data have been collected during culling dives by the COTs Control Program divers. Such data include species, size, sex, evident mating scars, time of the day, reef ID, and zone, and all data have been standardised by effort (e.g., CPUE). These data allow cross-layered analyses, recording sharks and rays across seasons, reef aspects (North, South, East, West), reef habitat (crest, flat, lagoon, slope, base), and reef zonation (green, blue, yellow). Culling dives are methodically performed every day, 4 times per day, across target reefs, which are divided in zones approximately rectangular and 500-700 meters long and placed as a grid on the reef map. During culling dives, divers are spread in a line of 8 people, 2.5m apart from each other and progressing along the zone. Data on sharks and rays are recorded at the end of each dive, associated with the zone targeted and the time of the day. This method resembles Underwater Visual Census methodology. Such data will be compared to existing past data to observe changes in population composition and species composition across similar reefs in the past 10.
AIM 4: Comparing diurnal underwater surveys and nocturnal underwater surveys of elasmobranchs. Understanding the effect of time-of-the-day on the accuracy of behavioural and abundance data.
After appropriate training in the handling and care of ROVs, the primary investigator and a group of trained volunteers will perform underwater surveys on scuba during the day, and ROV underwater surveys during the night time, from three different locations across different latitudes on the GBR.
Data collected will be standardised by effort and quantitatively and qualitatively compared to understand differences between diurnal and nocturnal sampling for elasmobranchs, aiming to control for additional factors which might bias the results (e.g. as tourists presence during the day, or full moonlight).
Results for AIM 1: Preliminary data on the identification of H. ocellatum has shown good results: the artificial intelligence designed to identify epaulette sharks has reported a 67% accuracy from the baseline accuracy test. The baseline accuracy test is fundamental to reliably observe minor changes in spot patterns from future pictures of the same individual. We predict no detectable change in epaulette sharks spot patterns for the duration of this study. However, the artificial intelligence designed for this study could be successfully applied to different species, and for longer studies, to detect changes in spot patterns. This tool will provide an easier, standardised method for validating photographic identification as a reliable tool for assessing shark and ray populations through time.
Results for AIM 2 and 3: preliminary data on sharks and rays sightings show different patterns of species composition, population structures and overall distribution across reefs, at different times of the year, possibly influenced by surface water temperature and atmospheric pressure. This suggests not only how fluctuating abiotic factors can influence shark and ray distribution in the tropics, but most importantly how the time of the year can have a major impact on the accuracy of data collected through UVS. Furthermore, considering previous studies reporting declines in shark and ray populations of the GBR, this study will show such decline through the comparison of UVS data from present days with 10-year-old data from previous studies. These results will highlight the effects that time has on data collection for sharks and rays populations, within the same year and after a 10 year period. This supports the importance of detailed, fine-scale and constant sampling to obtain an accurate picture of the sharks and rays population status on the GBR.
Results from AIM 4:
Training and practice will be required for operating the ROV at night-time, due to predicted challenges in operating such technologies. The sampling design is still to be defined but, considering the cryptic nature of elasmobranchs, we predict small sample sizes for sharks and rays sightings during ROV underwater surveys at night and during daytime surveys with scuba divers. Power analysis will help understand the minimum number of sightings needed for significance.
Communication / Education,
Quantitative marine science,
Sharks / Rays,
Stacy Bierwagen (AIMS)
Andrew Chin (James Cook University)
Rhondda Jones (James Cook University)