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- Materials and methods
Several other shark species lend themselves to such individual identification techniques, including the raggedtooth shark Carcharias taurus (Rafinesque 1810), also known as the grey nurse or sand tiger shark, which is a large brown shark with distinct spots or pigment marks on the flanks (Compagno 2001). Ireland (1984) first documented use of the pigment spots on the flanks of C. taurus in order to distinguish between two large males. Subsequently, Peddemors & Thurman (1996) and Allen & Peddemors (2001) successfully demonstrated that wild individual C. taurus could be distinguished using natural marks such as tears and notches in fins, fin spots and flank spots. The use of natural marks is also preferred over conventional tagging approaches because it is stressless, inexpensive and reliable over a much longer period, features that are particularly suited to species that are of conservation interest. World-wide, C. taurus is currently listed by the IUCN as vulnerable (Pollard & Smith 2000) and off the east coast of Australia as critically endangered (Pollard et al. 2003), while on the South African coast it is currently listed as not threatened.
In this paper we present a system of pattern-matching using the pigment marks or spots on C. taurus. Although a computer-aided identification system has already been reported for whale sharks (Arzoumanian, Holmberg & Norman 2005), our system allows simpler, yet more rapid, data entry and matching by allowing the user to select the key pattern features at the outset. This approach improves accuracy considerably, reduces processing time and allows analyses of larger databases than those that have been used to date.
- Top of page
- Materials and methods
The natural pigment marks on the flanks and their relative arrangement forms the basis from which identifications are made using the I3S software. The identifications were tested using 221 individually recognizable C. taurus. The ability to identify individuals with less than perfect representative images is of enormous benefit to field workers studying free-ranging animals in challenging marine environments, such as those off the South African east coast.
The identification algorithm is based on a two-dimensional affine transformation that assumes that a shark is a linear, rigid, two-dimensional object. Ideally, photographs should be taken at right angles to the shark's side, but even imperfect photographs taken at an oblique angle provided a correct match, thereby reducing the potential heterogeneity bias often associated with photo-identification studies (Hammond 1990). Correct identification would still be jeopardized if the body of the shark was flexing or turning. Nevertheless, even with imperfect images, the system has proved to be a useful identification aid, provided that the user is extremely critical of the suggested matches and verifies matches using other features. In studies with dolphins, well-marked individuals are often recognized by more than one feature, which may include a combination of attributes such as marked fins, shape of fin, shading patterns, scrapes, scratches and wound marks, as well as pigment patterns (Würsig & Jefferson 1990; Karczmarski & Cockcroft 1998). The investigator can then use other features, such as fin shape and notches, tears, scars and spots in the fin and, in adult male sharks, clasper size and form, to identify individual sharks. The pigment spots on C. taurus are largely unchanging over successive years, and can be traced from year to year, as illustrated by the example shown in Fig. 3. In this example, the tip of the first dorsal fin is unusually squared-off and serves as a double mark.
The key feature of the software is that it is not fully automated. The user must point out the reference points, which in the case of C. taurus are the fin origins, and the most distinctive marks. Finally, the user must select the best match from a ranked list of possible known shark images. As the user manually points out the natural marks, image artefacts such as particle reflection in the water, backscatter from incorrect flash position and flash overexposure of the flanks, can be ignored. Only those natural marks that can be clearly discerned by the human eye are selected, thereby ensuring the best possible choice. Additionally, the use of this software is beneficial as a clear image focus is not as stringent a requirement for spot patterns as it would be for other natural marks, such as notches and tears in fins. We believe that this is more beneficial to correct identification of individuals and represents a preferable option over the system reported by Arzoumanian, Holmberg & Norman (2005).
We found that pattern-matching performance improved with a greater number of reference images against which comparisons could be made. Thus the image catalogue should include at least three good-quality images of each individual for efficient identification. In many historical studies of photo-identification, only the best quality images are retained as the reference material because of limited storage capacity for photographs. The use of I3S therefore may require a larger catalogue of images to be maintained, but as it is all digital and the software searches the entire catalogue, irrespective of the order of image storage, we believe that a typical modern computer hard-drive would provide ample storage space.
Ideally, photographs of both sides of the animal should be obtained (Würsig & Jefferson 1990) but this is not always possible. We elected to consistently photograph the left side to avoid any possible confusion. Although the current application was specifically tailored to use only the left side of the animal, it is a simple step to include both sides of the animal in future versions. The recognition performance could be further enhanced by making a distinction between males, females and animals of unknown sex. Sex is difficult to determine in small individuals, when the claspers of the male may not yet be clearly distinguishable, or if the angle of the photograph does not allow the claspers to be seen.
An added benefit of our system is that only one computer-based package is required and the entire process, from image download, spot selection and matching, requires less than 5 min if the shark already exists in the database. If a new shark is recorded that has not been previously identified, then a more rigorous visual inspection of the database is necessary but still will be completed in a substantially shorter time than reported for other identification software packages (Arzoumanian, Holmberg & Norman 2005).
The I3S software therefore would be a useful tool for long-term studies that inevitably include large databases. The non-invasive nature of photo-identification mark–recapture studies makes them ideal for assisting in population estimates of critically endangered species such as C. taurus on the east coast of Australia (Otway, Bradshaw & Harcourt 2004). In this study at Aliwal Shoal, use of the I3S software substantially eased the process of correctly identifying individuals and allowed an estimation of the numbers of animals visiting the reef each year.
Additionally, this software can assist in obtaining more detailed data on the movements and residency status of individual animals. This study highlights the apparent philopatric nature of C. taurus to a particular reef system, with individuals apparently returning on a near-annual basis to this reef. Whether the Aliwal Shoal serves as a critical habitat for individuals of C. taurus, and thus may influence the entire population, requires confirmation of the nature and regularity of visits to the reef with more substantial data capture effort. Nevertheless, this work highlights the importance that protection of individual reefs may have for conservation of the species. The I3S software may then serve as an important tool in assuring accurate data analysis in international efforts to protect particular species (such as C. taurus) through proclamation of marine protected areas.
In its present form, the system has only been rigorously used and tested with C. taurus. The possibility that natural markings on the sharks may fade or change over time does not appear to be a concern. Even with intervals of several years between photographs, the sharks can generally be readily distinguished. Potentially the system could be adapted for other similarly shaped animals with spots (or other consistent features). Indeed, trials with tiger sharks and the shorttail stingray Dasyatis brevicaudata are being considered, while current tests with whale sharks are extremely promising (Speed, Meekan & Bradshaw 2007).