Small aquarium... wide research niche

The Shark Lab and Research Aquarium initially functioned as both a public aquarium and a unique research facility, offering South African and International students alike the opportunity to advance their academic careers. Most recently, this facility has realigned its focus and functions primarily as a research unit.

In a world where human pressure is threatening entire ecosystems, the need to understand the individual elements that make up such systems becomes progressively more urgent and the research required to achieve these goals, become paramount. Research projects conducted at the Shark Lab and Research Aquarium therefore are of great value to and dovetail with conservation efforts on an international scale.

A number of honours and masters projects have been completed at the Shark Lab and Research Aquarium. A project titled “Temperature Niche of Four Benthic Shark Species”, conducted by honours student R. Lombard, from the Department of Zoology and Entomology, University of Pretoria, aimed to show how benthic sharks react physiologically to ambient temperature changes in their environment by assessing respiration rates as an indicator of abiotic tolerance. An additional aim of this project was to ascertain if dissolved oxygen is the major driver of respiration as opposed to temperature, as well as to assess if any variations in responses occur amongst the three species used in the experiment. The species used, being the leopard cat shark (Poroderma pantherinum), pyjama cat shark (Poroderma africanum) and the puff adder shy shark (Haploblepharus edwardsii).

A second honours project, conducted by honours student, Monica Betts, also from the Department of Zoology and Entomology, University of Pretoria, was titled, “Intraspecific and Interspecific Interactions of Benthic Sharks”.

This study aimed to determine the interspecific and intraspecific interactions of benthic sharks through a series of manipulative laboratory experiments. These insights into how three otherwise similar benthic species interact in a captive setting under the same controlled environmental conditions, will hopefully inform on their inter-relationships in nature.

Questions posed for this project, considered the response of different individuals of conspecific sharks to the tank environment, the responses compared amongst the three species of benthic shark, the response of an individual shark in the tank environment to the presence of one, or more conspecifics, the response of an individual shark in the tank environment to the presence of one or more heterospecifics and how the findings of this study reflect on the likely interspecific relationships of the three benthic sharks in the wild

Current research projects at the Lab include amongst others, a Cognition experiment and a Tonic Immobilization study, as well as a project to determine the growth rates of select benthic shark embryos and a project looking at stress in select pelagic shark species. These species being the leopard cat shark (Poroderma pantherinum), pyjama cat shark (Poroderma africanum) and the puff adder shy shark (Haploblepharus edwardsii).

The tonic immobilization study examines various factors which may affect TI behaviour of three species of scyliorhindae. The aims of this study are to investigate differences in TI behaviour between dependant variables, such as success rate, time in tonic, time taken to go into tonic, and the tenseness or calmness of the individual specimens. These factors are then compared between various independent factors, which include species, gender, and size and respiration rate. Variation in responses is then used to critically compare and interpret the potential biological significance of this behaviour.

The Cognition project aims to assess the relative learning capabilities of the three benthic shark species already mentioned, using an open plan choice-based maze. These sharks are conditioned to distinguish a visually distinct colour, using food as a reward. Furthermore, the different species will be used to ascertain if differences in learning behaviour exists between benthic species.

Questions that were asked during this project included the following: Can these species of benthic shark be conditioned to associate a visually distinct colour by using food as a reward?  Is the ability to condition sharks to associate a visually distinct colour with food independent of shark species and is the duration that the conditioned response persists independent of shark species?

The aim of a very recent egg project is to gauge the growth rates of the embryos of select benthic shark species in different temperatures as well as the growth rate between these species. A minilogger is used to obtain the average temperature of ocean water in Mossel Bay to most accurately duplicate this temperature in the research tanks.

Over the previous two years, two masters projects have also been completed at the Shark Lab and Research Aquarium.

One of these projects, titled “Occupational patterns of sharks in Mossel Bay as a function of air and hydrostatic pressure”, looked at understanding the functional behavioral responses of the three previously mentioned benthic shark species as a result of the environmental factors. The researcher, Tristan Scott from the Department of Zoology and Entomology, University of Pretoria, wanted to demonstrate that movements in these species may be related to atmospheric pressure declines associated with approaching storms.

Dylan Irion from the University of Cape Town, also completed his masters titled “Identification of the Swimming Behavior of the common smooth hound shark (Mustelus mustelus) based on TriAxial Accelerometer Data”, at the Shark Lab and Research Aquarium.

Alan Jardine - Aquarium manager

The Ups and Downs (or Side to Sides) of Shark Research

If you’re reading this blog, chances are you’re well versed in the fate of the modern shark. Shark fin mafia, extinction, 38 million, ecosystem collapse, blah, blah, blah; there are a lot of buzzwords being thrown around by active and armchair conservationists alike. I don’t want to start any arguments so we’ll take a middle-of-the-road approach and just agree that these species are important, threatened, in need of much further research.

Historically we begin this research with direct (we say in situ) observations of the study species in their natural environment. Think Jane Goodall and her Gombe River Chimpanzees. From here we progress to higher order analyses with multidisciplinary syntheses and hypothesis testing (test tubes and bubbly liquids). The marine environment however, presents several unique challenges to this fundamental task. It’s bloody huge, often inaccessible, and the best visibility of 30 metres is but a fraction of some shark home ranges than can span thousands of kilometres. This is perhaps why we still know very little about many of the oceans inhabitants.

Fortunately though you are reading this from your shiny new iPad and we have made several advances in technology since Jane Goodall was out in the field. We can place tags on sharks that transmit their location to your very screen and find out just how they like to spend their weekends. As scientists, this allows us to shift our perspective from that of an outside observer and onto the animal itself. We remove the need to actually see the animal, and in turn remove many of those limitations to observation that I listed before.

This answers the ‘When’ and the ‘Where,’ but increasingly, scientists want to know the ‘Why,’ the ‘What,’ and the ‘How.’ So we put sensors on those tags. A current estimation identifies about 24 different types of available sensors measuring anything from temperature to heartbeat.

One such sensor, the accelerometer, allows for the detection of very fine scale movement. You’ve got one in your iPad and it is what detects the tilting and shaking of the screen when you play Temple Run. In the very same way, the accelerometers we place on sharks measure their tail movements and posture.

My work here at Oceans Research has been a ground truthing exercise whereby we test the ability of these accelerometers to measure shark tail beats, and from there extract specific swimming behaviours. Now that I’m into the final analyses before writing up the dissertation, I can show you how this is done.

After some manipulation, this is what I get from the sway axis of the accelerometer (the side to side movements). Essentially each peak and trough pair corresponds to one complete tail stroke cycle. So in the beginning we see some steady swimming, followed by a sweeping turn, some more steady swimming, and so on until the very end where we the shark stops moving al together before quickly resuming movement in  a quick burst of speed. And that’s pretty much it! By taking a little bit of physics into account, we can remodel the movement of the shark, even making some behavioural inferences, without ever having witnessed the animal.

Unfortunately science isn’t quite that simple and we have to ‘test’ hypotheses with ‘statistics,’ but that’s my problem, not yours. What’s that you say? My humour and brilliance has got you curious? Oh go on you! Fine, here’s a bit more…

Here is a comparison of several different methods for extracting those behaviours. At the bottom, marked ‘video’ is our direct observation, an ethogram, of the animal that will serve as the truth, against which we will compare all others. Each coloured bar indicates when a specific behaviour was observed. Marked ‘accel’ are the behaviours that I have manually observed from the accelerometer time series. The next one, marked ‘Eth’ are the behaviours extracted by an autonomous k-means clustering algorithm of the accelerometer record. Special software has analysed the data and grouped them together. Lastly, is the same analysis performed with some training. So in this case I have given the computer a set of criteria to use for each clustering before it automatically groups them together.

You can see clear differences in the efficacy of each method. Not immediately apparent however is the work involved in each method. Manually annotating the accelerometer record by hand is very time consuming compared with the split-second analysis performed by modern computers. So which method would you choose? Each has its own advantages and disadvantages, ups and down (side to sides). Leave a comment and tell me what you think! Here’s one thing to consider; we are comparing everything to a visual record, but who’s to say we can see everything? Perhaps the accelerometer can pick our subtleties not visible to the human observer. Food for thought!

For your viewing pleasure, here’s a short video demonstrating the ability of the accelerometer to identify specific tail beats. https://www.youtube.com/watch?v=zUfk3arpleU