What can we learn from a shark’s DNA?
Show notes
This week on the World of Sharks podcast, we are zooming in to examine the tiniest part of a shark – its DNA! The study of shark genetics is a rapidly advancing field with many different facets to it. Scientists across the world are using new, innovative technologies to unlock secrets hidden within the DNA of sharks, which can provide valuable insight into their biology, movements and evolution, as well as help combat some of the greatest threats facing them, including the shark fin trade. To walk us through this complex but hugely fascinating world, we are joined by Professor Mahmood Shivji, director of the Nova Southeastern University Guy Harvey Research Institute and Save Our Seas Foundation Shark Research Center (SOSF-SRC). For the last 20 years, Mahmood has specialised in integrating laboratory genetics-based and field-work approaches to solving problems in the management and conservation of sharks and rays, and since 2010 has led the research and education programmes of the SOSF-SRC – so it’s fair to say he knows a thing or two about what we can learn from a shark’s DNA! In this episode, Mahmood breaks down key genetic concepts – such as what on earth DNA sequencing is and what is meant by a ‘genome’ – explains how genetics can help inform conservation strategies for sharks and rays, as well as some of the ground-breaking discoveries he and the team at SOSF-SRC have made.
We begin our conversation, as always, with Mahmood’s most memorable ocean experience [05.44]. He takes us to a shipwreck on the west coast of Vancouver Island, Canada, which he and his dive buddies chose to explore. The journey to the site took four hours in their small, inflatable boats – but it was made all the better for the presence of some very active grey whales, who breached just metres from their vessels. But that was just the appetiser. Once they had arrived at the shipwreck, they found hundreds of spiny dogfish, a relatively small species of shark known for their large aggregations (you can listen to our episode on them with SOSF project leader Fenella Wood here). Mahmood describes it as “descending through a cloud of sharks”! Once they reached the bottom, the sharks were no longer at their depth but remained above them for the entire dive. It was so memorable that Mahmood can still picture it all these years later – even though he didn’t have a camera with him at the time.
Mahmood’s fascination with the ocean began a long way from Vancouver [08.14]. He grew up on the island of Mombasa, on the southern coast of Kenya. He remembers playing in the mangroves, seeing marine life every day, which he attributes his career to now. However, Mahmood didn’t start out studying marine biology – when he first attended university, it was to study economics! He had to take a biology class as a requirement for the economics degree, which he found even more fascinating and led him on a path to the marine sciences. But it was genetics that came first for Mahmood – the sharks came later [10.05]. He was working as a professor at the Oceanographic Center at Nova Southeastern University, focussed on ocean-related topics when he came across an article in the local newspaper discussing the difficulty of identifying shark body parts that were being landed by fishing vessels. Morphologically, the individual parts looked very similar to that of several other species, and it was hard to tell them apart by appearance alone – making it difficult to ascertain exactly what had been caught and, therefore, harder to manage fisheries effectively. But Mahmood had an idea. He contacted some of the scientists working at the fisheries management agency and asked them to send him some samples of the body parts in question and set to work developing methods capable of identifying a species from its DNA relatively quickly. Needless to say, it worked quite well – and brought Mahmood into the field of shark genetics.
But before we fully submerge ourselves in the deep end, we take some time to dip our toes into genetics and get to know the basics [15.23]. Put simply, DNA is the basic instructions behind how all life works. It is present in every living thing and dictates how our bodies look and function. It is a molecule made up of two long strands that are joined together in the middle by a number of interlocking chemical bases – like a ladder. There are four chemical bases – adenine, thymine, guanine and cytosine (also known as A, T, G and C) – that appear in pairs, and the order in which these appear are very important. They create a unique code that instructs the cells of the body to make certain things, and the differences between codes are what make two species different from one another. It’s what sets you apart from someone else. The colour of your eyes and hair, the size of your nose, even how things taste to you – they’re all coded for in your DNA. Geneticists like Mahmood extract DNA from the tissues of organisms and have special methods to read the code, understanding where certain traits come from and how they’re passed down from parents to offspring.
Sharks are no different. The unique combinations of As, Ts, Cs and Gs in their DNA can provide insight into an endless amount of things [19.31]. These can include aspects of their biology and behaviour, such as their migration patterns, mating systems, population structure and unique adaptations. We can also examine how certain traits have evolved through time and where certain species branched off from their ancestors. And we can also look into the future: DNA can tell us the susceptibility of a species to certain diseases or how they might cope with external stressors like climate change and overfishing. The focus of the SOSF-SRC is to use a range of genetic techniques to answer some of these questions and use that information to inform conservation practices for sharks and rays around the world.
One of the most recent achievements of the SOSF-SRC, and their many collaborators, was the sequencing of the entire genomes of two endangered species: the shortfin mako and the great hammerhead [23.50]. Now, if DNA can be considered the instructions, genomes are the entire manual. A genome is the entire genetic makeup of a species – it’s all the DNA put together. Sequencing means putting all the puzzle pieces together, figuring out which order the pairs of As, Ts, Cs, and Gs go in. Often, geneticists are working with a specific part of an organism’s genetic code, working out the composition of one part of it to understand where a certain trait comes from – this is known as DNA sequencing. Sequencing a whole genome requires huge amounts of work. The human genome has around 3 billion base pairs – sharks, as Mahmood tells us, have even more. The shortfin mako, for example, has a genome 1.6 times bigger than that of our own.
But once we have the genome sequenced, the possibilities of what can be discovered is almost endless. Before the shortfin mako and great hammerhead, Mahmood’s team were also the first to sequence the entire genome of the white shark [31.35]. In doing so, they discovered that the white shark has a very stable genome, which means that very few genetic mutations occur. Because of this, white sharks are less susceptible to diseases caused by mutations, like cancers and neurodegenerative diseases. In addition to this, they also discovered that white sharks have incredible wound-healing abilities. Within the white shark’s genome were sequences of DNA that code for wound healing. We have them too, but in white sharks, they are especially efficient, meaning that sharks are capable of healing from injury much faster than us. This makes sense as an adaptation, given that sharks usually bite one another during mating, which can leave them with pretty severe wounds. These are just two reasons why sharks have been so successful as a group of animals, all of which are written in their DNA.
Impressive abilities aside, a larger focus of the work of the SOSF-SRC is conservation genetics – in short, what can a shark’s DNA tell us about their capacity to adapt to external stressors [38.14]? Genomes can reflect the genetic health of a species. If there is a lot of diversity within the genes of a species, it means there is more chance that some of those genes may be for adaptive traits, providing a higher chance that that species can adapt to future changes. It also avoids inbreeding, which can limit a species’ ability to survive and reproduce. A lower genetic diversity increases the risk that a species may go extinct. Across the whole great hammerhead genome, Mahmood’s team found very low genetic diversity – lower even than many land species. They also discovered evidence of very high levels of recent inbreeding. Both of these findings hold very important implications for the conservation of the great hammerhead, as it places them at greater risk of extinction. On the other hand, the genome of the shortfin mako revealed the opposite – much more genetic variation and very little indication of inbreeding. This means their populations are large enough to prevent inbreeding, which is a very good sign for their conservation status.
Another exciting bit of research published recently by Mahmood’s team, led by Sydney Harned, looked at the genetic health of another species of hammerhead – the Critically Endangered scalloped hammerhead [45.20]. They focussed on the population of the Eastern Tropical Pacific, where hammerheads are fished extensively for their fins, and there are high incidences of Illegal, Unreported and Unregulated (IUU) fishing. Given the extent of exploitation, the researchers expected to find very low genetic diversity – but to their surprise, they found the opposite. It provides a glimmer of hope for this population and again holds important implications for the management of scalloped hammerheads of not just the Eastern Tropical Pacific but the world. The study also compared the genetic diversity of two other populations of scalloped hammerheads, which were found to be much lower – suggesting that the population of the Eastern Tropical Pacific might have an easier time ‘bouncing back’ from overfishing.
The field is rapidly advancing, with new technologies and methodologies being developed all the time. It’s something Mahmood is really excited about: “Genetics, DNA underlies how all life functions, and now getting all of this sort of really high resolution, highly detailed information about DNA at the level of whole genomes is allowing us, you know, in addition to understanding how sharks actually work- because as scientists we’re also interested in basic biology, how organisms work – but also from a conservation perspective, all this genomics information is telling us which species need to be prioritized for more conservation efforts – like in the case of the shortfin mako and great hammerhead.” [50.05].
About our guest
Professor Mahmood Shivji
Director, NSU Guy Harvey Research Institute and Save Our Seas Foundation Shark Research Center
Mahmood is a professor of marine science at Nova Southeastern University’s Oceanographic Center in Florida and a director of the SOSF SRC. He received his undergraduate degree in biological sciences at Simon Fraser University in Canada, his MSc from the University of California, Santa Barbara, and his PhD from the University of Washington. He has been a faculty member at Nova Southeastern University since 1993 and a director of the SOSF SRC since 2010.
Mahmood credits his life-long fascination with biology to growing up in Kenya, where he was routinely exposed to African wildlife and undersea environments as a child and teenager. His interest in marine science, in particular, was boosted when as an undergraduate student, he assisted one of his professors with kelp-bed ecology research in a pristine part of British Columbia. That experience proved transformative, leading to a career in marine and conservation science and education.
In addition to leading the research and education programmes of the SOSF SRC, Mahmood directs the Guy Harvey Research Institute, emphasising collaborative projects between the two entities to achieve larger and more impactful research and conservation outcomes. He specialises in integrating laboratory genetics-based and field-work approaches to study and solve problems pertaining to the management and conservation of sharks and rays, billfishes and coral reef ecosystems.
Mahmood’s work is on exhibit at the Smithsonian Museum’s Sant Ocean Hall in Washington DC, and his team’s research discoveries are frequently and widely reported in the national and international media.
