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Biopsy sampling dolphins in Sicily

When something finally happens that you have been thinking and dreaming about for a very long time there is often a sense of surrealism, like it’s not really happening and only a more lurid and tangible extension of those dreams which you have been having for so long. This is certainly true for where I find myself currently – in the tranquil Sicilian town of Torretta Granitola and hosted by scientists at IAMC-CNR having brokered a collaboration between this institution and Durham University. Since the very earliest days of my PhD research it was clear that there was a gaping hole in the geographic spread of the samples of Tursiops truncatus, or Bottlenose Dolphin, to which I had access. This might have been overlooked were it not for that hole to be sat squarely over a region that was of fundamental interest to my research question – how do environmental boundaries influence population structure of marine vertebrates. The Siculo-Tunisian channel, on which Torretta Granitola stands on the northern edge, is just such a boundary and the principle one around which my PhD was formed. To the East lies the warm, salty and deep water of the East Mediterranean Basin, to the West: the generally shallower Western Mediterranean Basin with its cooler waters influenced by the Atlantic. Research conducted by Dr Ada Natoli showed that there was a distinct genetic difference between Bottlenose Dolphins found in the Western Mediterranean Basin and those from the Eastern Mediterranean Basin and that the Siculo-Tunisian channel was the geographic region in the middle of these two groups. Could it be that the different environmental conditions found in the two basins has led to the discovered genetic differentiation?

To understand this more clearly, I need tissue samples from dolphins found in this region. With these we can conduct genetic analysis to see if the population split between the EMB and WMB is abrupt, i.e. the dolphins found here fall easily into one group or the other, or if in fact the dolphins here represent a more transitional grouping with geneflow in either direction or potentially even both. To do this requires biopsy sampling which can be done in a number of ways; rifle, scrubber, crossbow or even with a pole. After much research, reading and speaking to other scientists I decided to go with the use of a crossbow for a number of reasons. My principle reason was that many fellow scientists suggested that using a crossbow provided a higher sample return rate (particularly compared to a pole or scrubber) and this was important to me as I didn’t want to subject the animals to any more interaction was absolutely necessary. For me it would be quite tragic to cause any stress to wild animals, no matter how little, and yet come away with no samples to support the science that will eventually help to protect the animals themselves. Secondly, it is far easier to transport the crossbow and associated biopsy equipment across international borders than other methods such as a biopsy rifle. Thirdly the crossbow is an order of magnitude less expensive than a rifle.

So how does the crossbow work? The crossbow itself is a standard sports crossbow with a 150lb draw weight. This is the standard power used for biopsy sampling marine mammals. It must be strong enough to penetrate the skin of the animal and for the molded polyethylene flotation to cause the bolt to bounce back from the animal but not powerful enough for the bolt to injure the animal beyond required. The bolt itself is a specially designed item from a company based in Denmark called Ceta-Dart. It is an aluminium-carbon fiber shaft with three vanes and a molded polyethylene flotation. On the front is a threaded bar onto which you attach the cutting tip. The tips are 25mm deep, with an internal diameter of 7mm, and contain three backward facing barbs that hold onto the sample once taken. The bolt will float in the water after striking the animal and can be easily retrieved with a landing net. I’ll talk about the processing of samples in a future post.

With animal safety and welfare being of highest priority for me it was essential that I was accompanied by an experienced cetacean biopsy sampler. For this we flew in Tilen Genov, an extremely experienced biopsy sampler from Slovenia. Tilen is the President of the Slovenian Marine Mammal Society – Morigenos and I urge you to check out the amazing scientific research that this organisation does. Tilen provided us an opportunity to shadow him during the first week of the expedition as well as providing lectures and practical training on biopsy sampling.

One of the main issues to consider when conducting biopsy sampling is to be very aware of potential dangers to calves. Our basic rule is to never target mothers with calves or groups that contain calves. The main reason for this is due to the surfacing pattern of bottlenose dolphin calves, they typically come to the surface on the flank of the accompanying adult – putting their head firmly in the firing line. The last thing we would want to do is harm a calf so it is best to simply avoid the possibility altogether. In addition we never want to sample an individual animal more than once, not only as such samples would be superfluous but also to limit stress to an individual, so we run concurrent Photo-ID allowing us to keep track of who has already been sampled and identify potential target animals.

Next time I’ll tell you a little more about how we have been getting on…

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Sailing the length of the Atlantic Ocean

We shall not cease from exploration,

And the end of all our exploring

Will be to arrive where we started

And know the place for the first time.

T.S. Eliot, ‘Little Gidding’

The sky grew lighter. The wind, although warm, sent a shiver of chill right through me. Or was it the excitement? As my hands clutched the rusty metal hand rails I steadied myself as the ship rolled over to port in its steady and rhythmic movement. It was 6.45am and I had risen early to catch the sunrise as we ploughed through the waves on our course through the Atlantic, currently several hundred miles off Sierra Leone. The few clouds in the sky caught fire as the sun crawled upwards beyond the horizon. I have seen sunrises at sea before but nothing like the offerings of the tropical Atlantic. From the pastel chalks of predawn to the bold colour palette of a surrealist painter found in the few seconds before sunrise, sunrises here had it all. And the best bit? I still had another two weeks’ worth of sunrises to go.

I have recently returned from a long voyage at sea. I boarded the Akademik Tryoshnikov, a Russian icebreaker, in Bremerhaven Germany and stepped off in Cape Town South Africa. My reason for doing so was to take part in a Maritime University taking place during Leg zero of the Swiss Polar Institutes Antarctic Circumpolar Expedition (ACE). This University course, under the auspices of the Russian Geographical Society, taught oceanography and ocean sampling techniques to 49 students from 14 different nationalities and to say it was the trip of a lifetime was an understatement.

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The course was excellent, covering a huge and varied curriculum from CTD deployment to atmospheric circulation, from Antarctic winds to ocean gliders. It was run and taught, most amazingly, by three conveners whom all did a fabulous job. Equally as intellectually stimulating as the course however was the interactions with my fellow students. Coming from diverse academic backgrounds and from all over the world I learnt so much from our discussion over meals, our lively scheduled debates or the daily student lectures. What’s more than this I also gained 49 friends.

It is hard to describe the experiences of such an incredible journey so I’m going to enlist the help of my new friends to help me. Please check out some of their great blog articles from below:

http://annacresswell.wixsite.com/photography/voyage

http://spi-ace-expedition.ch/a-students-perspective-jordan-hollarsmiths-journal/

A voyage at sea – ACE Maritime University

We’ve all been there. Packing to go away, often on holiday, and realising that the list of things you need already far exceeds your precious luggage allowance, let alone the capacity of the bags themselves. Normally this stressful experience is diffused by a cup of tea and the descending logic that your destination is (usually) a warm climate and if pushed you could survive with just a pair of shorts, a t-shirt, some flip flops and your bank card. However, when your destination is not a fixed geographical point but a journey, by an unusual mode of transport and with some interesting activities along the way even a cup of tea seems to do little to help. Still, it is a good excuse to drink plenty of tea.

Next week I will be departing for Germany to join the research vessel Akademik Treshnikov for a journey down to South Africa. I will be making this journey as part of the Antarctic Circumnavigation Expedition (ACE) created by the Swiss Polar Institute with the support of Ferring Pharmaceuticals. Whilst the Akademik Treshnikov will go on to make an exciting three leg journey around Antarctica, I will only be joining the ship as far as South Africa. My reason for doing so is to be a part of the ACE Maritime University which is organized under the auspices of the Russian Geographic Society in order to broaden the scope of ACE and inspire a new generation of scientists.

The ACE Maritime University will host 50 postgraduate students from 10 different countries. Whilst onboard we will be following a fairly intensive schedule of lectures, workshops and practical training in many aspects of oceanography. With access to state of the art equipment and scientists who are leaders in their field I’m sure that the Maritime University will not only be an experience of a lifetime but incredibly educational and inspiring too. One aspect of the trip that I’m particularly looking forward to is meeting all the other people onboard. I believe that having such a diverse group of people can only be a good thing; I’m sure I will learn so much about the world and make some friends for life. A second aspect I am especially looking forward to, albeit slightly nervously, is the Equator crossing ceremony. This is something I have always wanted to experience and I’m sure it will be good fun. Most of all though I am looking forward to learning. With such a diverse and broad range of subjects planned to be covered in the Maritime University programme I’m sure it will be brilliant.

So how is my packing actually going? So to explain this let me first outline that I have only two bags – a 25 litre daysack and a 90 litre expedition duffel bag (oh and only a standard 23kg baggage allowance for my flights). Being part of the ACE Maritime University will involve travelling from the depths of European winter (read: I will need plenty of warm clothing) to the height of South African summer (read: I will need warm weather clothing). Our activities will be considerably varied too; from a reception hosted by the Swiss Ambassador in Germany (read: smart outfit required) to deckwork whilst at sea (read: wet weather gear and safety equipment needed) it suffices to say that if anybody has Mary Poppin’s handbag or Doctor Who’s Tardis going spare I would be most grateful. Please follow my twitter feed to stay up to date with my experience of the ACE Maritime University.

The Akademik Treshnikov, a Russian icebreaker that will host us for the ACE Maritime University and our journey down to South Africa.
The Akademik Treshnikov, a Russian icebreaker that will host us for the ACE Maritime University and our journey down to South Africa.

All marine biologists SCUBA dive right? Er….no actually…

A common reply when I tell people that I am a marine biologist is “Ohh I’d love to do that but I can’t SCUBA dive”. Let me firstly correct one huge myth; you do not need to be able to SCUBA dive in order to be a marine biologist. I can immediately think of many colleagues whom collectively study the full breadth of marine taxa yet not one of them have a SCUBA certification. The common public perception of marine biologists is one of a neoprene clad, tanned individual donning SCUBA equipment before rolling backwards off a boat into pristine blue waters. For 99% of marine biologists this is very, very far from the truth. That is not to say that 99% of marine biology isn’t glamorous or cool or exciting. I certainly think it is. Major marine biology discoveries are made all the time in laboratories and museum archives around the world. When this happens these marine biologists are often the first people in the history of humankind to comprehend this new information – now who can say that isn’t cool?

SCUBA diving is not essential for a career in marine biology. I have met marine biologists who can't even swim!
SCUBA diving is not essential for a career in marine biology. I have met marine biologists who can’t even swim!

However, I have been very lucky in my career so far in that I have been able to work in a variety of environments from remote beaches to ocean going research vessels and of course SCUBA surveys in some pretty nice locations. If you are set on a career in marine biology AND you want SCUBA to be part of your working life there are numerous ways you can set yourself on the path to this. I should mention however that this is not an exhaustive list and there are many more ways to integrate getting into the water with your career.

  • Choose a degree programme that has optional dive training.

Plymouth University in the UK offers the opportunity for its students on marine courses to complete the HSE SCUBA qualification over an intensive 4 week course.

  • Gain your qualifications recreationally.

This is the route I chose, having first learned to dive as a teenager. To follow this route you have many, many options. The main choice is which qualification agency to get qualified with. In reality it doesn’t matter as they all provide excellent training and there is an international recognition for all qualifications and an understanding  of grade equivalency through the excellent system of CMAS (Confédération Mondiale des Activités Subaquatiques) star grading. The PADI (Professional Association of Diving Instructors) scheme is often more common worldwide and attaining the Divemaster certification usually opens the doors to conducting scientific diving. In the UK the BSAC (British Sub-Aqua Club) provides an excellent training scheme with the added benefit of being club based which means there is often a pool of kit for beginners to use, there are regular dives to help you build up experience and courses are often cheaper too! Within BSAC, attaining the Dive Leader or Advanced Diver qualifications are the usual minimum for access to scientific diving opportunities.

  • Learn to dive whilst building survey experience abroad

Some organisations such as Frontier, Coral Cay Conservation or Blue Ventures can provide opportunities to not only gain your SCUBA qualifications but also contribute towards ongoing conservation and scientific work as well as have an amazing life experience in awesome locations – all at the same time. Be aware though that this can be a very expensive route into scientific diving.

  • Qualified already? Contribute to science now!

The excellent Seasearch scheme within the UK allows recreational divers the opportunity to contribute to our scientific body of knowledge every time they dive by simply recording the habitats and species they come across. Training is provided, all you need to do is go and dive (and report your results afterwards of course!).

For many, learning to dive is often what starts them on to a career in marine biology and it is sometimes what sustains many others. Every time you drop below the waves into this amazing alien world you can’t help be amazed, inspired and motivated. Remember though that for many marine biologists, and for many reasons, choose not to dive but still have incredibly successful and exciting careers studying our oceans. If this ends up being you then don’t forget that you are in good company.

I first developed my SCUBA skills in the cold quarries of the UK. Tough but an excellent training ground.
I first developed my SCUBA skills in the cold quarries of the UK. Tough but an excellent training ground.

Shark vs Man is No Contest: How You Can Help Sharks Now – An Ecophiles article

I recently had the opportunity to contribute to an online Ecophiles article about contributing to shark conservation for Shark Awareness Day ( 14th July!). This was an exciting and engaging piece put together by Melissa Hobson of Ecophiles.

“According to shark and marine conservation charity Bite Back, sharks have been around since before dinosaur-times. There are around 390 species of sharks in the world with 31 different types of shark living in British waters.

Most sharks have five rows of teeth and can have up to 3,000 teeth! Not surprising they’re the ocean’s top predator. Yet, unlike the shark’s portrayal in the film The Shallows where Blake Lively is surfing on a secluded beach and finds herself on the feeding ground of a great white shark, shark attacks on humans are incredibly rare.

In fact, sharks themselves are more at risk from another deadly predator: humans. So what can be done to help protect them from becoming further endangered?”

To read the full article please follow the link by clicking the image below.

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IAPETUS – Doctoral Training Partnership

I’m lucky and I know it. I’m lucky because my PhD studies are funded by the Natural Environment Research Council (NERC) through one of their Doctoral Training Partnerships or DTP’s (in my case IAPETUS – www.iapetus.ac.uk). Being part of the IAPETUS DTP has many advantages.

First and foremost is the supported feeling provided by being part of a cohort. In each funding year IAPETUS supports around 15 PhD students and these have all become firm friends. My IAPETUS cohort is split over the five partner institutions – Durham University, Newcastle University, St Andrews University, Glasgow University and Stirling University – and all studying in a range of scientific disciplines from oceanography to geology to glaciology to ecology and archaeology. The great positive of being brought together from such a wide range of backgrounds is that it is almost hard to talk in detail about our specific projects together, something that is often covered by laboratory colleagues. Instead we talk about the generalities of being a PhD student – of the struggle with samples, of frustrations with departments and maintaining a balance with regular life outside the PhD. Above all this creates a reassuring feeling of not being alone. Because of IAPETUS, I realise that no matter what discipline a PhD student is working in we all go through similar trials, frustrations and successes.

The second great advantage of being part of IAPETUS is the training opportunities it provides. From an induction day during November to a week at the Scottish Centre for Ecology and the Natural Environment (SCENE – http://www.gla.ac.uk/researchinstitutes/bahcm/researchfacilities/scene/about/) in cold January, training opportunities are plenty. These events have so far provided training in mathematical modelling, GIS, field sampling, experimental design, paper writing and presentation skills.

 

 

Additionally, it is a NERC requirement that we have a student conference/meeting once a year and this year we held the annual event in Majorca, Spain. This event was great and allowed for the best scientific poster session I have ever attended – see the photo if you don’t believe me! For the main part of our conference we were very kindly hosted by IMEDEA (Mediterranean Institute for Advanced Studies) and it was great to hear about some of the environmental research being conducted locally.

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From a personal PhD point of view, being on Majorca allowed me to visit Dr Joan Moranta at the Oceanographic Centre for the Balearic Islands to discuss barracuda sampling. I am very grateful to his support for my project.

In summary I am lucky and I know it. I am lucky to be part of IAPETUS and I would encourage anyone thinking of applying for a PhD to aim for becoming part of a DTP – you won’t regret it!

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An opportunity for learning…

One of the great things about studying for a PhD is the opportunities it presents for meeting new people, being exposed to new ideas and learning new things. Sometimes this arises in a more formal setting such as during seminar, conference presentation or training workshop but equally as often it occurs by chance meetings or discussions over coffee.  It’s often said that most real science is conducted in the pub!

Over the past few weeks I have had many of these opportunities. On the 15th of March, I and a few of my lab colleagues travelled to Cambridge University for the Evolutionary Genetics and Genomics Symposium (EGGS). This symposium was sponsored by the Genetics Society and provides an opportunity for researchers to share ideas and present their work. As a group we had decided that we would travel to the symposium and back in a single day – which made for a very early start and a late finish!

The symposium program had 15 talks scheduled through the day. The talks covered a range of topics from the evolution of viral resistance in rabbits (‘The rabbit strikes back: myxomatosis and the evolution of viral resistance’ – Joel Alves, University of Cambridge) to understanding the development of genitalia in Drosophila (‘Genetic and developmental basis of male genitalia evolution in Drosophila’ – Maria Daniela Santos Nunes, Oxford Brookes University). Sometimes it is easy to look at a conference/symposium program and all too readily dismiss talks as ‘not relevant’ or ‘unrelated’ to your own research. Sometimes this is indeed the case, but no matter what the topic of the talk there is something you can learn – from presentation skills, slide composition to even how not to do something!

Overall the day was a success, we heard some great talks, had chance to see some of the beautiful college buildings of Cambridge University and met some lovely people. We also looked around the fascinating collections of the Sedgewick Museum of Earth Sciences, a truly great institution – if you get a chance to go then really do! Thanks to the Genetics Society for sponsoring the symposium.

 

On the 21st of March I attended a three day Population Genomics workshop at Sheffield University. The workshop was funded by NERC and run by staff of the NERC Biomolecular Analysis Facility (NBAF) at Sheffield. Focusing on a variety of programs, the series of online tutorials and lectures during the workshop took us through a pipeline of bioinformatic data analysis. We could easily have spent weeks working through the problems provided but crucially the workshop provided an overview or taster of different methods and analyses. The knowledge and expertise of the workshop staff were incredible and I would recommend anybody with an interest to check out the services/opportunities provided at NBAF – http://nbaf.nerc.ac.uk/

In addition to these events I have also attended guest lectures both in my department and in my college at Durham. These can be especially varied. Early last month I attended two extremely dichotomous lectures on the same day, one on the effects of light pollution on wildlife and one on making medieval nautical charts! I love these opportunities for learning and it is one of my favourite aspects of my PhD so far. However, we mustn’t forget just how much I have learned from my colleagues. From lunch time chats to laboratory meetings I have probably learnt most from them, to the point I would say I couldn’t do my PhD without the support and knowledge of all the people around me on a day to day basis. A strong research group/team is invaluable and that is a lesson that I will remember forever.

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Social learning with the University College Sunday Seminar series.

23 new Marine Conservation Zones for the UK!

There has been much in the media recently about the proposed designation of the Ascension Island marine protected area. This designation, when it comes to fruition, will protect 234,291km2 of ocean from potentially harmful activities. While the Conservative governments’ ambition to create a ‘blue belt’ around the UK and its overseas territories is admirable it is important that we are not too captivated by achievements overseas and remember to protect those waters closer to home. Today we took a wonderful step towards that goal.

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The waters of Ascension Island will soon be protected. Image: Ascension Island from the sea by Emily Cunningham @eegeesea

In 2013 the UK government designated 27 Marine Conservation Zones (MCZs) in English and Secretary of State waters that in total protected 9,664km2 of our seas. The announcement this morning that of the 23 sites considered for designation as part of the second tranche of MCZs all will be formally designated is a fantastic triumph for conservation. This designation will protect a further 10,810km2 of our seas bringing the total protected area to 20,474km2. Our total of 50 MCZs in English waters will protect a fantastic array of nationally important habitats and species. For example, the Mounts Bay MCZ will protect important Zostera marina seagrass beds and the tiny stalked jellyfish Lucernariopsis campanulata. The Fulmar MCZ will protect an area of muddy seabed that is an important feeding area for seabirds and habitat for sea pens Pennatula phosphorea and burrowing megafauna. The Lands End (Runnel Stone) MCZ will protect an area important for the impressive and elegant Pink Sea Fan Eunicella verrucosa. These are just some of the features in some of the sites which will be protected as part of our rich natural heritage for future generations to enjoy.

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The new MCZs will protect important species like this Pink sea-fan. Picture by Paul Kay – http://www.marinewildlife.co.uk

These designations have come about as a result of the hard and tireless labours of many people. From conservation NGOs such at The Wildlife Trusts and The Marine Conservation Society, government departments and organisations such as Defra and JNCC to the countless members of the public, businesses and stakeholder groups that were actively involved in the consultation process. To all of them I say thank you. This achievement is remarkable not just for the habitats and species it protects but for the process in which it was reached. In contrast to many other marine reserve designations in other countries, the path to today was stakeholder led. This means that the UK government asked us, the people, what we wanted and they listened.

We must now remember that the journey is not over. In their landmark Nature paper Edgar et al (2014) made compelling arguments that in order for Marine Protected Areas (essentially a synonym for our MCZs) to maximise their success they must meet five key requirements:

  1. They must be no take
  2. They must be well enforced
  3. They must be old (>10 years)
  4. They must be large (>100km2)
  5. They must be isolated by deep water or sand.

Even ignoring point three as these are new sites then none of our new MCZs meet these criteria and some will never be reached for well thought out and practical reasons. Instead the UK government is aiming for an ecologically coherent network of MCZs. This means protecting a variety of habitats and species from damaging activities using smaller, geographically close zones whilst allowing sustainable use. We now have 50 zones and this is closer to what we would call a ‘network’ but it is still not enough, we need to fill in the ecological gaps and protect even more of our amazing marine wildlife and habitats. In particular we should for further protection of undervalued muddy seabed habitats that are both sensitive to disturbance and are home to a unique and biodiverse array of fauna.

So what can you do? Firstly I would urge you to become a Friend of Marine Conservation Zones at http://action.wildlifetrusts.org/ea-action/action?ea.client.id=1823&ea.campaign.id=28581 to be kept updated on important information and progress, to be given guidance on how to respond to consultations and to show your support for the local and national work of The Wildlife Trusts in campaigning for better protection for our seas.

Secondly, congratulate the people who made the announcement today possible. Write to Defra or your local MP and tell them how pleased you are with the progress they have made but remind them that there is still much to be done and that you look forward to even more protection for our seas in the future.

Thirdly, remember that the sea is for everybody. Be open minded to other people’s views and requirements for the marine environment. It is only by working with other stakeholders will we achieve protection for our seas that is both real and long lasting.

Finally, celebrate. We should be proud of the progress the UK is making in marine conservation, we are true international leaders in this area. Tell your friends and family about how great our seas are and what great headway was made to protect them today.

 

Edgar, G.J., Stuart-Smith, R.D., Willis, T.J., Kininmonth, S., Baker, S.C., Banks, S., Barrett, N.S., Becerro, M.A., Bernard, A.T., Berkhout, J. and Buxton, C.D., 2014. Global conservation outcomes depend on marine protected areas with five key features. Nature, 506(7487), pp.216-220.

 

Sequencing

The past few weeks have been very busy. I was due to be running my first sample set on the sequencer in January but due to a last minute drop out by another grad student I was bumped up to be on the end of November/start of December run. Running the Illumina HiSeq (the sequencer) is an expensive undertaking so in order to make it economical we fill the 8 sequencing lanes with samples from 8 different researchers, thus spreading the cost across projects. The trouble is that if somebody drops out then a replacement must be found quickly because otherwise the run is delayed and everybody suffers. So, with only four days notice I began to prepare my DNA libraries.

In order to sequence Restriction site Associated DNA (RAD) tags from many individuals at the same time and in the same lane we need to make sure that the sequence read from each sample is individually identifiable during the later analyses. To do this we follow the protocol of Peterson et al (2012) 1, adapted by Dr Kim Andrews (Hawai’i Institute of Marine Biology, University of Hawai’i). For me this involved taking 72 samples post enzyme digestion, ligating one of 12 unique barcodes to every sample in 6 groups. Samples from different locations were randomised across the 6 groups. Then the samples in each group were pooled before one of 6 unique indices were added to each pool; thus giving two levels of identification and allowing us to pull out individual samples after all 6 groups were pooled to make the final library.

This sounds simple enough but there are quite a few more quality control and quantification steps involved and when trying to do this in a rush it can be difficult. This whole process can be completed in 3 days if all goes perfectly. It would be advised to take longer however. In any case, I had problems with pool 5 and pool 6 and despite 12 and 13 hour stints in the lab to try and recover these pools we eventually had to drop pool 5 altogether. However, we managed to get out completed library to the sequencing facility in time (just!) and we have just had our preliminary data back. My PhD Christmas present is 233 million reads of DNA. That should keep me busy in the new year!

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The Illumina HiSeq next-gen sequencer at DBS Genomics

 

  1. Peterson, B. K., Weber, J. N., Kay, E. H., Fisher, H. S. & Hoekstra, H. E. Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species. PLoS ONE 7, e37135 (2012).

Dear Welsh Government, I have a solution and it involves a crossbow.

The Bae Ceredigion (Cardigan Bay) Special Area of Conservation (SAC) constitutes an area of importance for the largest population of bottlenose dolphins Tursiops truncatus in the United Kingdom1. Any readers that have been following the #scallopgate discussion on Twitter will know that the Welsh Government is currently considering re-introduction of limited scallop dredging into some new areas of the Bae Ceredigion SAC beyond which they currently operate.

As a brief synopsis, I refer readers to the excellent blog of Sam Andrews : https://thehoboscientist.wordpress.com/2015/11/22/how-special-is-a-special-area-of-conservation/

So where are we now? I would say we are in a bit of a ‘no man’s land’ and stuck between the scientists who say their science is good and the conservationists who say it isn’t. This stalemate is down to a misunderstanding of what the other group is trying to say and the common tendency for humans to have short-sighted baselines. But I believe science has an answer that may help to resolve some of these issues. Let me explain.

Conservationists have been quick to argue that the Bangor University report is defunct because any recommendations based on its findings are starting from a non-natural baseline of what the seabed should be. The scientists involved have since been very open in defending against this ‘shifting baseline’ accusation2. Professor Michel Kaiser, of Bangor University, has on multiple occasions, quite rightly, pointed out that not all environments are biologically rich and diverse and that the ultimate climax community is very much dependent on environmental conditions. Prof Kaiser and other Bangor scientists have stated that owing to the dynamic environment found within the SAC the seabed would never return to a complex and 3D community as one never existed in the first place. The fauna found in these habitats are adapted for a turbulent and storm-ravaged ecosystem and that scallop dredging, if well managed and controlled, will have limited impact upon them.

There has been some suggestion that the seabed within the SAC may be too hard to be a suitable foraging environment in the way that it is for tropical bottlenose dolphins and so any impact on this food resource would have limited effect for the dolphins anyway. However the more robust and scratched rostrum found in the Bae Ceredigion SAC dolphins suggests that in fact they may be uniquely adapted for such a challenge and that it is indeed a key resource, a point that is critical to the conservationists argument. They argue that this food resource is especially important to mothers with calves that have limited ability to hunt fast moving fish and other prey.

Dolphin rostrum comparison
Tropical (left) bottlenose dolphin known for soft sediment feeding and Bae Ceredigion (right) dolphin. Notice the apparently more robust and heavily scratched rostrum of the Bae Ceredigion dolphins. Is this evidence for feeding in a harder sediment? Picture credits: Left – http://www.arkive.org Right – CBMWC

If the scientists are right and the environmental conditions are such that recovery from scallop dredging can happen in less than a year then by extended logic we can deduce that the seabed conditions in Bae Ceredigion SAC now are, minus the effects of the endemic beam trawl fishery, as they were prior to industrialized fishing. I must stress that the effects of beam trawlers on a virgin seabed should not be underestimated but let’s put that aside for now and assume that the effects are minimal compared to those of scallop dredging. If that is the case and the habitat is (nearly) as healthy as it has always been then the top predators of that habitat – in this case the dolphins – should exhibit a stable population, especially if the key food resource for calving mothers (the breeding element of the population) is healthy. Now I understand that we may be foolish to call our marine environment healthy, especially in terms of other fish stocks that may be important food resources to the dolphins at other key life stages or the impacts of water pollution, but let’s not muddy the waters too much here. In a simplified system if our impact is minimal the number of dolphins in the population today will be the same as it was two hundred, three hundred or even a thousand years ago. If this is not the case then the conservationists may have a valid point that our baseline has shifted and the Bae Ceredigion SAC may need more protection, not less.

Fortunately science has given us a way to examine some of these hypotheses, we just have to take a rather different approach. In my opinion the population biology and ecology of the dolphins found in Bae Ceredigion SAC is poorly studied. I didn’t say unstudied or not studied, I mean poorly studied but that is for another post. Current research focusses mainly on photo identification (Photo ID) surveys that allow us to estimate the current size of the population. It gives us no real capacity to estimate past population sizes beyond 1989 (the oldest photo ID records of any real note), in many cases this is not beyond the current oldest living generation. However, modern genetic techniques allow us to do just that. Genetic bottleneck tests allow us to fundamentally examine declines in abundance of a population. In reality they actually test for signals of population decline in the effective population size (Ne) but for cases like the Bae Ceredigion SAC the general effect is still the same. They work by detecting departures from expected values under mutation-drift equilibrium.

Conducting these tests on the Bae Ceredigion SAC dolphins would be relatively straightforward, especially with modern sequencing methods and techniques. Having this information would allow us to infer just what impact man has had on the dolphin population of the SAC and that would have a lot of bearing on not only the current debate but many other future management decisions too such as those about marine renewables or sea defense construction. If the population of these top predators has remained stable for a long time then this would take substantial wind out of the conservationists’ sails. If their population has changed significantly then this would afford us the opportunity to re-examine the effectiveness of the Bae Ceredigion SAC and its management. Either way we can’t move forward without this kind of information.

So what is stopping us? The answer is gaining access to samples. Bottlenose dolphins are highly protected species and taking biopsy samples can only be done under strict regulations and license. If this could be gained the procedure is simple and involves experienced scientists using a crossbow or rifle (hence the title) to take a small skin and blubber tissue sample from dolphins at the surface. This procedure has been shown to have minimal effect on the animal’s wellbeing if done correctly6 and the information that could be gained would be substantial. Furthermore access to tissue samples would allow us to examine more closely the feeding ecology of the dolphins through stable isotope analysis. This would also be useful to the debate as it would give us information on just how important the benthic infauna is to the dolphins as a food resource.

Although it may be too late for this debate owing to political timescales, our data collection strategy must be progressive and must put the dolphins at the heart of the decision making process. We must not be afraid of new ways of approaching a problem and be prepared to cast off old strategies, particularly if we are continuing with a certain approach simply because that is ‘how it has always been done’.

 

 

  1. Parsons, K. M., Noble, L. R., Reid, R. J. & Thompson, P. M. Mitochondrial genetic diversity and population structuring of UK bottlenose dolphins (Tursiops truncatus): is the NE Scotland population demographically and geographically isolated? Biol. Conserv. 108, 175–182 (2002).
  2. Will Scallop Dredging in Cardigan Bay be an Environmental Disaster? CFOOD – Science of Fisheries Sustainability at <http://cfooduw.org/will-scallop-dredging-in-cardigan-bay-be-an-environmental-disaster/&gt;
  3. JNCC. Cardigan Bay/ Bae Ceredigion – Special Area of Conservation – SAC – Habitats Directive. at <http://jncc.defra.gov.uk/protectedsites/sacselection/sac.asp?EUCode=UK0012712&gt;
  4. Dayton, P. K., Thrush, S. F., Agardy, M. T. & Hofman, R. J. Environmental effects of marine fishing. Aquat. Conserv. Mar. Freshw. Ecosyst. 5, 205–232 (1995).
  5. Lambert, G. et al. Impact of scallop dredging on benthic communities and habitat features in the Cardigan Bay Special Area of Conservation. Bang. Univ. Fish. Conserv. Rep. No 59 (2015). at <http://fisheries-conservation.bangor.ac.uk/wales/documents/59.pdf&gt;
  6. Tethys Research Institute. Biopsy sampling and intrusive research. (2013).