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!



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.

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.

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.

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.



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!

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).

The problem with samples…

My current focus is on sourcing samples, both Barracuda (BRC) and Bottlenose Dolphin (BND). My hunt for BND samples is going smoother, but only slightly. Fortunately, two ex-PhD students of my supervisor, Dr Ada Natoli & Dr Stefania Gaspari, have been very kind in allowing me to take sub-samples from their own personal archive of BND samples. Dr Ada Natoli has a substantial collection of BND samples stored here at Durham within the School of Biological & Biomedical Sciences. This archive covers samples from across Europe and contains 20 from the Italian region.

By Italian region I am referring to any samples coming from the Adriatic, Ligurian, Tyrrhenian and Ionian seas. Most of these 20 samples are from Northern Italy and not the area around Sicily that is of most interest to my project. This is not to say that Northern Italy samples are without value, far from it as I require samples that area to allow me to determine the steepness and exact position of the genetic transition between populations. The Adriatic is also of interest owing to its strong environmental North-South gradients in variables such as salinity and depth. This is important as it will allow us to ask just how concise a habitat change needs to be in order to influence population structure.

Dr Stefania Gaspari’s archive of BND samples is housed at the University of Lincoln under the care of Dr André Moura. I spent time last week at the Joseph Banks Laboratories, University of Lincoln, measuring DNA concentration of samples within the archive. This then allowed me to compile a list of useable samples from the Italian region based on the requirements that taking the 250ng of DNA needed for RADseq library preparation would not compromise the archive coverage. After identifying 58 suitable samples Dr Gaspari kindly allowed me to take my required volume of sample. Much like Dr Natoli’s archive the geographic distribution of samples acquired from Lincoln showed considerable sparsity around Southern Italy and Sicily. This is something that we may have to address in time.

Joseph Banks Laboratories, University of Lincoln
Joseph Banks Laboratories, University of Lincoln
I love the external decoration of the Joseph Banks Laboratories
I love the external decoration of the Joseph Banks Laboratories

The collection of BRC samples has brought with it plenty of different obstacles. Selecting Yellowmouth Barracuda as our comparative fish species has been the first challenge. The requirements for this position stipulated that the fish be a large, high trophic level species that shows regional residency and some evidence of population differentiation across the Siculo-Tunisian Front (STF). Tuna species show evidence of genetic differentiation across the STF (Carlsson et al 2004) but often travel long distances within the Mediterranean and beyond ( Davies et al 2011; De Metrio et al 2002) and so do not meet the regional residency requirement. Many other fish such as the Tortonese’s Goby, Chub Mackerel and Mackerel and others all exhibit genetic differentiation across the STF (Mejri et al 2009; Zardoya et al 2004) but are not high trophic level predators. Quickly the Yellowmouth Barracuda became a firm focus. It feeds at a high trophic level (Barreiros et al 2002), has shown hints of genetic differentiation across the STF (Milana et al 2014) and some evidence of being regionally resident (Barreiros et al 2002).

I then began to start investigating how I could acquire BRC samples and through communication with native Italian researchers and very helpful fishing enthusiasts on the online fishing forum Mercatino Della Pesce it has become apparent that I cannot simply collect samples from Italian fish markets as they are seen there infrequently. So far I have one sample of BRC, kindly donated to me by Salvatore Papasergi from Palermo, Sicily. Where the rest of my samples will come from remains to be seen…

Barreiros, J. P., Santos, R. S., & Borba, A. E. S. D. (2002). Food habits, schooling and predatory behaviour of the Yellowmouth Barracuda, Sphyraena viridensis Cuvier, 1829 (Perciformes: Sphyraenidae) in the Azores.

Carlsson, J., McDowell, J. A.N., Díaz‐Jaimes, Píndar. O., Carlsson, J. E., Boles, S. B., Gold, J. R., & Graves, J. E. (2004). Microsatellite and mitochondrial DNA analyses of Atlantic bluefin tuna (Thunnus thynnus thynnus) population structure in the Mediterranean Sea. Molecular Ecology, 13(11), 3345-3356.

Davies, C. A., Gosling, E. M., Was, A., Brophy, D., & Tysklind, N. (2011). Microsatellite analysis of albacore tuna (Thunnus alalunga): population genetic structure in the North-East Atlantic Ocean and Mediterranean Sea. Marine biology, 158(12), 2727-2740.

De Metrio, G., Arnold, G. P., Block, B. A., De la Serna, J. M., Deflorio, M., Cataldo, M., … & Seitz, A. (2002). Behaviour of post-spawning Atlantic bluefin tuna tagged with pop-up satellite tags in the Mediterranean and eastern Atlantic. ICCAT Col. Vol. Sci. Pap, 54(2), 415-424.

Mejri, R., Lo Brutto, S., Hassine, O. K. B., & Arculeo, M. (2009). A study on Pomatoschistus tortonesei Miller 1968 (Perciformes, Gobiidae) reveals the Siculo-Tunisian Strait (STS) as a breakpoint to gene flow in the Mediterranean basin. Molecular Phylogenetics and Evolution, 53(2), 596-601.

Milana, V., Ciampoli, M., & Sola, L. (2014). mtDNA sequences of Sphyraena viridensis (Perciformes: Sphyraenidae) from Italy: insights into historical events and the phylogeny of the genus. Biological Journal of the Linnean Society, 113(2), 635-641.

Zardoya, R., Castilho, R., Grande, C., Favre‐Krey, L., Caetano, S., Marcato, S., … & Patarnello, T. (2004). Differential population structuring of two closely related fish species, the mackerel (Scomber scombrus) and the chub mackerel (Scomber japonicus), in the Mediterranean Sea. Molecular Ecology, 13(7), 1785-1798.

The PhD begins…

Two days ago the PhD adventure began in a flurried frenzy of packing, buying, unpacking, travelling and meeting more people than I can remember meeting in such a short period for a very long time. I have moved into Brackenbury halls, the postgraduate accommodation for members of University College (more affectionately known as ‘Castle’), Durham University. My room is light, airy and spacious and all of my fellow ‘Castlemen’ flatmates were extremely welcome and friendly.


The next two weeks is a diary packed maelstrom of inductions, socials and events designed to allow us to settle into life at Durham University. Particular social calendar highlights include Croquet and lawn games as well as a BBQ river cruise! Of course there is the more practical side of laboratory inductions and equipment training and there seems to be a good balance of fun and serious events planned.


For now I’m happy being swept along in the excitement of it all but I am looking forward to getting stuck into the work. Hopefully I’ll be able to post more pictures and a research update when I get chance. Floreat Castellum!

Collecting fossil shark teeth


Carcharocles megalodon
Carcharocles megalodon

I’ve been collecting fossil shark teeth now for about seven years and I wanted to tell you about what is a rewarding, educational and fun hobby. What started as just a couple of teeth bought from a fossil shop has now reached over one hundred ‘display’ specimens, representing over ninety species including some pretty rare ones, and hundreds more in my ‘swap or sell’ collection. My interests and preferences in shark tooth collecting have grown and changed as my collection (and experience!) has expanded over the years. I’ve also learnt some good lessons over the years and wanted to share these with you in the hope that I might tempt more people into this fascinating hobby.


Ethics. Firstly I don’t collect jaws or modern teeth. EVER. I refuse to contribute to market pressure that increases the threats that sharks face. They have enough. Even if I knew one hundred percent that a modern tooth hadn’t caused the death of a shark, such as being collected from the bottom of an aquarium, I still think it has no place in my collection. Having one is a slippery slope and there are some internet dealers who will advertise ‘sustainably sourced’ teeth that have in fact come from fisheries bycatch. By buying one you are saying that there is a use for the bycatch when actually it would be better if we looked to address the issue and reduce bycatch of sharks. It has been estimated that one hundred million sharks are killed by humans every year; there is no sense in collectors adding to this tragedy. The reality is that nearly all modern shark lineages are at least a few million years old and fossil examples can be found for extant species if you know where to look or who to ask. You can collect teeth both ethically and without compromising your collections potential.


Information. The most important thing in any collection and especially a biological one is to keep records and label your specimens. Luckily I decided very early on that this was important to me and now add labels to teeth as soon as they come into my collection. Each tooth has a label with at least the Genus, Species, Age and Locality. Furthermore I also keep an Access database with many additional items of information about each specimen contained such as Source, Cost, and particular Stratigraphy etc. Whilst this may seem excessive it is important that any specimens you collect yourself have at least basic information accompanying them or they are scientifically worthless.


Display. There are many ways to display fossil shark teeth and my own collection has changed over the years. One of the most basic and common ways to display teeth is in a Riker Mount; essentially a black box with a see through lid and soft mounting fabric inside. Many collectors use these but often forget to add information labels, essentially reducing their teeth to nothing more than decorative stones. I keep mine in individual plastic display boxes which not only protects the specimen well but keeps the information label with it. At first I had my teeth simply arranged on a shelf in their little boxes but after I had about forty specimens I purchased some larger acrylic display boxes that stacked together. These worked well initially but they do get scratched and look old fairly quickly.

My first display cases.
My first display cases.

As my collection grew I purchased lighted glass display cabinet as well as some acrylic stands and steps to better display the specimens. These looked great and were a fantastic talking point for guests! I even added some plastic prehistoric shark models to allow visualisation of the living animals.

post-7075-0-16444300-1326701049 post-7075-0-22757400-1326701058 post-7075-0-46052100-1326701064

My latest incarnation of collection display is a little less aesthetically pleasing but far more practical. I now have a metal Bisley drawer set. This allows me to keep all my collection, plus swaps, spare boxes and mounting materials together and in a compact storage option. This has been especially useful for moving and taking my collection to display for special events. Ultimately display is personal preference and there are many more options than the ones I have highlighted – just don’t forget the information labels!

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Specialisation. When you first start collecting a fossil shark tooth is a fossil shark tooth and you simply collect whatever you can. As your collection grows however you can find that your collection may become unwieldy and you may need to specialise. What you specialise in is entirely personal preference and what you find most interesting. It could be a particular family, a particular locality or a particular geological age or something else entirely. Your interest may even change over time. I have found myself being drawn to the smaller sharks and especially the catsharks or Scyliorhinidae so for the foreseeable future this is where my collection will begin to focus.


Source. Where do you acquire specimens from? Like I said I started with just a few specimens from a local fossil shop but most fossil shops will stock only two or three species and often with poor locality information. If you are lucky enough you may live near a local fossil hunting site. In the UK there are many good hunting grounds including Bracklesham Bay, Burnham-on-Crouch, the Isle of Sheppey and others. It is wise to do a little research online to find if you can collect fossils close to your location and www.ukfossils.co.uk is a great place to start. Just remember to collect safely, check tides if appropriate and always ask the landowners permission before collecting.

If like me you live far from good collecting areas then purchasing over the internet is the best option. I’ve listed a few great internet resources at the end of this blog. A word to the un-initiated. Be cautious if you are purchasing shark teeth through online auction sites. There are some good dealers that sell this way but specimens often come poorly labelled or with little information. That said some items are often mislabelled and if you are prepared to do some research you can often pick up a bargain, purchasing a rare specimen labelled as a more common one. You have to know what to look for though. Alternatively there are many excellent established dealers with their own websites (see the foot of this blog post). Fossil shark teeth vary in price depending on species, quality, locality and rarity. You can pick up some specimens for just a few pounds each or you could buy a seven inch pristine Carcharocles megalodon tooth for upwards of ten thousand pounds so there is something for every budget.

Joining forums is another great way to acquire material too. Often other collectors will offer to swap specimens and it’s also a great way to learn new things and meet new people. There are some very knowledgeable and generous people to be found on online fossil forums. Just remember they are a community however and you have to give something back.


Collecting shark teeth is a great way to learn about the evolution of these fascinating animals as well as venture into scientific disciplines such as palaeontology, marine biology and even museum curation! I would encourage anyone with an interest in sharks to give it a go.

Don’t forget to follow my Twitter feed as each day throughout June I’ll be highlighting a specimen from my collection.


www.buriedtreasurefossils.com – One of the most comprehensive dealer websites stocking many top quality and rare species.

www.megalodonteeth.com – A great, easy to navigate site run by a very friendly dealer. A good place for beginners and experienced collectors.

www.lowcountrygeologic.com – A well-presented site with a good selection of species.

www.fossiliferous.co.uk – A fantastic UK based site run by a very friendly dealer. He collects all material himself so every specimen comes with excellent information.

www.heskensfossils.nl – Some unique and rare specimens.

www.ukge.com – Excellent source of collecting equipment and display material.

Current research

My current research is focussed on developing molecular markers for deep water sharks and is being conducted at Edge Hill University with fellow early career researchers David Goodson, Thom Dallimore and Carl Barker. Deep water sharks are poorly understood relative to their shallow water counterparts but are often even more vulnerable to anthropogenic pressures. Deep water fishing fleets are increasing in size every year and it is well known that many deep water sharks aggregate in single sex or age cohort groups meaning a single trawl can have a very significant impact to localised populations. It is vital that we understand more about these deep water species in order to effectively manage conservation efforts. Key to this understanding is knowledge on population structure and connectivity. The vital first step on this road is the development of molecular markers to enable comparisons.


The shark samples I am working on all come from the Rockall Trough, an area of deep water off the coast of Scotland, and were collected whilst on board the FRV Scotia during a Marine Scotland deep water survey. I am principally targeting the sharks Galeus melastomus and a selection of sharks from the genus Apristurus, including some additional samples very kindly supplied by Dr Ana Verissimo of CIBIO – University of Porto. I am also attempting to replicate the excellent work completed by Helyar et al (2011) who developed microsatellite markers in Centroselachus crepidater. Whilst initial thoughts were to jump straight to population examination through the use of Amplified Fragment Length Polymorphisms (AFLPs) we were encouraged to attempt to develop microsatellite markers by Dr Jim Provan (Queens University Belfast) whilst presenting a poster at the BES Ecological Genetics Group 59th Annual Conference. With his guidance that is exactly what myself, fellow Technician David Goodson and PhD students Carl Barker and Thom Dallimore are now attempting. Please follow me on Twitter for updates and other exciting Marine Vertebrate news.


Helyar, S., Coscia, I., Sala-Bozano, M., & Mariani, S. (2011). New microsatellite loci for the longnose velvet dogfish Centroselachus crepidater (Squaliformes: Somniosidae) and other deep sea sharks. Conservation Genetics Resources, 3(1), 173-176.


The origins of great whites

There is great debate within the scientific community with regards to the true ancestral origins of the modern White Shark Carcharodon carcharias. There currently exist two main hypotheses on the correct phylogenetic placement of C. carcharias. Both hypotheses talk in terms of sharing a more recent common ancestor with an extinct species (Smith 1994). The older of the two hypotheses suggests that C. carcharias is descendant from the ancestral lineage of megatoothed sharks such as Carcharodon megalodon and that the megatoothed sharks should be placed within the family Lamnidae. The more recent hypothesis suggests that C. carcharias is descendant from the ancestral lineage of the extinct Mako shark Isurus hastalis and that the megatoothed sharks should be separately placed within the family Otodontidae. It is important to be clear that neither theory suggests an absolute direct descendancy from the afore-mentioned species as the scarcity of fossil evidence could not support such a claim.

4cm tall Fossil Carcharodon carcharias tooth from Miocene (~20 million year old) sediments in the Atacama Desert of Chile. (Photo credit: Wikipedia)
4cm tall Fossil Carcharodon carcharias tooth from Miocene (~20 million year old) sediments in the Atacama Desert of Chile. (Photo credit: Wikipedia)

Proponents of the megatoothed descendancy hypothesis (Applegate and Espinosa-Arrubarrena, 1996; Gottfried et al., 1996; Martin, 1996; Gottfried and Fordyce 2001; Purdy et al., 2001) base their conclusions upon aspects of shared tooth morphology between the modern C. carcharias and principally the extinct C. megalodon. These similarities include: similar tooth morphologies between juvenile C. megalodon and adult C. carcharias; fine tooth serration in both adult C. carcharias and C. megalodon; shared chevron-shaped neck area on the lingual surface of the upper anterior teeth, a mesially inclined large intermediate tooth and second anterior teeth symmetry (Gottfried et al., 1996; Gottfried and Fordyce, 2001; Purdy et al., 2001). Under this phylogenetic regime the megatoothed sharks are placed within the family Lamnidae and retain their genus Carcharodon.

The evolutionary history of Carcharodon megalodon is well understood from a large quantity of fossil evidence including many transitional specimens. The direct ancestry of C. megalodon can be traced at least as far back as the late Pliocene in the form of the large mackerel shark Otodus obliqus although if Cretolamna appendiculata is considered a chronospecies then this ancestry can be extended into the Lower Cretaceous. O. obliqus had large non serrated teeth with distinctive side cusps. During the middle Eocene the side cusps of O. obliqus reduced in size and the edges developed slight serration. This Eocene species is classified as Carcharocles auriculatus. A massive increase in shark body size accompanied by further reduction in teeth cusps and increased development in serrated edges marks the introduction of Carcharocles angustidens during the late Oligocene. Carcharodon megalodon finally evolved from C. angustidens during the early Miocene and is characterized by a further increase in body size, further development in serrated tooth cutting edges as well as a complete loss of teeth side cusps. The megatoothed descendancy hypothesis suggests that the origin of Carcharodon carcharias is derived in a form of dwarfism of Carcharodon megalodon (Ehret et al 2009).

The Isurus hastalis descendancy hypothesis argues that owing to a shared overall tooth shape and labio-lingual flattening in tooth morphology in both the later ‘broad-form’ I. hastalis (specifically the suggested transitional fossil Isurus xiphodon as described by Purdy et al. 2001) and Carcharodon carcharias, the megatoothed sharks should be viewed as a distinct and non related taxon (Casier 1960). This phylogenetic regime would see the megatoothed sharks placed in the separate family Otodontidae, containing other extinct genera such as Otodus and Parotodus, with Carcharodon megalodon being renamed as Carcharocles megalodon (Casier, 1960; Glickman, 1964; Capetta, 1987). Proponents of the Isurus hastalis descendancy hypothesis also argue that not only are tooth serrations in the megatoothed sharks much finer than those found in C. carcharias but that megatoothed sharks teeth lack enameloid in the neck area whereas C. carcharias does not (Nyberg et al. 2006).

The evolution of Isurus hastalis itself is reasonably well documented in the fossil record. All Mako sharks can find their ancestry in the Eocene epoch (approximately 50mya) with the arrival of Isurus praecursor. During the Oligocene epoch a new Mako shark, Isurus desori, appears in the fossil record. Fossils of Isurus desori are found to be almost cosmopolitan in their distribution and it is from this species that Isurus hastalis is likely to have evolved during the early Miocene. Initial forms of Isurus hastalis are relatively small and considerably longer than their width, thus these initial forms are often referred to as ‘narrow-form’ with later examples being referred to as ‘broad-form’ as their width increases in the mid to late Miocene (Alter 2013).

Casier (1960) makes suggestion of a possible transitional fossil in Isurus escheri where teeth were found to show slight fine marginal serration. Isurus escheri inhabited the waters of the Atlantic Ocean around the mid Miocene (approximately 10mya) and likely derived from the ‘narrow-form’ Isurus hastalis. Unfortunately it would appear that Isurus escheri would be an evolutionary dead-end as fossil evidence of their existence disappears within just a few million years.

True Carcharodon carcharias fossils with all modern characteristics represented have been dated back to the late Miocene with specimens being recovered from California, Maryland and Japan showing that by this time C. carcharias was already thriving across the Pacific and Atlantic Oceans (Gottfried and Fordyce, 2001; Stewart, 1999, 2000, 2002; Hatai et al., 1974; Tanaka and Mori, 1996; Yabe, 2000). A fossil recovered from Peru and described by Muizon and DeVries (1985) was suggested as another transitional fossil in favour of the Isurus hastalis descendancy hypothesis on account of weak tooth serrations but this evidence is countered by Purdy (1996) and Purdy et al. (2001) who observe that this fossil (known internationally as the Sacaco sp. on account of its discovery in the Pisco formation of the Sacaco basin, Peru) is predated by the aforementioned C. carcharias discoveries.

Based upon the simplified evidence presented it would seem that the decision is of only two possible phylogenies. It seems this view is now over-simplified as new fossil and genetic evidence (Martin 1996; Martin et al 2002) shows that the Carcharodon lineage may have split from that of the Mako sharks much earlier than suggested here and that Isurus was not in fact a true Mako but truly of the Carcharodon lineage and should therefore be placed in the genus Cosmopolitodus to indicate as such (Glikman 1964).

For now there remains great scope for research into the ancestry of Carcharodon carcharias and it is likely that debate over the matter will continue for decades to come.



In addition to the literature cited below I would refer the reader to an excellent online article by Steven A. Alter based on his many years as a collector/dealer:


In addition to the many excellent articles published online by Jim Bourdon at:




Cappetta, H. 1987. Chondrichthyes II. Mesozoic and Cenozoic Elasmobranchii; in H.-P. Schultze (ed.), Handbook of Paleoichthyology. Volume 3B. New York, NYVerlag Dr. Gustav Fischer193 pp.

Casier, E. 1960. Note sur la collection des poisons Pale´oce`nes et E ´ oce`nes de l’Enclave de Cabinda (Congo). Annales du Muse´e Royal du Congo Belge (A.3) 1, 2:1–48.

Ehret, D. J., G. Hubbell, and B. J. Macfadden. 2009. Exceptional preservation of the white shark Carcharodon (lamniformes, lamnidae) from the early pliocene of peru. Journal of Vertebrate Paleontology.  29:1 1-13.

Glickman, L. S. 1964. [Sharks of the Paleogene and their Stratigraphic Significance] . Nauka Press, Moscow: , 229 pp. [Russian].

Gottfried, M. D., and R. E. Fordyce. 2001. An associated specimen of Carcharodon angustidens (Chondrichthyes, Lamnidae) from the late Oligocene of New Zealand, with comments on Carcharodon interrelationships. Journal of Vertebrate Paleontology 21:730–739.

Gottfried, M. D., L. J. V. Compagno, and S. C. Bowman. 1996. Size and skeletal anatomy of the giant “megatooth” shark Carcharodon megalodon; pp. 55–89 in A. Kimley, and D. Ainley (eds.), Great White Sharks: the Biology of Carcharodon carcharias. San Diego, California: Academic Press.

Martin, A. F. 1996. Systematics of the Lamnidae and origination time of Carcharodon carcharias inferred from the comparative analysis of mitochondrial DNA sequences; pp. 49–53 in A. Kimley and D. Ainley (eds.), Great White Sharks: the Biology of Carcharodon carcharias. San Diego, California: Academic Press.

Martin, A. F., A. T. Pardini, L. F. Noble, and C. S. Jones. 2002. Conservation of a dinucleotide simple sequence repeat locus in sharks. Molecular Phylogenetics and Evolution 23:205–213.

Nyberg, K. G., Ciampaglio, C. N., and G. A. Wray. 2006. Tracing the ancestry of the great white shark, Carcharodon carcharias, using morphometric analyses of fossil teeth. Journal of Vertebrate Paleontology 26:806–814.

Purdy, R. 1996. Paleoecology of fossil white sharks; pp. 67–78 in A. Kimley, and D. Ainley (eds.), Great White Sharks: the Biology of Carcharodon carcharias. San Diego, California: Academic Press.

Purdy, R., Schneider, V. P., Applegate, S. P., McLellan, J. H., Meyer, R. L., and B. H. Slaughter. 2001. The Neogene sharks, rays, and bony fishes from Lee Creek Mine, Aurora, North Carolina; pp. 71–202 in C. E. Ray, and D. J. Bohaska (eds.), Geology and Paleontology of the Lee Creek Mine, North Carolina, III. Smithsonian Contributions to Paleobiology no. 90.

Smith, A. B. 1994. Systematics and the fossil record: documenting evolutionary patterns. Blackwell Scientific Publications, Oxford, England.

Stewart, J. D. 1999. Correlation of stratigraphic position with Isurus-Carcharodon tooth serration size in the Capistrano Formation, and its implications for the ancestry of Carcharodon carcharias. Journal of Vertebrate Paleontology 19(3, Supplement):78A.

Stewart, J. D. 2000. Late Miocene ontogenetic series of true Carcharodon teeth. Journal of Vertebrate Paleontology 20(3, Supplement): 71A.

Stewart, J. D. 2002. The first paleomagnetic framework for the Isurus hastalis-Carcharodon transition in the Pacific Basin: The Purisama Formation, Central California. Journal of Vertebrate Paleontology 22(3, Supplement):111A.