genetics – Dr. Daniel M Moore

September 19, 2018September 19, 2018 Daniel M Moore

Ligers, Zorses and Bottlenose Dolphins

Most people do not realise that there are numerous species of Bottlenose Dolphins; the exact number is a subject of strong debate and depending on the background of whom you ask will strongly influence the number they give. For example, a conservationist, a geneticist and a taxonomist are unlikely to agree on such matters. However, there are at least three species formally recognised by everybody, each with their own behavioural and physical characteristics. Of the three recognised species Tursiops truncatus, known as the Common Bottlenose Dolphin, is the species that most people are familiar with. This is owing to it’s near global distribution (it is found in every sea except those in the polar regions), its prevalence in popular culture – be it films or TV and of course its popularity in aquariums during the latter half of the 20^th century. The second of the three species, Tursiops aduncus, is more often referred to as the Indo-Pacific Bottlenose Dolphin and as its name suggests is found in the Indian and Pacific Oceans only. Whereas T. truncatus is found in both coastal and offshore environments T. aduncus is principally only found in coastal waters. The third species, Tursiops australis, known as the Burrunan Dolphin is found only in coastal waters of parts of Australia.

One of the most controversial topics in in the field of biology is the subject of what defines a species. Certainly in most high schools, pupils are taught that animals belong to the same species if they can reproduce and form fertile offspring. This is undoubtedly complete fallacy and a recent topic of research that I have been involved in significantly proves this. This research, led by Dr. Tess Gridley of the University of Cape Town, has just been published and I provided the genetics elements included in the paper. The research focuses on the production of fertile hybrids by two species of Bottlenose Dolphin when kept together in captivity. Hybrids are the offspring of two different species – famous examples include the Liger (the offspring of a Lion and Tiger) and Zorse (yes you guessed it, the offspring of a Zebra and a Horse).

Hybrids — Hybrid animals are remarkably common. Here we see a Liger (Lion and Tiger hybrid) on the left and a Zorse (Zebra and Horse hybrid) on the right.

First of all, let’s deal with the elephant in the room. Yes, this research is based on dolphins kept in captivity. Let me be absolutely clear that I am in no way an advocate for keeping any species of cetacean in captivity. When the individual dolphins on which this research focusses were taken into captivity it was the 1970s, at which time our understanding of cetacean biology, in particular their emotional intelligence, was significantly inferior to our understanding today. Like all areas of knowledge, our understanding progresses through time and moral humans adapt their behaviour and actions to take account of this improved understanding. Flipping this on its head, we should be reticent to judge people who made decisions in the past with which we would normally condemn when judging by todays understanding, morality and societal will. Times and understanding were different then and as long as we are willing to, pragmatically and sensibly, adapt our actions today to take account of our improved understanding then we should look forward and not back. No, we should not be taking new cetaceans into captivity but those that currently are kept in aquaria, like those in this study, provide an opportunity to expand our knowledge of cetaceans such that we can continue to improve our decision making in the future; thus, having greater benefit for the conservation of wild cetaceans.

Our research focussed on two dolphins and their offspring. The first, a male Tursiops truncatus by the name of Gambit, and the second a female Tursiops aduncus by the name of Frodo. As well as physical characteristics (Frodo has speckling on her underside, a feature common in older Tursiops aduncus), we confirmed their species identity genetically. This is done using DNA extracted from blood taken from routine veterinary check-ups. The principal finding of this study revealed that hybrid and backcross offspring were fertile – proven by a second generation in both cases.

Backcross fertile — One of the apparently fertile backcross offspring featured in this research.

The underside of Frodo, showing her belly speckling that is a common feature in mature Tursiops aduncus individuals.

This finding is important for two reasons. Firstly, it adds further weight to current scientific thoughts on evolution as a process. We like to think that evolution is a linear process and that once a new species is formed it is permanent until such time that it may go extinct due to some natural disaster or change in environment. We know, however, that this is not the case at all. There are a number of emerging examples that show species emerged in the past, likely as a result of physical separation, but then disappeared again when the physical barrier was removed because they simply merged and interbred with their parent species. A great example of this comes in the form of the Common Raven. We also know that reticulation, or the interbreeding of species during speciation is common and demonstrating the production of fertile hybrid offspring in this study provides a mechanism for this to happen.

Perhaps more importantly, however, this study demonstrates the potential resilience of Bottlenose Dolphins to adapt to changing environments. By producing fertile offspring, the success of gene flow events between different species of Bottlenose Dolphin may allow them to adapt to a more coastal or more pelagic way of life more readily should the need arise. We should take encouragement in this new understanding; although life in our oceans is currently under a great many threats it is likely that, thanks to the plasticity of evolution, the famous smile of a Bottlenose Dolphin will continue to greet us for many generations to come.

This research is published in PLoS ONE, Sepember 2018. You can download a copy of the paper here.

Full paper citation:

Gridley, T., Elwen, S.H., Harris, G., Moore, D.M., Hoelzel, A.R. and Lampen, F., 2018. Hybridization in bottlenose dolphins—A case study of Tursiops aduncus× T. truncatus hybrids and successful backcross hybridization events. PloS one, 13(9), p.e0201722.

November 30, 2015 Daniel M Moore

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 (N_e) 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’.

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).
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/>
JNCC. Cardigan Bay/ Bae Ceredigion – Special Area of Conservation – SAC – Habitats Directive. at <http://jncc.defra.gov.uk/protectedsites/sacselection/sac.asp?EUCode=UK0012712>
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).
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>
Tethys Research Institute. Biopsy sampling and intrusive research. (2013).

May 6, 2015June 22, 2015 Daniel M Moore

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 59^th 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.