Thomas Kent ID paper published


The Identification of a 1916 Irish Rebel: New Approach for Estimating Relatedness From Low Coverage Homozygous Genomes


Charlotte from Kenya

I’ve been assigned a particularly special task for my MSc evolutionary biology thesis. Under the supervision of Dr Jens Carlsson, and John Byrne (conservancy director/wild explorer), my project will examine eDNA in Kenya.

Galana conservancy is a wildlife reserve situated on the boarder with Tsavo East national park, in Southern Kenya. It contains masses of African wildlife. For my thesis, I’ll be focusing on Plains Zebra (Equus quagga) and giraffe (Giraffa camelopardalis). I’ll be collecting their scat in order to extract DNA. DNA like this is classified as eDNA (environmental DNA). Environmental DNA has the ability to revolutionise genetics.
So, what is it? An animal sloughs off skin cells, saliva, faeces, mucus, blood etc which are left in the environment and which contain traces of DNA. This is eDNA. The DNA can then be extracted and analysed for use in population genetics, management, species barcoding, and species monitoring. Population genetics measures the genetic diversity, richness, and level of inbreeding in a population. It’s essential for the long-term management of an animal population. Environmental DNA using scat has had little study. Therefore, the aim for my study is to develop a technique using eDNA from giraffe and zebra scat. This data could hopefully be used at a later point for population genetics (there has been little pop gen on zebra and giraffe either).
So here in Galana, I am running a sampling programme for collecting giraffe/zebra scat over the next 10 days. I have already carried out 2 days of sampling, which went well (aside from tracking a herd of giraffe for a good 45 minutes without a hint of poo and then watching them disappear off into the distance).
The trip is quite amazing so far. As well as zebra and giraffe, I’ve seen Impala, oryx, baboon, hippos, a lionness, warthogs, water buffalo, secretary bird, gazelle, elephants, gerenuk, crocodiles, as well as the animals I’ve probably forgotten to mention here.
More updates on poo patrol later.

Memorandums of Understanding signed between UCD and Pwani University, Kenya


December 10th 2015
Venue: Kenyan Embassy Dublin.

It is with great pleasure that we would like to announce that University College Dublin and Pwani University, Kenya have agreed upon Memorandums of Understanding to facilitate academic and student exchanges between our two countries.

The agreements follow an intense period of negotiation and consultation between University College Dublin and Pwani University in Kenya and were facilitated throughout by the NGOs Friends From Ireland, The Galana Wildlife Conservancy Kenya, the Watamu Marine Association Kenya and the Agricultural Development Corporation of Kenya. This initiative has the support of the Irish Ambassador to Kenya Dr. Vincent O Neill, the Cabinet Secretary for the Environment in Kenya, Professor Judi Wakhungu, and the M.D. of the Agricultural Development Corporation Kenya, Dr. Andrew Tuimur and has been kindly facilitated over recent months by the Kenyan Ambassador to Ireland Mr. Richard Opembe.

In addition to the announcement of the MOUs we are also announcing the following:

1. The creation of a Scientific Field Research Station at the Galana Wildlife Conservancy in Kenya, designed to promote knowledge and open up this critically endangered environment and its endangered wildlife to Kenyan and International students of the Sciences.

2. The commencement, by Friends From Ireland of the Galana Secondary School building project complex adjacent to the Primary and Infant School complexes constructed by FFI over the last three years.

3. The intention to support an application to have the Galana Wildlife Conservancy considered for inclusion as a World Heritage Site.
This is a new approach to community-conservation-education challenges in developing countries and has brought together voluntary National and International community and conservation groups, business groups, state agencies and those in relevant political offices, to ensure that promises are kept and goals are achieved.

This new model of multi-agency partnership, bringing volunteering and education together to tackle community and conservation challenges in Kenya will herald the beginning of a significant scientific study of this crucial eco-system and its endangered species, the development of the community which shares that environment and the development of educational facilities from infancy to third level education. It is a model that works through inclusion, the realistic consideration of community, cultural and conservation concerns, the management of realistic goals based on what can be achieved by listening to the issues on the ground and planning processes that start with real dialogue.


I would like to thank The Kenyan Ambassador H.E. Mr. Richard Opembe for inviting us to make the announcement from the Embassy. I would also like to thank the representatives of University College Dublin, Friends From Ireland and the Minister, Mr. Damien English for supporting our endeavours. Indeed we wish him well on his visit to Kenya. For more information following this release please contact me at or through the following websites

Information on upcoming community and conservation projects for 2016 will follow through these websites and related Facebook Pages

Portraiture at sea


As the expedition is coming to an end and the science part is over, on this stormy day heading back to Galway, I would like to present what has been secretly going on throughout this cruise, namely, portraiture at sea. I am the artist on board, a recent graduate from the Angel Academy of art, in Florence (Italy), a classical painting school, and I was here to do an experiment: portrait the crew and scientists on board. Portraiture has a long historical tradition, it has been done for centuries and it still holds incredible charm for me today. I am fascinated with faces and expressions and here I had great inspiration, also because I know the people in person, talk and interact with them, which makes a great difference. Trying to capture them in a drawing has been challenging for me, as my work is only at its start, and also a great honour because I think the people who represent the soul of this ship should be celebrated; and a portrait is the best way because it is not a photo, it has much more life and depth than a photo, and it connects people.

Above is a group photo during the “exhibition” that was held last night, (the venue was in the sitting room!) and it includes few of the subjects of the portraits. A big thanks to everyone and a special thanks to Raissa for her great support!

Blog by Alice Antoniacomi

Sponge Gardens – Chemistry of the deep

mud volc3

Our control site (non-chemosynthetic) was a deep underwater peninsula at the mouth of the Mediterranean Sea. This rocky bottom and fast flowing nutrient rich waters provide the perfect habitat for sponges and other filter feeders like corals. These beautiful animals grow in large numbers along the seabeds. Sponges are soft bodied, sessile organisms which lack a physical defence so in order to deter predation they often produce interesting toxins. These toxins are often active against human infections and diseases offering us new treatments for a range of human afflictions such as cancer and MRSA. The active compounds are extracted from the organism and screened in numerous biological assays around Ireland and the world.

Despite the strong underwater currents and uneven surfaces our team of extremely skilled ROV pilots managed to collect several samples so we can return these organisms to our lab to better understand and describe the chemistry of these deep water invertebrates. In addition to looking at the chemistry of the sponge itself we are interested isolating and screening the microbes contained within the three dimensional matrix of the sponge tissue. Should any of these microbes be producing bioactive compounds this will afford us a renewable source of the chemistry without having to return to deep waters of Cadiz.
Blog by – Ryan Young

Chimney Henge – a story of gas escape and chemosynthetic bacteria

The Hesperides mud volcano, Gulf of Cadiz, is a complex structure of three mounds, ~200m high, 2 km x 4km in size and with east-west oriented ridges extending to the east. The mud volcano is flanked to the west and south by a crescent-shaped moat, and to the north by pock marks 500m in diameter. The flanks of the mud volcano are covered in a sticky grey mud with a 10-20cm thick cover of light-brown coloured pelagic foram (plankton skeletons) sand. In places on the flanks there are tongues of fallen cylindrical chimneys of carbonate, up to 1m long and 30cm in diameter. These tongues of fallen chimneys and mud are elongated down the slope of the mud-volcano.

mud volc1
The origin of these carbonate chimneys is thought to be a result of methane and hydrogen sulphide gas seeping from deep below the mud volcano (from several kilometres beneath the seafloor) and its interaction with bacteria and seawater. The bacteria live off the methane (CH4) increasing the alkalinity of the sediment pore fluids and anaerobically oxidising the methane to bicarbonate (HCO− 3) and the sulphate to sulphide (HS−) which reacts with calcium ions in the seawater resulting in the precipitation of carbonate (CaCO3) and the generation of hydrogen sulphide (equation 1). The flow of methane up through the sediment causes the chimneys to grow around the methane bubble streams generating the cylindrical structures we call chimneys and the sulphide supports other types of bacteria.

(Eq. 1) CH4 + SO2− 4 →HCO− 3 + HS− + H2O → +Ca+2 → CaCO3 + H2S +H2O

The chimneys we see at Hesperides are mostly fallen, lying on their sides on the flanks of the mud volcano. It has been suggested by other scientists that these chimneys are formed inside the sediment that has since been eroded by strong currents to expose the chimneys which have then then fallen over. But we have discovered at the summit of the Hesperides mud volcano a forest of upright carbonate chimneys, up to 2m tall and 50cm in diameter, embedded in the mud ‘lava’. This we have named ‘Chimney Henge’, because the circular arrangement of the chimneys resembles the famous Stonehenge Neolithic monument in England. The summit of the volcano is also where we see bacterial mats, escaping methane gas and the youngest mud flows.

mud volc2

We propose that the carbonate chimneys grow both in the sediment and in the water column immediately above the seafloor at the summit of the mud volcano where methane flow is focused. These chimneys are then pushed down slope after being incorporated in subsequent eruptions of mud and gas as the mud volcano edifice grows. This process also explains why the fallen chimneys are found on the volcano flanks where they form tongues of chimneys and mud oriented down slope, having been carried there in mud flows erupting at the summit.

The abundance of carbonate chimneys at Heperides mud volcano show that there has been a long history of intense methane gas escape and mud eruptions supporting chemosynthetic life here for many thousands of years.

Blog by – Bramley Murton


ROV Holland I returning from a night dive

ROV Holland I returning from a night dive

Jens and Jeanne and the team have been busy surveying the first sampling site on the Deep-links expedition. Maria Judge, of the INFOMAR programme in the Geological Survey of Ireland, used a multibeam echosounder to create an in-depth map of the terrain. Using this mapping info the crew were able to determine which sites may have the most chemosynthetic activity and be the most interesting to explore.

Multibeam map of Hesperides provided the scientists with a good picture of where to sample.

Multibeam map of Hesperides provided the scientists with a good picture of where to sample.

At the bottom; a deep-sea crab tries to protect its new-found loot.

At the bottom; a deep-sea crab tries to protect its new-found loot.

The depth at the site is over 1000m taking the ROV approximately one hour to reach the sea-floor. At this depth, in total darkness, the marine species have unique and varying adaptations to survive. Sediment samples have been taken using push and gravity cores and water was sampled with a CTD and water sampler at varying depths for biological and chemical analysis. After enjoying many days of fine Spanish weather the ship was forced to retreat further into the bay to wait out some big swells but are now taking the opportunity to sample another mud volcano closer to shore.