EGG heads talk ecological genetics in Dublin

Using genetics to understand ecology is fascinating. The data reveal things that often cannot be found by observation alone, such as patterns of cryptic diversity, migration pathways and the source of colonising populations.

But life in ecological genetics research is peculiar because we sit on a border between two fairly different fields of science. In an ecological crowd we’re called the ‘genetics person’ while among geneticists we’re seen to have only a rudimentary knowledge of ‘real’ genetics and our comments on ecological theory are sometimes met with funny looks. So spending time in an ecological genetics crowd is refreshing and, last week, about 30 members of the British Ecological Society did exactly that.


The BES Ecological Genetics Special Interest Group (affectionately known as EGG) meet every year and 2017 was their first meeting in Ireland. It was a strategic move from the organising team headed by Dr Gemma Beatty (Aberystwyth University) to expand their Irish membership. The conference took place in the picturesque National Botanic Gardens, Glasnevin, Dublin. Continue reading “EGG heads talk ecological genetics in Dublin”

Research haikus

Last month, the Zoology Department’s Dr. David Kelly launched his first book of Japanese short form poetry, Hammerscale from the Thrush’s Anvil. At the launch of the book, David invited us in the audience to try our hand at writing our own haikus.

Taking him up on his challenge, and taking inspiration from his book, a few of us in the School of Natural Sciences have penned our own poems based on our areas of study. We even have a contribution from David Kelly himself!

Trying not to sacrifice coherency at the alter of syllable number was a rather new struggle for most of us, but we managed and, I’d like to think, emerged with a greater appreciation for the poets in our midst. Read on for our science-y foray into the arts!

(Paula Tierney @_ptierney)


Yellow red fish eyes

Maybe that’s a nematode?

No, it is more fish

Paula Tierney


Carbon fixed by plants

Then sequestered in the soil

Helps to keep Earth cool

Matt Saunders


Hoverflies hover

Syrphidae flying over

Gardens of flowers

Sarah Gabel


Monochrome poets

Curved claws etching musky spoors

Into the cold night

Aoibheann Gaughran Continue reading “Research haikus”

Ecology & Science in Ireland: the inaugural meeting of the Irish Ecological Association


In the years to come, 140 ecologists working in Ireland will look back with fond memories of being part of the inaugural meeting of the Irish Ecological Association (24th-26th November). We will remember hard-hitting plenaries, compelling oral presentations, data-rich posters, influential workshops and the formation of the IEA’s first committee. The lively social events might be harder for some of us to remember…

There could not have been a more fitting way to open the conference than the plenary seminar from Professor Ian Montgomery (QUB) on Thursday night. Within the hour, he managed to given an incredibly detailed summary of the natural history of Ireland, showing how Ireland had been an island for 16,000 years and presenting evidence that human occupation dated back 13,000 years. Ian stepped us through successive mammal invasions, classifying them as true ‘natives’ and more recent ‘invasives’. His seminar was open to the public and the audience included local farmers with strong concerns about the impacts of invasive mammals on their stock.

We were welcomed the following morning with an energetic plenary from Professor Jane Memmott (U Bristol), covering her strikingly diverse career. She took us on a journey from life as a medical entomologist, to tropical ecologist living in a Costa Rican jungle tent, to invasion biologist in the land of invasives – New Zealand, to her more recent work on biodiversity in urban and farmland systems. Quantitative food webs were the central theme. Using both simple and complex food webs, based on enormous data sets, Jane clearly showed that we only see the full story about ecosystem dynamics by examining links between trophic levels. Continue reading “Ecology & Science in Ireland: the inaugural meeting of the Irish Ecological Association”

Trump and the future of “America’s best idea.”


In 1872 Yellowstone National Park was established as the first National Park not only in the USA, but in the world. President Ulysses S. Grant signed into law the Yellowstone National Park Protection Act, and so the National Parks were born. Today 59 National Parks exist throughout the United States, covering approximately 51.9 million acres with the goal of maintaining in perpetuity both wildlife and their habitat. Since 1916 the National Park Service (NPS) has been entrusted with the care of these National Parks, and this year they celebrate their centenary.

The National Parks have been referred to as “America’s best idea”, an ideology that has spread across the globe promoting the conservation of what little natural habitat and resources remain. What began as a single National Park in 1872 has spread to over 100 nations and been built up to approximately 1,200 National Parks.

In the wake of Trump’s shock election win, researchers, scientists, conservationists and a significant proportion of the public are lamenting for our natural world.It is no secret that Donald Trump does not openly believe in climate change, refusing to accept the overwhelming scientific evidence. Not only this but he has also promised to dismantle the Paris Agreement which sought to limit the temperature rise associated with global warming to below 2°C in order to reduce the risks and impacts of climate change.

Today the NPS actively teaches about, and warns of, the dangers of climate change to both the National Parks and the natural world at large. However, it is feared that the NPS will be silenced under a Trump Administration. Under the second Bush Administration talk of climate change by the NPS was prohibited under a decree from the Secretary of the Interior. Similar circumstances are expected under a Trump Administration, with Sarah Palin expected to be made Secretary of the Interior. If this comes to fruition then Palin would oversee the extraction of natural resources on approximately 500 million acres of public land, including the iconic National Parks, such as the Grand Canyon and Yosemite. Palin’s stance on natural resources leaves little hope as she has actively campaigned for the drilling of oil within the Alaska National Wildlife Refuge, the nation’s largest Wildlife Refuge, at the expense of the wildlife within it: “If a caribou needs to be sacrificed for the sake of energy … I say, ‘Mr. Caribou, maybe you need to take one for the team.’” Continue reading “Trump and the future of “America’s best idea.””

Tropical Field Course Kenya

IMG_1564We’ve just returned from our annual Tropical Ecology Field Course in Kenya with our final year undergraduates. Our trip took us on a journey through the rift valley to the theme of biodiversity, conservation and sustainable livelihoods. Here are some of the sights of the trip:

Visit to Lake Nakuru National Park where water levels have been on the rise creating these eerie tree graveyards!
A Grey Crowned Crane on the shores of Lake Baringo where we were camping.
A hike along the soda lake of Bogoria



Maribou stork looks on
Little fruit bats keeping a close eye on us!
An olive baboon and her baby eyeing us suspiciously!
The gorge at Hell’s Gate National Park, Naivasha- look out Simba!


Author: Deirdre McClean

Photo credits: Deirdre McClean and Ian Donohue

The Wakatobi Flowerpecker: the reclassification of a bird species and why it matters

Wakatobi Flowerpecker - Male

I posted previously about my PhD research studying bird populations from the tropical and biodiversity-rich region of Sulawesi, Indonesia. I am happy to announce that the first paper as part of this research has just been published in the open access journal PLOS ONE. To read the full paper for free, click here. This work is a collaborative effort from staff in the Department of Zoology in Trinity College Dublin and Haluoleo University in Sulawesi. Here, I’d like to discuss the wider importance of the findings of this study.

My current research focuses on bird populations from peninsular South-east Sulawesi and the nearby Wakatobi Islands. The main focus of this paper was to reassess the taxonomic status of a population of birds from the Wakatobi Islands (i.e. whether these birds represent a species or subspecies). The birds in question belong to the flowerpecker family (Dicaeidae); a group of small and colourful, arboreal passerines found from Southeast Asia to Australia. The Wakatobi birds were originally described as a separate species (Dicaeum kuehni) from those on mainland Sulawesi by the renowned avian taxonomist Ernst J. Hartert. However, for reasons that remain unclear in the literature, the Wakatobi birds were later reclassified as a subspecies of the Grey-sided Flowerpecker (Dicaeum celebicum) from mainland Sulawesi. Therefore we decided the Wakatobi populations were deserving of reassessment. From comparisons of plumage and morphology (that is, the measurement of various features such as a bird’s wing and bill), as well as estimates of genetic divergence and phylogenetic relationships between Wakatobi and Sulawesi populations, our results suggest the Wakatobi birds deserve to be recognised as a distinct species. We have therefore recommended the Wakatobi populations be reclassified as Dicaeum kuehni, a species found only on the Wakatobi archipelago and put forward the common name ‘Wakatobi Flowerpecker’.  For more detailed methods and results check out the paper.

“So what?”, you might say. Well, despite centuries of work from naturalists aiming to estimate the number of different species that exist or have existed on Earth (be they animal, plant, fungus, bacteria, etc) and further understand their evolutionary relationships, we still have a lot to learn! Therefore, this research adds another tiny piece to this enormous and incomplete jigsaw. Through a greater understanding of life on Earth we can attempt to answer some of the great philosophical questions, such as ‘Where and how did life start?’; ‘How and why do new species appear?’;  ‘Why has life evolved to become as it is today?’; and ‘How have we, as humans, come to be?’. Anyway, let’s be honest, who doesn’t enjoy learning of a recently discovered species or simply one they haven’t heard of before (be they as cute as the recently discovered olinguito or as frighteningly ugly as the goblin shark)? But the endeavour to discover species and classify and quantify the diversity on life on Earth brings us much more than entertainment and endless fascination, it also has very practical applications. Data on the distribution and conservation status of species are one of the major sources of information used to inform conservation policy. Therefore, as we are in the midst of an extinction crisis, it is vital that these data are accurate.

In order to maximise our understanding biodiversity, particularly in the remote and poorly known Sulawesi region of Indonesia, we require multi-disciplinary research. For example, take a look at Figure 1 below. On the left are a male (above) and a female (below) Grey-sided Flowerpecker from mainland Sulawesi. On the right are a male (above) and a female (below) Wakatobi Flowerpecker. They look very similar, right? This is true. However there are subtle but consistent differences in plumage between the species (again, see the paper for more info on this). Without the collection of detailed morphological data and the generation of genetic sequences, we may have incorrectly concluded that these make up just one species, when in fact they are morphologically distinct, reproductively isolated and genetically very different. This demonstrates the need for modern research, not just in Sulawesi, but globally, to employ integrative research, combining traditional comparisons of colour, size and shape with modern genetic and phylogenetic analyses.

Figure 1. Plumage comparisons-p18pjcggcs1dgo1ulm1sor9s214bc
Figure 1. A comparison of plumage characteristics between male (top row) and female (bottom row) Grey-sided Flowerpeckers (left) and Wakatobi Flowerpeckers (right).

Despite the knowledge that the Sulawesi region is home to a large number of remarkable birds that are found nowhere else in the world, it has remained relatively poorly studied. Furthermore, there has been a lack of integrative ornithological research in the area and very little genetic sampling. Therefore, it is likely that avian species richness for the Sulawesi region is underestimated and that numerous bird species are awaiting description. On top of this, Sulawesi’s biodiversity is facing major threats from a rapidly expanding human population and mass habitat destruction, among other things. Unless we can encourage more multi-disciplinary research within the region, we will likely fail to recognise evolutionarily distinct lineages and run the risk of losing them forever.

Our current findings inspire many further questions. For example, why have the flowerpeckers on the Wakatobi islands become so different to their close relatives on mainland Sulawesi? In other words, what are the evolutionary pressures that have driven the divergence of the Wakatobi Flowerpeckers? By investigating these questions, we hope to learn more about the evolutionary processes of speciation and adaptation to living on islands. As the Wakatobi Flowerpecker is found only on the Wakatobi Islands, the protection status afforded to the islands may require reassessment. Furthermore, considering one unique bird species has evolved on the Wakatobi, could there be more? Watch this space.

Author and Images:  Seán Kelly, kellys17[at], @seankelly999

Biodiversity face off

Between the 1st and 2nd of May several members of the Trinity Centre for Biodiversity Research got their game faces on for the inaugural Intervarsity BioBlitz Challenge. For the first time the Trinity fox and co were pitted against the best biodiversity on offer from the DCU, NUI Galway and UCC campuses.

The stakes were high but the goal was simple; identify more species on campus then any other college in a 24 hour period and become the first college biodiversity champion of Ireland!

Kicking off Trinity’s effort to win the championship the birdwatchers were up bright and early to catch the dawn course. With 19 species identified it was the Sparrow hawk that caught the eye (but evaded the camera lens) of our inner city campus birds.

While the birders were digesting their findings some early morning pond dipping was throwing up its own surprises with a three-spined stickleback found in what looked an inhospitable pool out the back of the Zoology Department.

The unlikely source of our only campus fish, the three-spined stickleback
The unlikely source of our only campus fish, the three-spined stickleback

Meanwhile in the more hospitable setting of Trinity’s own little secret garden some black ants were having a midday honeydew snack from their aphid herd during our plant identification walk.

The ant in focus can be seen feeding on the sugary secretions of the aphid, which in return for feeding the ants gains protection.
The ant in focus is feeding on sugary secretions from the aphid, which benefits from the ants’ protection in return.

Although many of the 32 species of invertebrates were found amongst the plants and pools, it was in the nooks and crannies of various building walls that Trinity’s diversity of arachnids, such as the snakes back spider, were found to reside.

Segrestria senoculata spider awaiting unsuspecting passers-by
Segrestria senoculata spider awaiting unsuspecting passers-by

While many volunteers were out rummaging in the leaf litter, Rachel Kavanagh was busy coordinating efforts at the central hub in the Science Gallery. There were also some inquisitive guests from St. Mary’s Boys school learning about pollinators with Green Bee Education.

Students from St. Mary’s Boys school building solitary bee shelters.
Students from St. Mary’s Boys school building solitary bee shelters.

As the day passed-by collecting and identifying specimens the deadline quickly approached and results were coming in. Galway won with a massive 581 species, with Cork on 451 leaving the race to avoid the wooden spoon between the Dublin Campuses. Unfortunately despite the heroic efforts of everyone, especially the botanists who identified 245 species of plants, Trinity could not avoid the dubious wooden spoon award, finishing with 346 and losing by just 27 species.

However while we didn’t win their was plenty of consolation prizes to be found as @EndangeredDAVE left some postcards and paintings of endangered Irish species in various spots around campus.

One of the many beautiful pictures distributed around campus by @EndangeredDave.
One of the many beautiful pictures distributed around campus by @EndangeredDave.

With an impressive 346 species recorded in an inner city campus and an incredible increase on previous years (16 species in 2012 and 126 species in 2013) TCD’s form is only on the up with the Trinity fox looking to be the top dog in next year’s event.

Look out for bioblitz events near you this weekend!

Author and Images: Kevin Healy, healyke[at], @healyke

Mooching in Madagascar

I recently returned from a short stint of fieldwork in Madagascar. The purpose of our trip was to run some behavioural tests of echolocation in tenrecs but things didn’t exactly go according to plan. Therefore we had plenty of time to explore and experience some of the wonders of the 8th continent.

Here’s a few of our wildlife highlights…

Shower lizard
Our friend from the shower
Spider webs
Enormous spider webs which span an entire river bed!
Moth case
Case from a bagworm moth
Spot the Indri (like four year olds in panda suits..)
Tree frog
What a poser
Just hanging around
Camouflaged frog
Spot the frog
Red bellied lemurs
Inquisitive red bellied lemurs (Eulemur rubriventer)
Hemicentetes semispinosus
Tenrec in a bucket! Hemicentetes semispinosus

 Author and Images: Sive Finlay, sfinlay[at], @SiveFinlay

Seminar Series: Nathalie Pettorelli, Institute of Zoology, London

space monitoring

Part of our series of posts by final-year undergraduate students for their Research Comprehension module. Students write blogs inspired by guest lecturers in our Evolutionary Biology and Ecology seminar series in the School of Natural Sciences.

This week, views from Sharon Matthews and Sinead Barrett on Nathalie Pettorelli’s seminar, “Monitoring biodiversity from space: a wealth of opportunities”.

Space, the final frontier for ecology?

Okay, you got me.  I am a trekkie who is fanatical about anything space related. So when I saw that this week’s seminar was to do with conservation biology from space, I was hooked!  Dr. Nathalie Pettorelli from the Institute of Zoology, London spoke with passion and enthusiasm about a new wave of ecology; monitoring species and ecosystems from space.

We were treated to information about remote sensing and how data from satellites can be used to help ecologists in the tasks of assessing population size and habitat condition. Earth observation (EO) data is free and is ripe for the picking.  Satellites are able to “boldy go where no one has gone before” or very few people have (sorry, I will stop with the star trek quotes now!).  They can get information on places that are often inaccessible and inhospitable for the lowly researcher like Antarctica and the Sahara desert.

One of the major tasks ecologists face is estimating the size of a population.  Dr. Pettorelli talked about an ingenious research project that used information from satellites to gain an estimate of the population of emperor penguins (Aptenodytes fosteri) in Antarctica.  Emperor penguin populations may be affected by climate change in the next few decades due to changes in sea-ice distribution and therefore it is important to get an estimate of the extant population.

Frettwell et al. (2012) examined quick-looks from three different very high-resolution satellites.  These have a resolution of ~ 10m and are able to show great detail.  The researchers looked for staining on images and classified it as snow, penguin, shadow or guano.  When areas with penguins were identified, they analysed the penguin pixel area through regression equations.  The statistics gathered from this were used to convert the area of penguins to population numbers.

In this study, the identification of a penguin from a pixel area was done by human interpretation and this led to some error especially in areas of high guano staining.  This could be resolved with future development of higher resolution satellites.  However, there were other issues that arose from using this technology.  Researchers identifying penguins from pixels made an assumption that a pixel constituted one individual when it may in fact have been an individual with a chick close to it.  This can affect the estimated population size.  The kind of error association with using satellites makes me think that this satellite approach should be backed up with other methods such as field study where possible.

Remote sensing can allow research to be undertaken over a broad spatial and temporal scale.  One of Dr. Pettorelli’s projects involved using EO data to assess a game reserve in central Chad for its ability to sustain a reintroduction of the Scimitar-horned Oryx (Oryx dammah).  A vegetation index (an indication of ‘greeness’) and annual mean precipitation, were assessed over a 27-year period for this game reserve. The results showed that precipitation was a main driver of vegetation dynamics and there was an intense greening in the south of the region.  Dr. Pettorelli also found that there was a contraction of the transition zone from north to south. This was an area that was identified as most suitable for the oryx.  This study showed how remote sensing can help inform ecologists about variation in a region over time.  It can greatly enhance the success of reintroducing a species into a suitable area.

There is no doubt in my mind that data from remote sensing can help ecologists in their work but I don’t think it should be used in isolation. Ecosystems involve a complex mix of interactions of many variables. Therefore, this approach could be used alongside other tried and tested (down to earth) methods of studying ecosystems and biodiversity.

Author: Sharon Matthews


Evidence of Global Change is Sky High

As we all know, climate change is affecting the world in which we live. One aim of scientists is to find out the extent of this change. At a seminar given recently in Trinity College Dublin, Dr. Nathalie Pettorelli from the Zoological Society of London informed us about a new method of doing this. With benefits including the cost, its sustainability, reproductivity and standardised information, satellite usage as a way to monitor biodiversity seems like an excellent option.

Dr. Pettorelli mentioned the vast array of options of satellites available for monitoring depending on what you want to find out in the study. For example, very high resolution imagery has been used in order to count penguins in colonies, Landsat has been used to study the gorilla habitat in Virunga and LiDAR satellites which give a 3-D image have been used in the Bavarian forest. But what interested me most was when Dr. Pettorelli mentioned the ability to monitor vegetation indices and how this technique was used in the reintroduction process of the Scimitar-horned Oryx in Ouadi Rimé-Ouadi Achim Game Reserve in central Chad.

The Scimitar-horned Oryx was last found in the wild in the 1970’s. However it has been kept in captivity and there were plans of reintroducing it back into this area in central Chad. In order to do so, a habitat assessment was undertaken to establish whether the area would still be suitable for the species to live in. The primary productivity over the past number of years was viewed using remote sensing (satellite) techniques. It was seen that the vegetation in the north had significantly dried while the area to the south showed intense greening. Because the Oryx lives preferably in sub desert regions, suitable habitat here was declining and it was not advised to reintroduce this animal to the area.

To me, this shows just how important this method of monitoring is. Due to the increased changes that come about as a result of climate change, species are no longer suited to their natural habitat. Although it wasn’t mentioned in detail in the seminar, it struck me that one use of this satellite method of monitoring would be to use it in assisted migration. This is a method of conservation that involves humans undertaking a translocation of an animal or plant species. This is used when a species can no longer survive in their habitat and so must be moved to a more suitable area. This method of conservation is debatable as there are many associated risks involved including the impact on original species in the new habitat. However, with scientists doing research on this to study possible effects, it may save a species from dying out. Suitable habitat needs to be found for assisted migration to work. The methods that Dr. Pettorelli uses in her habitat assessment in central Chad could be the ideal way to find these habitats needed. This highlights the need for this new method of data collection. Because it is done at such a big scale, it seems like an excellent way of finding large habitats suitable for a new species, whether it’s a tree or a large carnivore.

Changes are occurring globally as a result of anthropogenic actions, and species worldwide are dying out as a result of this. It is clear from the numerous examples mentioned at the seminar that there are many uses of satellite imagery in monitoring biodiversity worldwide. After hearing Dr. Pettorelli talk about this subject, I left realising just how important technology such as satellites are in a time when global change is sky high.

Author: Sinead Barrett


Kenya- A Summary through the vegetation

Campsite at Ol Pejeta, with Acacia xanthophloea in the background.
Campsite at Ol Pejeta, with Acacia xanthophloea in the background.

During the first week of November I travelled to Kenya to help out on the Tropical Field Ecology course, run by Ian Donahue in the Zoology Department.  Final year students from Zoology, Environmental Sciences, and Plant Sciences attended, and I was the postgraduate representative from the Botany Department.  While I should under no circumstances be considered a true Botanist-I study plant-animal interactions, and my botanical skills are mediocre at best- I did my best to learn about the amazing tropical flora of this region.  I’m sure others will write about the trip in detail, but I thought I would summarize our experience using the dominant or interesting plants we saw in each place we travelled.

Day 1&2- Arrive in Nairobi: After spending the night in the United Kenya Club, we awoke to a 5 hour drive north to Laikipia County.  Along the way the most striking plants were ornamental and known to a number of the students already- for example, colourful Bougainvillea was visible from quite a distance, as were the beautiful flowering Jacaranda trees- neither of course are native to the region.

Day 3-Ol Pejeta Conservancy, Laikipia County: We camped for the next two days in Ol Pejeta, and although we experienced quite a bit of rain, it was one of the most beautiful places I’ve ever seen.  The campsite was on the river and surrounded by Acacia xanthophloea, known to the locals as “Yellow fever acacia” for its medicinal properties.  It has a yellow-green bark which makes it quite distinctive.  On game drives we saw a lot of scrubby shrub species, none in flower.  It was difficult to identify many of the species in the conservancy but we were told many of them belong to the genus Euclea.  We also got our first glimpse of Solanum incanum but more on that later.

Solanum incanum at the Chimpanzee sanctuary in Ol Pejeta
Solanum incanum at the Chimpanzee sanctuary in Ol Pejeta

Day 4- Nakuru: Compared to Ol Pejeta the flowering flora here was a breeze to identify! Although a lot of it comprised invasive species, such as Lantana and Datura species, and of course the conspicuous Solanum incanum (also known as Sodom’s Apple).  S. incanum gives the management at Nakuru serious trouble, growing uncontrolled in areas that are over grazed or disturbed by humans.  In addition to the invasives we saw a lot of Leonotis mollissima and identified a lovely shrub called Tarchonanthus camphorates from its camphor scented leaves.

Day 5-11-Baringo County: And finally, after quite a lot of driving (during which we saw some impressive Euphorbia candelabra specimen), we arrived in Baringo County.  Our first day here we went for a hike at Lake Bogoria, and spotted two species of interest.  First, the indigenous Adenium obesum, or Desert Rose.  Some of the students carried out their mini-project on the nectar secretion and flower visitation of this species, and found nectar volume varies with time of day.  Second, we saw Salvadora persica, known as the “toothbrush tree.”  Our local guide told us people chew the twigs to promote dental hygiene.  Throughout the county, two new species of Acacia were also evident- Acacia tortilis (The Umbrella Thorn, accurately named after its shape) and Acacia mellifera.  Women in the area highly value A. mellifera because the honeybees they keep apparently favour it for making particularly sweet honey.  And finally, one cannot forget to mention the damaging invasive Prosopis juliflora.  Native to Mexico and Central America, it was introduced to try and control soil erosion and now has spread throughout the county.  It is difficult to remove as it can regenerate from the roots, and is not particularly useful as fuel, food for livestock or fencing.

Adenium obesum, Desert Rose at our campsite in Baringo, Robert’s Camp
Adenium obesum, Desert Rose at our campsite in Baringo, Robert’s Camp

This description is simply the most obvious vegetation we saw on the field course.  The diversity of flora and fauna was overwhelming and I think the students, demonstrators, and staff alike were impressed and awed by the environments we were fortunate enough to experience.  Kenya is truly an amazing place!

Author and Picture Credits;

Erin Jo Tiedeken, tiedekee[at], @EJTiedeken