Tag: Postgraduate research

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Bird Feeders

AWBVDSC_2691.jpeg-p194p512d2km1im218hp1hk2sjt-0It’s coming up to winter so people will be conscious that our garden birds need a helping hand to get through the cold months. Bird feeders will be stocked, bread served up and water dished out. In the UK alone, almost half of households provide supplementary food for birds throughout the year. And although songbirds are usually the species that come to mind when we think of provisioning food the same principle can apply to more exotic birds, notably vultures. Indeed conservationists have supplied extra food to these scavengers for decades. Instead of bread or berries, a carcass is left out for the vultures to feed on. A recent paper of ours advocates this technique for a population of African White-backed Vultures in Swaziland.

This country is home to the densest breeding population of this species so we should do our best to conserve them given the huge declines suffered by vultures throughout the Old World. In the paper we showed times when there isn’t enough food in Swaziland to feed the whole population which means the birds are forced to forage farther afield, most likely in South Africa. On the face of it this doesn’t seem problematic because South Africa has huge populations of herbivores which could supply carcasses to vultures. But the birds must fly over unprotected areas as well. This increases their chances that they’ll encounter a poisoned carcass, perhaps set out by a farmer to kill the terrestrial carnivores harassing his livestock.

It’s well known that vultures are particularly sensitive to poisons, especially NSAIDs. Their group foraging behaviour makes them even more susceptible too, the discovery of a carcass by one individual will bring in the rest of the soaring birds in visual range. The hope with creating vulture restaurants is the birds will focus on foraging for carrion in Swaziland, minimising the risk of poisoning.

Yet there are well known problems with supplying supplementary food for animals in general. They may act as an ecological trap for instance, drawing the birds into an area only for the fickle humans to stop the supply of food. Carrion is an unpredictable resource so vultures forage in a characteristic way to improve their chance of encountering it. If food is supplied in a predicable way there is a fear we may disrupt these behaviours. Another recently realised danger in providing supplementary food is that it can attract unwanted guests. Sites tailor made for vultures in South Africa were shown to draw in jackals and hyenas.

Given these issues practitioners need to think carefully about how they provide food. Perhaps the best approach is a series of sites supplying food at random which would best represent the distribution of naturally occurring carrion.

Author: Adam Kane, @P1zPalu, kanead[at]tcd.ie

Photo credit: Munir Virani

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PhD students and the cult of busy

 

busyAcademics often remind me of the Four Yorkshire Men in the old sketch (not actually originally a Monty Python sketch, but famously performed by them in their live shows – comedy nerd out over, carry on), except rather than trying to outdo each with how deprived we were as kids, we’re always trying to outdo each other with tales of how busy we are. We do it so often that it becomes hard to draw the line between how much this reflects how busy we really are, and how much is just “bragging” to assert how important we are. Somehow, we associate importance/success with being constantly busy, and think that good scientists work stupidly long hours and rarely take a day off. This is so inbuilt into our working culture that we feel guilty when we only work 9-5 or have the occasional lazy afternoon!

Worryingly the cult of being busy starts with PhD students. It’s insane the number of times I hear PhD students turning down opportunities (both academic and recreational) because they are “too busy”. Of course there are always going to be periods where you are truly “too busy”. The last few days before you submit a paper, the weeks leading up to a conference, or when you’re in the final stages of writing up. But in general there is nothing in your PhD that is so important that you can’t delay it for a few days/weeks/months. Most times your supervisor won’t mind waiting a few extra days for a draft (they are also busy!), and you can always email journal editors for extensions when writing reviews or returning corrections.

Full disclosure – I was the kind of PhD student that drives me crazy now. I refused to go to seminars unless they were completely related to what I was working on, I rarely read papers for lab meetings, and in my final year I stopped going to morning coffee, ate lunch at my desk and bit the head off anyone who came to my office to chat to my labmates (to be fair this got totally out of control when we got an espresso machine in the office and almost every postdoc in the building came by at least once a day! I’m blaming you Ezard! :P). I regret my tunnel vision now. There were so many things I could have taken time out to learn – things that would have saved me lots of time during my PhD and later in my career. This year I finally taught myself LaTeX for example, which would have saved me months of blood, sweat and tears formatting my thesis. I also wish I’d taken more time to learn to program properly. I’m now working hard to improve my coding, but see that if I’d taken a few months to do this in my PhD, I’d have saved myself a lot of heartache.

I guess my message to PhD students is to try and be less busy, and make more of an effort to enjoy the PhD experience! Easier said than done I know! I am sympathetic – I remember how it felt as a student. I remember feeling terribly inadequate compared to the high achieving PhD students and postdocs around me. I remember the crushing sense of panic and stress as my hand-in date approached and I still hadn’t got past my first chapter. I remember thinking that every hour doing something unrelated to my PhD was an hour wasted. But what I should have known, and what I’ll remind PhD students now, is that your PhD is about so much more than your thesis. Yes, you are judged on your thesis, and you will have to defend it. But you should also be training yourself to become part of the scientific community. Whether you stay in academia or not, it’s pretty unlikely that you’ll ever work on the exact topic of your PhD again. So you’ll need an awareness of other things that are happening in the world of science! You’ll also need to develop other skills, like presentation skills, teaching, and outreach. You can’t do that if you only focus on your PhD topic and nothing else.

But how can we be less busy (and hence less stressed)? This is something I’m constantly trying to deal with myself (if you think you’re busy as a PhD student, don’t ask a Faculty member how busy they are!). A few things I’ve found useful are as follows:

1. Learn to stop when something is “good enough”
Many of the traits that make us good academics, like attention to detail and the desire to do our best at things, can also lead to terribly stressful perfectionism. Instead try to establish when something is “good enough” rather than “perfect”. This is something I’m trying to improve at myself, and I’ll admit that it’s difficult. However, as a PhD student your supervisor should be able to help. Sometimes you can leave stuff like properly formatting references until you’re ready to submit a paper. If you’re really struggling with one section, maybe send the rest to your supervisor for comments, rather than waiting until it’s all perfect (but ask them first).

I find deadlines help me with this – for example, I have a habit of constantly fiddling with lectures so if I have two weeks to make one, it will take me two weeks. However as time goes on, the amount of improvement approaches an asymptote, so two weeks of effort doesn’t create a lecture much better than one that takes me a week. Therefore I give myself strict amounts of time I’m allowed to work on each lecture. After that time passes it’s done. It’s not perfect, but I doubt the students would notice the difference. The same goes for conference presentations and paper drafts.

2. Use “waiting time” efficiently.
PhD students often forget in their rush to finish something and hand it to their supervisor, that their supervisor will take time to return it with comments. If you know this is going to happen you can use that waiting time more wisely. It’s often a good time to format references, add details to manuscript central if you’re submitting a paper, fiddle around with your thesis template etc. Also talk to your supervisor about when they have time to give you comments. There’s no sense in rushing to hand in a draft chapter the day before your supervisor goes on holiday for two weeks leaving you twiddling your thumbs.

3. Schedule time for non-essential reading or for learning skills
As a PhD student I stopped reading widely near the end of my PhD. However, at postdoc interviews I often got asked about what papers I’d read recently that I’d enjoyed. These questions are designed to see how broad your knowledge is, so citing the technical paper you just read on your PhD subject is not going to impress. Additionally, if you want to stay in science (academia or otherwise), you probably should have a basic knowledge of the current controversies in the field. The only way to do this is by reading. However, it’s hard to read non-essential stuff. The easiest way to ensure you do it is by scheduling a bit of time each week (maybe Friday afternoon or Monday morning) to do it. If you choose a time you usually get very little work done it won’t eat into your productivity. I often use this kind of scheduling to learn programming skills or to play with a new R package.

4. Say yes to opportunities!
Of course there’s a limit to how much you can say yes to. But remember that your time as a PhD student is probably one of the most flexible times of your life, especially if you don’t have kids yet. Your schedule is mostly yours to make. So if you can’t get anything to work, spend the day in a local museum and catch up one evening or at the weekend. If you live in a rainy place (cough cough Ireland) and the sun is out, take the afternoon off and go for a bike ride or a walk – you can work a little longer tomorrow when the sun disappears! If you get offered skills training take it, particularly if it’s free and doesn’t require traveling too far. If your friend wants a hand on tropical field work for a couple of weeks, and you have the money, go with them! It’s a great chance to see an exciting country in a whole new light. Go to seminars and conferences. Talk to your colleagues at coffee time. Take a proper lunch break. It’s amazing how much you can get done in short bursts when you need to, especially if you’ve scheduled in proper breaks.

5. But learn to say no to time sucks…
Not everything people ask you to do is going to be useful, and/or fun. If in doubt, speak to your supervisor before saying yes to things (you can then also use the old “my supervisor is an ogre and won’t let me help you, sorry” excuse). For example, organising an event like a conference or an outreach event, is a great thing to have on your CV. But once you have one of these on your CV the gains of organising a second one are low. These things often take up ridiculous amounts of time and energy. The same goes for teaching. It’s great to get teaching experience, but try and get quality experience with different kinds of teaching rather than saying yes to everything. Be strategic in what you spend your time on, based on filling gaps in your CV, and preferably on what you want to do after your PhD.

6. Talk to someone if you need help.
Finally, if you’re really struggling with feeling busy and overwhelmed, talk to someone! Sometimes in academia we have the habit of not talking about problems. This leads us to believe that everyone else is coping, and we’re the only ones struggling. The truth is EVERYONE struggles sometimes. Talk to your friends/PhD colleagues about how you feel – they’ll soon make you feel less alone. Talk to your supervisor, or another faculty member, about ways of coping with stress. And remember most places have a student counseling service if things are too hard to discuss.

Now go forth, be less busy, more happy and more productive as a result!

DISCLAIMER – Your PhD is not all about your thesis. BUT finishing your thesis on time is the most important thing at the end of the day. This post is not about encouraging slacking off, it’s about encouraging efficient working practices. Research has shown that people working 35 hour weeks get as much done as those working 60 hours (long-term, short-term there are gains in working long hours). So use your time wisely, work hard when you have the energy and motivation to do it, and speak to your supervisor if you’re worried about your progress. They are here to help!

Author: Natalie Cooper, @nhcooper123, nhcooper[at]tcd.ie

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Night Life! Friday 26th Sept

Night Life no writing

This Friday, members of EcoEvo@TCD, as well as others from the Botany and Zoology departments and Trinity Centre for Biodiversity Research will present Night Life! in the Zoology building at Trinity College Dublin. The event is FREE to attend and we will be open from 6pm-10pm with the last entry at 9.30pm.

Night Life! is an opportunity to meet researchers and to find out the kinds of things we do. Prof. Yvonne Buckley will give you a taste of our research highlights, Kevin Healy will wow you with his research on snake venom (yes there will be snakes!), Sive Finlay will perplex you with the mysteries of tenrec evolution (if you don’t know what they are, come along and find out, they’re really cute!), Sean Kelly will explain how he discovers new bird species in Indonesia, Deirdre McClean will reveal the fascinating social lives of microbes, Thomas Guillerme will dazzle you with the lasers on his 3D scanner and the jaws of a shark, Claire Shea will amaze you by explaining why babies kick in the womb, Adam Kane will intrigue you with models of T.rex and maybe some vultures, and other students will be available to answer your burning questions about biology, evolution and ecology. So if you’re at a loose end on Friday night, come along and say hi!

Night Life! forms just one part of Discover Research Dublin, an annual event funded by the European Commission as part of European Researchers’ Night. The event is hosted by Trinity College Dublin, in partnership with the Royal College of Surgeons in Ireland. As well as Night Life! the evening will feature over 50 fun, interactive and free events and activities which will give you direct contact with researchers and allow for discovery, questions and participation. The event aims to challenge perceptions about researchers and show the creativity and innovation that exists in research across all disciplines. Activities are grouped under four broad themes – Body Parts, Creativity in Research, Meet the Researchers and Living Thought/Thinking Life.
We encourage you to visit, explore, discover and enjoy!

Author: Natalie Cooper, @nhcooper123
Image: Kevin Healy, @healyke

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What’s it like to study Zoology?

ZooEntrance

Tell someone on the street that you study Zoology and you can pretty much guarantee what their follow up question will be; “so you want to work in the zoo?” Well not quite. Of course some zoology graduates conform to the general stereotypes; the zookeepers, conservation managers and wildlife handlers who keep the rest of us supplied with a steady stream of tales of adventurous exploits and envy-inducing pictures on Facebook. But that is only one side of what you can do as a zoologist. It’s not all about frolicking with cute animals. There’s a healthy dose of molecular and lab-based research, theoretical studies and unavoidable number crunching which make up significant portions of life as a zoologist. Not to mention the diverse career opportunities, in areas such as science communication, education, policy and management, that are available to zoologists who venture beyond traditional research jobs.

A group of Transition Year students (15/16 year olds) recently spent a week in the department learning about what it’s like to study and work as a zoologist. Some of their questions and misconceptions prompted me to write this blog. Consider it the lowdown on zoological life if you will.

Zoology is not just about cute animals

If your interest in zoology stems from a desire to spend your days playing with puppies or equivalent bundles of cuteness then be warned. Such opportunities do arise during a degree course but they are relatively limited. You will spend more time in lecture rooms, dissecting dead animals or behind a computer than you will interacting with live animals. Of course field courses, summer research opportunities and final year undergraduate projects do offer many opportunities for hands-on, practical experience but these are the exceptions rather than the rule for life as an undergraduate zoologist. Post-graduation is another story entirely: there’s puppies, meerkats, elephants and dolphins aplenty if that’s what you want!

Zoology is not stamp collecting

Modern zoology stems from the long scientific traditions of enthusiastic naturalists: the genteel country gentlemen who wiled away the hours with contemplations of beetles and the exotic explorers who bravely ventured forth into unknown lands. These origins have created a common misconception that modern zoology follows the same veins; we may collect DNA sequences rather than butterflies now but surely it’s all just descriptive stamp-collecting at heart? Well, no. The methods and techniques used in zoology research are just as scientifically rigorous and complex as the “machines that go ping” which grace any physics or chemistry lab. Zoology is no more exempt from number crunching and computational methods than any other scientific discipline. You don’t have to be a maths whizz or computer nerd but a career in zoology, no matter what branch, will inevitably involve quantitative and not just qualitative analyses.

(Most) Zoologists are not hippy dippy animal lovers

A common misconception about being a zoologist is that it’s a just a fancier term for people who are only concerned with animal rights and issues. So we should all be strict vegans who spend our holidays trying to board Japanese whaling ships and we would rather halt economic progress than lose a single species of ant to extinction. Inevitably there is an element of truth to these ideas. We chose to study zoology because we’re fascinated by the natural world and the logical progression of such interests is a desire to protect and conserve all aspects of life on our planet. But our pro-animal tendencies don’t equate to making us anti-human!  Zoology teaches us to develop and apply appropriate, practical and realistic management and conservation actions to protect biodiversity while also enhancing human economic and social livelihoods.

Zoologists don’t just do field work

I chose to study science generally and zoology more specifically because I was adamant that I didn’t want to be stuck at a desk in an office. Guess where I spend most of my days now? Zoology isn’t all about trekking through jungles or diving on ocean reefs. Most research zoologists spend the majority of their time indoors whether that’s at the lab bench or behind a desk. The difference lies in the fact that, unlike a “normal” desk job, zoology provides plenty of opportunities to get out of the office whether that’s catching vultures in Swaziland, perusing museum collections, island hopping in Indonesia or traveling the world for conferences.  These are the undoubted highlights of any research project but they represent the cream of zoological life: usually you will spend far more time working at your computer than exploring the outside world.

Zoology is…great!

Don’t be fooled by the apparent negativity of the points above. I love studying zoology. I love the diversity of the subject, the breadth of knowledge to which we are exposed, the fascinating research questions we study and our undeniably awesome opportunities to travel.  I fell into zoology by accident rather than design and I could not be happier with my choice of subject. Research careers in zoology are varied and exciting but a zoology degree is also great preparation for so many opportunities beyond the realms of traditional research. Zoology is suited to people who are interested in nature, the environment, biology in general or anyone who is a confirmed lifelong disciple of Sir David. Zoologists are well equipped to take up any variety of career paths.

Our horizons both include and extend beyond the zoo gates!

Author: Sive Finlay, sfinlay[at]tcd.ie, @SiveFinlay

Image Source: Wikicommons

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School of Natural Sciences Postgraduate Symposium 2014: Part 4/4

B.terrestris

On the 20th and 21st of February we had our annual School of Natural Sciences Postgraduate Symposium. Over the course of two days many of our PhD students presented their work to the School. We also had two interesting plenary talks from Dr Sophie Arnaud-Haond (Ifremer) and Dr Lesley Morrell (University of Hull). Unfortunately our third speaker, Dr Fiona Jordan (University of Bristol) had to cancel due to illness.

For those of you who are interested in exactly what we work on here at EcoEvo@TCD, here are the abstracts from the PhD student presentations. Check out the TCD website for more details!

Ruby Prickett*: Geographical, ecological and genetic characterisation of perennial biomass grasses

*Unfortunately Ruby was unable to attend but we still have her abstract

Evidence suggests that increasing CO2 concentration from fossil fuels in the atmosphere is contributing to global climate change. There is great interest in producing energy from biological sources such as willow (Salix spp.), and the grass Miscanthus. This project aims to contribute to the development of grasses of the C4 genus Miscanthus and several C3 species (Dactylis glomerata, Festuca arundinacea and Phalaris arundinacea) for use as biomass crops, particularly on marginal land. This project aims to produce maps and species distribution models for each of the four species, to identify potential areas for production and their impact on biodiversity; to collect new accessions of Dactylis and Phalaris in the Northwest Europe and Miscanthus in Asia; and to assess the genetic diversity within each species.

Rebecca Rolfe: Identification of Mechanosensitive Genes during Skeletal Development: Functional evidence associated with the Wnt Signalling Pathway

Mechanical stimulation is important for the correct formation of the skeleton. Mutant embryos that develop with an altered mechanical environment result in defects in ossification and joint formation in the limb. We tested the hypothesis that mechanical stimuli influence the regulation of genes important in skeletal development by analysing the transcriptome of muscle-less and control skeletal tissue. We found 1,132 independent genes are differentially expressed with significant enrichment of genes associated with development and differentiation and cell signalling. In particular, multiple components of the Wnt signalling pathway are affected. An investigation of the functional effects of over/ectopically expressing Wnt pathway components in the developing chick will be tested using in ovo and ex ovo electroporation. It will be used to assess whether manipulation of the Wnt pathway in the developing joint mimics the phenotype that is seen when mechanical stimulation is removed, to identify whether or not disturbing the pathway alone causes the phenotypic disturbance seen when mechanical stimulation is removed.

Anurati Saha: The Influence of Mechanical Forces for the Definition of Articular Cartilage

Articular cartilage covers the terminal ends of bones at synovial joints. It allows pain-free movement with injury or degeneration leading to diseases such as osteoarthritis. Current treatment is whole joint replacement but stem cell regenerative therapies would offer a more sustainable solution. Previous research in the lab has shown that appropriate mechanical stimulation from movement of the embryo is required for normal joint formation; joints fuse when movement is absent. My project aims to increase our knowledge of mechanical regulation of joint development in a number of respects and to explore application of such findings to achieve stable differentiation of cartilage for alternative regenerative therapies.

In the first year of my PhD, I investigated the potential of embryonic limb bud cells to form cartilage in micromass culture. This allowed me to establish a protocol to achieve chondrogenesis and revealed the stage of maximum chondrogenic potential. This part of my work will be developed to compare the response of embryonic limb bud cells and adult progenitor cells from different sources (bone marrow and joint derived) to mechanical stimuli in 3D scaffolds, potentially valuable in the refinement of protocols for regenerative therapies

Claire Shea: Mechanotransduction in Skeletal Development: From Embryonic Development to Regenerative Therapies*

*Highly commended

Why do babies kick? Why do astronauts in zero-gravity lose bone mass? What are the causes of osteoporosis and osteoarthritis? The human skeleton allows us to move, but also requires movement for its own development and maintenance. Mechanical forces impact developing tissues, making embryonic movement (kicking and stretching) necessary for normal skeletal development. Understanding how a healthy skeleton forms is also important for skeletal disease therapies which seek to generate replacement tissues by recapitulating the normal developmental pathway with cell cultures. Wnt is a cell-signalling system known to be vital to many aspects of embryonic patterning, and has been implicated in mechanotransduction by our lab. My work focuses on identification of Wnt component genes responsible for transducing mechanical signals such as tension, hydrostatic pressure, or shear into a genetic response in developing joints and bones. To characterise gene expression patterns in normal vs. mechanically-altered environments, and to assess the role of Wnt, I use genetic mutants (mouse) and gene electroporation (chick). My goal is to apply this in vivo information to in vitro efforts, where stem cells embedded in 3-D scaffolds will be treated with an optimal genetic and physical environment to form functional, stable adult bone or cartilage tissue.

Sive Finlay: Tremendous tenrecs: curious convergence and distinctive disparity*

*Best talk 1/2

Understanding patterns of variation in morphological diversity, such as convergence and disparity, remains a challenge in evolutionary biology. In particular, questions of convergence and the predictability of evolution are central to the long-standing debate about the relative influences of historical contingency and determinism in evolutionary processes. Theoretical models indicate that some degree of convergence is expected by chance in most phylogenies. Therefore, quantitative analysis and explicit tests of superficial patterns are essential if we are to identify and understand significant cases of evolutionary convergence. However, most quantitative methods of identifying convergence were developed using relatively few groups for which detailed morphological and ecological data were already known. I want to test the wider applicability and usefulness of such quantitative methods by applying them to a new study group.

Malagasy tenrecs appear to be both disparate from each other and convergent with other “insectivore” mammal species. I’m assessing the evidence for significant morphological disparity within tenrecs and convergences among tenrecs and other mammals using a combination of geometric morphometric techniques and phylogenetic comparative methods. Subsequently, I will establish whether there are correlations between morphologically similar species occupying convergent ecological niches.

Kevin Healy: The evolution of potent venom in snakes*

*Highly commended

The ability of a predator to capture its prey is a fundamental element of ecological interactions. Such interactions can broadly be described as following general scaling laws underpinned by factors such as predator-prey body size difference’s, or habitat complexity. Unlike many predators, the ability of snakes to subdue and capture prey is mediated not by physical size but by their highly evolved venoms. Based on general predator prey scaling predictions I explore the hypothesis that venom potency is affected by ecological factors relating to the ability to quickly subdue prey. The factors I predict to increase venom potency include large prey size and low prey metabolic rate, as they reduce the speed of the venom affects, and habitat complexity, as more complex habitats would allow prey more opportunity to escape. Understanding the general drivers of venom evolution can lead to insights into the evolution of snakes and other venomous species and point to perhaps other untapped venom derived bio-resources.

Erin Jo Tiedeken: The impacts of Rhododendron nectar toxins on Ireland’s bees: deadly meal or valuable forage?*

*Best talk 2/2

Bees provide the valuable ecosystem service of pollination while visiting flowers and collecting nectar. We are currently experiencing a “pollinator crisis,” as pollinating species decline in response to anthropogenic pressures. Moreover, bees may exhibit species-specific responses to drivers of decline.

Rhododendron ponticum is an invasive flowering shrub that causes ecological and economic damage in Ireland. R. ponticum produces floral nectar in order to attract pollinators, but paradoxically this nectar contains neurotoxins called grayanotoxins. Our study investigated the impact of grayanotoxins on three bee species; Apis mellifera, Bombus terrestris, and a solitary Andrena species. For each species we tested whether consumption of nectar grayanotoxins had an impact on (1) survival, (2) consumption rate, and (3) behavior. Our results demonstrate that bees have critically different responses to grayanotoxins. Grayanotoxins are acutely toxic to honeybees, however, bumblebees exhibited no lethal or sublethal effects. Solitary bee survival was not affected, however bees exhibited temporary neurological symptoms after eating grayanotoxins. Rhododendron reduces available forage for honeybees and some solitary bees but could provide an important food resource for certain bumblebees. Our results demonstrate that studies of pollinator decline should include multiple species and should not extrapolate to species other than those included in the study.

Image Source: Wikicommons

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School of Natural Sciences Postgraduate Symposium 2014: Part 3/4

Rhododendron

On the 20th and 21st of February we had our annual School of Natural Sciences Postgraduate Symposium. Over the course of two days many of our PhD students presented their work to the School. We also had two interesting plenary talks from Dr Sophie Arnaud-Haond (Ifremer) and Dr Lesley Morrell (University of Hull). Unfortunately our third speaker, Dr Fiona Jordan (University of Bristol) had to cancel due to illness.

For those of you who are interested in exactly what we work on here at EcoEvo@TCD, here are the abstracts from the PhD student presentations. Check out the TCD website for more details!

Brian Murphy: The biocontrol and biofertilisation potential of fungal root endophytes

Fungal infections of crops are often devastating and costly. However, not all fungal infections are detrimental, and some are beneficial. Beneficial root infections often involve symbiotic root endophytes. Benefits to plants infected with endophytic root fungi include an increase in seed yield, enhanced resistance to pathogens and improved stress tolerance. Here, we report that grain yield in cold-stressed barley can be significantly increased after inoculation with a fungal root endophyte provided that a threshold level of nutrients is provided. We also show that endophytes derived from a wild barley species may provide similar benefits for barley grown under drought stress with low nitrogen input. These results suggest that locally-derived fungal root endophytes may have potential for reducing agricultural nitrogen input whilst maintaining acceptable yield. The full potential of these organisms is still to be determined and further studies are urgently required to develop specific beneficial root– endophyte associations, or combination of them, that are tailored to particular crops for maximum impact in agriculture. Many fungal root endophytes are amenable to axenic culture, sporulate readily and can be multiplied rapidly, suggesting that they could be developed as effective crop treatments in stressed crops and may have the potential to increase crop yield provided that the environmental and partner-specific conditions are met. The discovery of previously unrealised benefits associated with these fungi holds great future promise for developing economically and ecologically viable crop

Alwynne McGeever: The quantification of tree population dynamics*

*Highly commended

This project aims to quantify how the populations of Elm and Pine have changed geographically in Europe over the last 6000 years. Achieving this involves 3 tasks; (1) collecting pollen data on these species from the European pollen database (EPD), (2) comparing the timing of events in the populations at different geographic scales using the R package Bchron and (3) a focused study on the dynamics of Scots Pine in Ireland. Task 3 has two sub-tasks; (a) investigating the native status of Scots pine in Ireland, (b) investigating the past growth of Scots pine on bog surfaces in Ireland. This work will discuss the progress so far. Data has been successfully obtained from the EPD. Probability distributions of when events in the populations occurred in Ireland, the UK and Austria have been plotted, allowing the timing and synchronicity to be compared. The growth of Scots pine on bog surfaces in Ireland in the lead up to the Pine decline was also analysed, for which there were 3 distinct phases over the last 9000 years. The principle remaining work involves plotting events for every country in Europe and extracting pollen from a core to investigate a putative native population of Scots pine in the Burren, Co. Clare.

Aidan Walsh: The identification of important areas of plant diversity in Ireland

Records of vascular plants from the island of Ireland have been collated into a single plant distribution database. Rare and threatened plant species records were identified and subsequently mapped at the tetrad (2km by 2km) scale. We examined the overlap in spatial coverage between areas designated for the protection of biodiversity in Ireland and tetrads containing rare and threatened plant species. A proportion of the locations of these species occurred in the wider countryside and will not benefit from the protection provided by designated areas. For example, 22% of tetrads with records of Flora Protection Order species occurred outside of designated areas in the Republic of Ireland. The combination of designated areas and landscape within 4km of the designated areas contained over 90% of the locations where records of rare and threatened plant species occurred. These results indicate the importance of both designated areas and the wider countryside for biodiversity conservation, and offer an opportunity for the spatial targeting of conservation actions. The project will ultimately develop a method to identify important areas of plant diversity at the tetrad and hectad (10km x 10km) scale.

Susannah Cass: Is the grass ‘greener’? Biodiversity impacts of legume-supported grasslands.

Biodiversity is of great importance for the delivery of many key ecosystem services in agriculture (Altieri and Rogé, 2010) such as pollination, weed suppression, soil conditioning and pest control. Legume crops have a long history of use in traditional agricultural systems for the ability to fix atmospheric nitrogen (Graham and Vance, 2000) but have suffered a decline due to the ready supply of cheap inorganic fertilisers over recent decades (Graham and Vance, 2003). The Legume Futures project (EU FP7) aimed to investigate the potential for promotion of wide-spread legume-supported cropping in Europe, and the potential environmental impacts of such systems. We surveyed non-crop vegetation and earthworm (Lumbrucideae) biodiversity in semi-permanent and permanent agricultural grasslands, with and without legumes, at four established field sites belonging to the Legume Futures consortium (www.legumefutures.de). We found that responses to legume-supported cropping were different for non-crop vegetation and earthworms, and were dependent on the measure of biodiversity – abundance, species richness, diversity indices etc – considered. Mixed grass-legume swards supported more even and more diverse (Shannon’s H’ Index) non-crop vegetation communities but had less obvious impacts on earthworm communities.

Danielle McLaughlin: The molecular and morphological impact of notochord manipulation on the foregut in 3D explant culture

The notochord is a vital structure of vertebrate embryos, defining the anterior-posterior axis and strongly influencing molecular patterning and morphology of adjacent tissues such as the dorsally located neural tube. Despite their close proximity, the influence of the notochord on the ventrally located foregut as it separates to form oesophagus and trachea is undetermined. Oesophageal atresia is a relatively common congenital birth defect of unknown aetiology in which irregular foregut separation results in discontinuity of the oesophagus. In a well established model of this condition, the adriamycin mouse model, structural abnormalities of the notochord, frequently referred to as branches, are a distinctive feature. These notochord branches have a clear association with the site and severity of co-existing tracheo- oesophageal malformations. Further clinical and experimental examples of developmental disruption of the notochord occurring in conjunction with gastrointestinal tract anomalies including oesophageal atresia exist. We hypothesise that the notochord contributes essentially to the outcome in oesophageal formation and we have established an in vitro technique of 3D explant culture to examine the morphological and molecular impact of physical notochord

Sarah Hearne*: Limitations of the Fossil Record in Understanding Macroecological Trends

*Unfortunately Sarah was unable to attend but we still have her abstract

“To know your future, you must know your past” (Margaret Jang)

Since the fossil record was first recognised as the history of life on earth it has been an invaluable aid to understanding the evolution and diversity of life. It has been used to help explain and understand past and present distribution of biota across the globe and has increasingly informed our understanding of how life reacts to changes whether sudden, such as asteroid impacts, or gradual, such as climate change. Yet there are a host of biases inherent in the fossil record that make interpretation difficult. Many of these biases are either unknown or ignored by many researchers despite the fact that they are significant and limit the ability of the fossil record to reveal macroecological trends. Until these biases are accepted as problematic and efforts are made to counter them, macroecological interpretations of the fossil record will be little more than speculation.

Paul Egan: Variation of nectar toxins in space, time and habitat – is there evidence for functional significance?

The presence of toxic secondary metabolites in nectar represents somewhat of an ecological paradox. Although a number of explanations have been offered which pose a functional significance of this phenomenon; empirical tests of these hypotheses remain scarce. Here we employ use of an invasive species (Rhododendron ponticum) ideally suited as a model system, and investigate expression of diterpene grayanotoxins in nectar. Through comparisons within and between the species’ native and invasive range, possible post-invasion evolution and plasticity of this trait is explored in response to a number of spatial and environmental factors. In addition, a functional basis to toxic nectar is tested through examination of two potentially opposing processes: A.) if or how toxin levels are regulated in nectar over the course of phenological development of flowers, and B.) the extent to which phenotypic correlation with other plant tissues may in fact explain expression of toxins in nectar (e.g. as due to anti-herbivore defence in phloem, leaves, flowers etc.). In general, our findings reveal some important factors which influence nectar toxicity, indicative of both independent and adaptive regulation of this trait within plants. Our current studies seek to further test this purported adaptive function, examining the simultaneous and opposing selection pressures posed by pollinators and herbivores on toxin production, and the resultant impact on plant fitness.

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School of Natural Sciences Postgraduate Symposium 2014: Part2/4

Trex

On the 20th and 21st of February we had our annual School of Natural Sciences Postgraduate Symposium. Over the course of two days many of our PhD students presented their work to the School. We also had two interesting plenary talks from Dr Sophie Arnaud-Haond (Ifremer) and Dr Lesley Morrell (University of Hull). Unfortunately our third speaker, Dr Fiona Jordan (University of Bristol) had to cancel due to illness.

For those of you who are interested in exactly what we work on here at EcoEvo@TCD, here are the abstracts from the PhD student presentations. Check out the TCD website for more details!

Aoife Delaney: Eco-hydrology of humid dune slacks*

*Highly commended

Dune slacks are hollows in coastal sand dune systems where the groundwater table is close to the surface. Many dune slacks flood in winter to form temporary ponds which can last from a few weeks to several months. Humid dune slacks are an Annex I habitat (2190) and in accordance with Article 17 of the Habitats Directive they have been mapped and assessed in Ireland on the basis of their vegetation. During monitoring in 2013, Humid dune slacks (2190) were assessed as Unfavourable-Inadequate and topics for further research were identified. The extent and effect of water abstraction and wastewater from recreation facilities has not been firmly established in Ireland, and work relating biological communities to water quality or depth and duration of flooding has focussed almost entirely on vegetation up until now.

This project will assess variation in vegetation, mollusc and water beetle communities present in dune slacks in Donegal, Mayo, Kerry and on the east coast. It will also investigate the effects of land management by comparing biological communities of sites which are under different management regimes such as extensive pasture and golf courses. The hydrological functioning of dune slacks will be related to biological communities they support.

Anne Dubearness: Systematics of the genus Embelia Burm.f. (Primulacae — Myrsinoidae)*

*Highly commended

Primulaceae subfamily Myrsinoideae is a species-rich tropical group containing over 2000 species, with several taxonomically difficult genera with poorly defined limits and many novelties needing description. Within the subfamily, Embelia is a genus of climbing shrubs distributed mostly in South and South-East Asia and tropical Africa. The last monograph of this genus (made by Mez in 1902) recognised 8 subgenera and 92 species, but the total number of species is currently estimated at 140. The systematics of this group needs investigation using a modern phylogenetic approach: indeed, Embelia displays extensive morphological variation (especially regarding the position, shape, size and merosity of the inflorescences) and is only distinguished from other Myrsinoideae by a climbing habit and distichous leaves. This project aims to combine molecular and morphological data in order to investigate the systematic of Embelia at 3 levels: first of all the monophyly of the genus must be tested, then the existing subgenera must be assessed and refined in order to produce a taxonomic framework of the genus, and the final focus will be on the subgenus Euembelia Clarke, which contains more than 65 species and could certainly be split into several sections.

Thomas Guillerme: Combining living and fossil taxa into phylogenies: the missing data issue*

*Highly commended

Living species represent less than 1% of all species that have ever lived. Ignoring fossil taxa may lead to misinterpretation of macroevolutionary patterns and processes such as trends in species richness, biogeographical history or paleoecology. This fact has led to an increasing consensus among scientists that fossil taxa must be included in macroevolutionary studies. One approach, known as the otal evidence method, uses molecular data from living taxa and morphological data from both living and fossil taxa to infer phylogenies. Although this approach seems very promising, it requires a lot of data. In particular it requires morphological data from both living and fossil taxa, both of which are scarce. Therefore, this approach is likely to suffer from having lots of missing data which may affect its ability to infer correct phylogenies. Here we assess the effect of missing data on tree topologies inferred from total evidence supermatrices. Using simulations we investigate three major factors that directly affect the completeness of the morphological part of the supermatrix: (1) the proportion of living taxa with no morphological data, (2) the amount of missing data in the fossil taxa and (3) the overall number of morphological characters for all of the taxa.

Florence Hecq: Effects of scale and landscape structure on pollinator diversity and the provision of pollination services in semi natural grasslands

Over recent decades, humans have been changing the environment more rapidly than in any other period of history. Technological advances and new agricultural policies have led to a simplification of landscape structure resulting in the loss and fragmentation of habitats for flower-visiting insects which play an important ecological role as pollinators. Pollinating insects are very mobile and are influenced by the availability of flowers and nest sites over a scale of several kilometres.

In this study, we investigated the effects of the complexity of landscape structure on the diversity of four pollinating taxa and on the provision of pollination services to four plant species. Pollination data were collected in 19 semi-natural grassland sites in north midlands region of Ireland and related to the composition and configuration of surrounding landscape at two spatial scales (500m and 1km radius around sampling sites). Landscape structure was characterised by digitising each landscape feature with aerial photographs and GIS, and then ground-truthed using field-based surveys. Knowledge of these pollination/landscape scale relationships is crucial for a better understanding of pollinator diversity patterns and should be helpful for future conservation management decisions; ensuring essential levels of pollination services to wild plants are maintained.

Lindsay Hislop: Does nutrient enrichment moderate the effect of water level fluctuations on littoral communities?

Freshwater abstraction from lakes in order to support a growing human population is rapidly becoming a major global stress on lacustrine ecosystems. The consequent amplification of water level fluctuations disproportionately impact lake littoral zones, which contain the majority of their biological diversity. However, remarkably little is known about the impacts of amplified water level fluctuations on littoral assemblages and less still is known about how they interact with nutrient enrichment, one of the most pervasive and important of human disturbances on the biosphere. To address this, we established an experiment in large outdoor pond mesocosms where we quantified the effects of water level fluctuations and nutrient enrichment, both separately and together. We found that the impacts of water level fluctuations on both primary producers and benthic consumers varied significantly along the depth gradient. However, we found no interactions between nutrient enrichment and water level fluctuations. Given that the problem of amplified water level fluctuations is likely to be exacerbated considerably by predicted increases in climatic variability and enhanced water demand, our findings have profound implications for the conservation and management of global aquatic biodiversity.

Nuria Valbuena Parralejo: The impact of artificial sub-surface drainage on greenhouse gas emissions, change in soil carbon storage and nutrient losses in a grazing cattle production system in Ireland

In Ireland, over the 33% of milk is produced on a Heavy Soils farms. Heavy Soils are characterised by low permeability and often form in high rainfall areas. The combination of both can lead to waterlogging, promoting soil compaction which significantly affects the grass production. Drainage has been shown as an effective tool for improving the soil permeability. Little data is available to assess the effect of the artificial subsurface drainage of a grassland production system, on greenhouse gas emissions, change in soil carbon storage and nutrient losses. This experiment will be carried out in Teagasc Solohead Research Dairy Farm (latitude 52° 51’ N, 08° 21’ W; altitude 95 m a.s.l.). Different treatments (i) mole drain winter, (ii) mole drain summer, (iii) gravel mole and (iv) control were imposed in one site of the farm in 2011. A new experiment will be set up at a different site on the farm in summer 2014 with (i) control and (ii) gravel mole into collectors. Nitrous oxide (N2O) flux measurements, soil respiration measurements, soil total carbon and total nitrogen analysis, soil nitrogen mineralisation and net nitrification, water analysis, water table measurements and herbage production will all be perform in both sites over two years.

Adam Kane: Ontogenetic dietary partitioning in Tyrannosaurus rex*

*Highly commended

Obligate scavenging in vertebrates is a rare mode of life, one which requires very specialized morphologies and behaviours to allow the scavenger to cover enough area to find sufficient carrion. Yet, a number of studies have suggested that Tyrannosaurus rex occupied this niche with others arguing for its role as an apex predator. In this study we move away from the polarised predator-scavenger debate and argue that T. rex underwent an ontogenetic dietary shift, increasing the proportion of carrion in its diet as it aged due to both the increased availability of carrion through direct intraspecific and interspecific competition and also by exploiting resources unavailable to its smaller competitors, namely bone. We follow an energetics approach in our study to explore the effect of this previously unrealised resource on the ecology of T.rex and look at the impact of the proposed ontogenetic dietary shift.

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School of Natural Sciences Postgraduate Symposium 2014: Part1/4

tcd logo

On the 20th and 21st of February we had our annual School of Natural Sciences Postgraduate Symposium. Over the course of two days many of our PhD students presented their work to the School. We also had two interesting plenary talks from Dr Sophie Arnaud-Haond (Ifremer) and Dr Lesley Morrell (University of Hull). Unfortunately our third speaker, Dr Fiona Jordan (University of Bristol) had to cancel due to illness.

For those of you who are interested in exactly what we work on here at EcoEvo@TCD, here are the abstracts from the PhD student presentations. Check out the TCD website for more details!

Sven Batke: High energy weather events – long term responses on forest canopies and epiphytes

High energy weather events are often expected to play a substantial role in biotic and abiotic forest dynamics and large scale diversity patterns but their contribution is hard to prove. In this study we modelled cumulative hurricane impacts at Cusuco National Park, Honduras. The model was validated on the ground and microclimate and epiphyte data were collected along the forest profile and the modelled hurricane impact gradient. During this talk preliminary data will be presented that highlights the importance of including such events in understanding current abiotic and biotic canopy dynamics.

Qiang Yang (Marvin): The multidimensionality of ecological stability: A theoretical study

Understanding the factors that determine the stability of biological communities has been a focal point of ecological research for decades. However, a challenging aspect of stability is its many components, including asymptotic stability, resilience, resistance, robustness, persistence and variability. However, in spite of its multidimensionality, the few studies that measured multiple components of ecological stability simultaneously considered them as independent and therefore analysed them separately and we know remarkably little about the mechanisms underpinning relationships among components of stability and whether there are any general features of these relationships that are common across ecosystems.

Here by simulating the dynamics of distinct food-web structures following a range of perturbations on the species abundance in these food webs in silico we quantify 1) the general relationships among different stability components, 2) the effects of the strength of perturbations (i.e. the extent of biomass loss), the structure of food webs (i.e. trophic levels and connectance) and the individual species (i.e. its trophic position, generalist/specialist, omnivorous/monophagous) on the multivariate relationships among components of ecological stability in a range of food-web structures.

Mirjam Ansorge: Infectious diseases in squirrels and their importance for human health*

*Highly commended

It is well known that emerging infectious diseases like HIV or SARS have their origin in primates, and understanding the drivers for parasite sharing between humans and our closest relatives is an important factor for human health. However, some of the worst pandemics in history came from more distantly related animals. For example, the bubonic plague, which erased almost half of Europe’s human population in the 13th century, and was transmitted by fleas living on rats. This suggests that we should also investigate diseases in species that are not closely related to humans but that do come into contact with humans regularly. Squirrels are ubiquitous and share our parks and forests. Because they are considered non-threatening and often used to human presence, they are likely to have contact with humans and therefore to transmit parasites and vectors, such as fleas. These contacts can result in serious diseases in humans such as plague. I reviewed the recorded distribution of disease carrying squirrels in the USA from 1978 to 2002 and analysed the geographic range of parasites and parasite species richness in squirrel species. I will also discuss the importance of squirrels for human health.

Sai Krishna Arojju: Association mapping of agriculturally important traits in perennial ryegrass (Lolium perenne L.)

Linking genotypes to phenotypes and explain the natural phenotypic variation in terms of simple changes in DNA sequences is a major objective in plant breeding. Association mapping is a method which can be employed to search for genotype-phenotype correlations in individuals without population structure to identify co-segregation of genetic markers and phenotypes. This project aims to conduct an association mapping study in 1800 genotypes of Lolium perenne under three experimental regimes (1) simulated grazing management, (2) silage management and (3) persistency grazing management with 2 clonal replicates in a randomised block design. Each replicates consists of 40 blocks with 50 plants. 30 populations with different background have been selected for this study (10 released varieties, 8 half-sib breeding families, 8 full-sib breeding families and 4 Irish ecotypes). Genotyping will be performed by developing genotyping by sequencing (GBS) libraries for Illumina HiSeq2000 sequencing and we will also combine this with phenotyping on a range of forage quality traits including biomass accumulation, lignocellulose determination, flowering time, tillering capacity and digestibility on Lolium accessions. Variations in candidate genes of forage quality traits will also be examined.

William Burchill: Closing the farm nitrogen balance at Solohead Research Farm

Nitrogen use efficiency on Irish dairy systems tends to be low and leads to high farm-gate N surpluses (N imports minus N exports passing though the farm gate). The objective of this study was to quantify all N flows on a white clover based system of dairy production at Solohead Research farm from January 2011 to December 2012 and to account for surplus N. The system was rotationally grazed at a stocking density of 2.35 cows ha-1 received annual fertiliser N input of 112 kg ha-1 (BNF) was quantified using two 15N isotope techniques. A 15N gas flux and  static chamber method were used to quantify N2 and N2O emissions, respectively. Inputs (fertiliser N, BNF, feed and rainfall deposition) and outputs (milk and livestock sales) of N (kg ha-1) from the system were 274 and 80 respectively, with a farm-gate surplus of 194 kg ha-1 in 2011. Total measured N losses (kg ha-1) were 210 including 19, 43, 25, and 123 as N leaching, NH3, N2O and N2, respectively. The results of the present study indicate that a large proportion of Irish dairy systems N surpluses are returned to the atmosphere as environmentally benign N2 gas.

Donna Hawthorne: Fire, human and climate interactions throughout the Holocene

Significant changes in global and regional climate as well as changes in vegetation, land use, agriculture and policy, have promoted an increase in fires in the Irish landscape. To understand these changes the interrelationship between fire, climate and people will be explored. Past climatic oscillations have been studied at 8 sites throughout Ireland in an attempt to understand the current climatic changes which may mirror future patterns in climate. The landscape character and fire regime of each of these sites will be reconstructed and will seek to develop a model of risk assessment and management for future fire in the Irish landscape. The data span from the early Holocene to the present day, drawing on charcoal and pollen data, radiocarbon dating, and mineral and chemical data from lacustrine sediments. This work presents the first chronological comparison of regional fire activity across various locations throughout Ireland, and provides a base line level of data which can be drawn on in future scenarios when fire frequency is expected to increase. This work is in its third year of a four year PhD programme and preliminary discussions and results will be presented.

Louise Esmonde: Toxicity assessment of the agricultural pesticide Roundup Pro Biactive using Myriophyllum aquaticum and other test organisms.

Pesticide use in Ireland has increases over the last number of years yet its impact on the environment and in particular freshwater ecosystems is still not fully known. This study examines the toxicity of agricultural pesticides on non-target organisms with special reference to submerged macrophytes. In this study the toxicity of the herbicide Roundup Pro Biactive (active ingredient glyphosate) was examined using the plant species Myriophyllum aquaticum. Plant shoots were exposed to Roundup Pro Biactive concentrations of 0.01%, 0.1%, 1%, 5% and 10% for a period of 14 days. After the test period the response of the plant to the herbicide was measured in terms of wet weight, dry weight, shoot length, root length and root number with Relative Growth Rates (RGR) and EC50 values being calculated at each concentration. Preliminary results show a clear difference between the relative growth rates of control and test specimens. At concentration above 1% significant reductions in relative growth rates were recorded and physical deterioration of shoots was observed at concentration above 0.1%. Further studies will focus on the toxicity of five other agricultural pesticides on these same test species.