EcoEvo@TCD, Author at EcoEvo@TCD

08/11/201602/11/2017

Iguana vs Snakes | Planet Earth 2

Most of us were glued to the hugely anticipated premier of Planet Earth 2 this Sunday. We watched lovesick sloths meander through the mangroves, giant dragons battle it out on Komodo, and penguins getting fecked off cliffs by monstrous waves.

But if there was one scene that got us talking more than any other it was the literal race for survival that took place between a newly hatched marine iguana and an ominous pack of southern black racer snakes. The baby iguana had us shouting at the telly and clutching our faces while we watched its mad dash to the freedom of the ocean’s edge, avoiding the snakes’ fangs.

A racer snake gauntlet stands between hatchling iguanas and the safety of the sea! #PlanetEarth2 pic.twitter.com/LkFiEB30IJ

— BBC Earth (@BBCEarth) November 6, 2016

While we hoped against hope that the hatchling would make it, David Attenborough reminded us that for the snakes this was also a matter of life and death. Snakes have to eat, and for them the iguana hatching season means their best chance all year for hunting food. Continue reading “Iguana vs Snakes | Planet Earth 2”

17/10/2016

Studying worms – a Nobel calling

Professor William Campbell with Professors Celia Holland (front right) and Yvonne Buckley (front left). Back row L-R Professor Holland’s parasitology research group: Dr Peter Stuart, Gwen Deslyper, Maureen Williams, Rachael Byrne and Paula Tierney

“Parasites are not generally regarded as being loveable. When we refer to people as parasites we are not being complimentary, we are not praising them. We tend to think that a parasite is the sort of person who goes through a revolving door on somebody else’s push. This is unfair. It’s unfair to real parasites… It is time for parasites to get a little more respect!” – Professor William C. Campbell during his 2015 Nobel Prize acceptance speech.

In 2015, Prof. William C. Campbell, a Trinity Zoology graduate, won the Nobel Prize in Physiology or Medicine, for his discovery of ivermectin. The drug can be used to treat a wide range of parasites, but is most widely known for its effectiveness against river blindness. In 1987 the pharmaceutical company Merck enabled the free distribution of the drug to developing countries.

This Nobel Prize, which Prof. Campbell shared with his then colleague Prof. Satoshi Ōmura, is an important accomplishment not only for the Professors themselves as the cherry on top of their careers, but it is also important for the wider academic community.

This Nobel Prize is of importance to what Prof. Celia Holland described as ‘the international worm community’. This community has been struggling for many years to get recognition and funding. This prize therefore finally highlights the importance of parasitic worms. A lot of these parasites are often, despite their wide prevalence, classified as ‘neglected tropical diseases’. Neglected tropical diseases mainly affect the poor communities and are often forgotten in research and in the ‘public health agenda’. It remains to be seen whether some parasites will ever be able to shake their neglected status, but this Nobel Prize and associated international attention could be a great step in the right direction.

Hopefully, other pharmaceutical companies will take note of this prize. Giving away lifesaving medicine should be celebrated. We all know of the negative press pharmaceutical companies have gotten such as the recent price hikes in epi-pens. However, we tend to forget and ignore when pharmaceutical companies go to great lengths to help those in need. I see this prize also as a celebration of Merck for showing how it can be done differently. Because, really, what is the point of us producing any medical research if it doesn’t translate into affordable medicine?

During Prof. Campbell’s visit to TCD, the provost announced a new lectureship position in parasitology in honour of Prof. Campbell and the work he has done for the international worm community. Needless to say that this position would not have existed without Prof. Campbell’s Nobel Prize. Parasitology is a struggling field worldwide and every lectureship position is one to be valued and celebrated. This lectureship shows the commitment of the university to parasitology and will reinforce Trinity’s leading role in parasitological research within Ireland.

Additionally, this is an inspirational story for a lot of people. The story of ivermectin is a great motivation for parasitologists like myself. I work on a parasitic nematode called Ascaris, which infects 800 million people worldwide every year. Much like river blindness, it is also a neglected tropical disease, and as is often the case for these types of diseases, there isn’t much interest or funding going around. So it’s great at the start of my PhD to see that this type of research can also be honoured and valued.

I’ve read interviews of Prof. Campbell where he said that this prize meant the end of his retirement. I’m sorry to hear that his well-deserved retirement has been shaken up, but Prof. Campbell took one for the team and is promoting parasitic worm research to whoever wants to listen, just as he did before, only now he has a broader audience.

Author: Gwen Deslyper (seen charming Bill at 1:49 )

26/07/2016

Formally informal conferences

One of my favourite parts of working as a researcher during the summer (aside from quiet campuses with less students around) definitely has to be the “conference season”. Indeed, I don’t need to convince many people that conferences are one of the lively and exciting parts of doing science that rightly mix traveling, networking (and sometimes drinking) and learning about so many new things (and sometimes hangovers).

One of the problems though is that they can sometimes be overwhelming. It’s hard to find a balance between the right amount of networking (how many friends/collaborators do I want to meet and how many new ones do I want to make) and the right amount of learning (which talks do I want to attend and how much can I get from them). Although everyone has their own technique to deal with these questions, it seems to me that it boils down to the number of people attending the conference and the objectives of the conference organisers. One solution is to aim conferences towards a more manageable size with a clear emphasis on networking and learning.

One such conference is the annual BES Macro conference! As has became a happy ritual over the last 4 years, I was awaiting July with impatience for this year’s one organised in Oxford by Natalie Cooper and Rich Grenyer. As a disclaimer though, I do not consider myself as a macroecologist at all (most of my work is on macroevolution methods). So why do I go every year? I don’t even know what macroecology is! Well one of the first points is that this conference covers a vast array of topics, this year reaching far beyond the classic bird species richness heat maps with presentations on microbe populations in tree holes and sampling biases in the fossil record! The second point is because I think this conference contains all the ingredients that I think make a good conference:

First, mix different career levels:
For early career scientists like myself it can sometimes be a bit intimidating to mainly hear talks by “veteran” scientists. In fact I often think to myself just before giving a talk, how lame mine will be in comparison to the other people. Not that mixing different career levels makes my talk less lame (!), it has at least the benefit of making me feel better. It also has the undeniable benefit of making it easier to network with the big wigs if you spoke in the same session as them. At BES Macro 2016, each session was a good mix of every career level making it much more casual. Even the plenary speakers ranged from Professor Tim Blackburn to About-to-be-doctor Hannah White!

Second, make most of the talks short:
People have mixed feelings about lightning talks: from the speaker’s point of view, when you have exciting results it can be frustrating to convey your message in 5 minutes. Also these talks are sometimes more difficult to write than a classic 10-15 minutes one! However, from a listener’s point of view, think about how much more you absorb, on average, from these extra 5-10 minutes that make a classic talk? On a couple of talks: probably much more; on 2 days or more of conference: probably not that much! Besides, if 5 minutes was not enough and just peaked your curiosity, it makes an excellent opportunity to network (“Hi, I really enjoyed your talk. About that, [insert your burning question here]?”).

Third, add a nice dose of transferable skills:
Another point of conferences that can be negative is that you chain-listen to many many talks all day long. That has the benefit of giving a good overview of your field of research but can also make you slightly sleepy! One solution to break this continuous rhythm of talks is to do it with discussion sessions that can either be about transferable skills or about big questions in the field. For example, at BES Macro 2016 we had an excellent discussion session on reproducibility and another on the classic “What is Macroecology?” question.

And finally, don’t forget to add some rants:
What makes a good conference lies also in how much you feel part of the field of research covered by the conference. One way to convey that is to be part of or at least listen to the “hot” debates shaking the field. In this conference for example, we had two “official rants” by Shai Meiri and Adam Algar on what is going wrong in macroecology (but still how much cool work is done).

And of course, the main ingredient is the attitude of the people towards the conference. As Rich Grenyer put it in his welcoming introduction: “this conference is formally informal.”

Hope to see you at the next conference!

Photo credit: Thomas Guillerme

Original post

29/04/2016

Making the most out of a post doc interview

Making the most out of a post doc interview

(Even when you don’t get/want the job!)

So you’ve just finished your PhD and sent out a frantic flurry of post doc applications, amidst all of the excitement, you’re invited to interview; how should you proceed? Below are some of the things I learned from my first post doc interview recently:

A couple of weeks ago I embarked on a new first for me; my first interview! I grant you that it is unusual to be having one’s first interview at the age of 26; I had worked, but never interviewed in the formal sense, with a panel of strangers. There seem to be three broad classes of post doctoral jobs advertised; a) those advertised by a particular lab, usually with a particular person, where you are interviewed directly with the person you are hoping to work for. b) Grants like IRC or the Wellcome trust where you write a proposal and often, while a panel reviews this, you never have to actually interview in person. c) The kind I’ve just done; where a centre or department gets money and so you are interviewed by a panel from the department (and university in general sometimes), but not by the person you are applying to work with. With some trepidation I accepted the interview. I wasn’t sure at this stage that I actually wanted the position if offered but decided to take the opportunity to interview for experience alone at any rate. Here are some of the things that I learned and would advise (though remember, this is an n=1!):

Before the interview:

If the position is somewhere that you need to fly/travel to, arrive a day early if you can. This will relieve some of the stress of any travel delays and help get you in the zone
If the person you would be working with is not actually going to be on the panel try to arrange a meeting with them before the interview (day before if possible). This gives you the chance to meet if you haven’t done so before but also get their opinion as to the position. I got lots of great tips when I did this about what the panel may be looking for but also some valuable insights.
Tying in with the above, if you can visit the building it is going to be in beforehand, particularly a university, it really helps to get a feel of the place, the workspace and see whether this is somewhere you would enjoy spending your time.
Meet the other candidates! I know that this is perhaps a little controversial and may not work for everyone, but I ended up meeting some of the other candidates going for the job while I was there and found it really useful for a few reasons. Firstly, and mainly, it helps to remind you that these are people too, also nervous, which certainly made me feel more comfortable, knowing others were in the same boat. The other big reason is that it enables you to meet people at a similar stage and potentially with similar interests to you, which is always nice!
Try not to fret too much about whether you want the job until/if you’re offered it! This is something I really struggle with but the truth it, you owe it to them to give a good interview, particularly if they are paying for you to come over, but after that, then it is entirely up to you and you can pick and choose. It is you that you have to put first and if that means that after all you don’t want the job, that’s ok!
Do your research! It certainly helps if you already have a connection to the place but doing some research on both the department and the people in close proximity; who work on something similar or complimentary to what you are proposing. It helps for this to think outside the box too; I referenced a Prof in Physics even though this was a biology post.
Chat to the admin staff, it is usually they who have gone to the effort of timetabling the whole affair and booking rooms for you, so make sure to thank them and also ask what it’s like to work there. They have nothing to gain/lose in this so they will be very honest!

During the interview:

Be friendly! Whatever the outcome of the interview or your decision, these are potential future collaborators and leaving a good impression will mean a lot.
Take a moment to respond to questions. A moment considering your response can come across more confident than leaping into an answer before they have finished asking.
I was always taught that in a conference presentation, when asked a question, to answer the room rather than just the questioner. Certainly make them your primary contact but being sure to address the room as well. I think this works for interviews too, ensuring to engage the whole panel in your answers, I think this speaks to your communication skills and also just generally keeps everyone together.
Name drop to wazoo! Talk about the people in the department or School that you might work with or seek advice from, talk about other people already in your network that might not be in theirs and how you might get them to contribute for seminars etc.
Where will you be in 5 years? The dreaded question! Be honest here; in my case I had just submitted my PhD corrections the week before (a point one of the panel chuckled at during the interview…), so I did not have the grandiose expectation that I would be in a faculty position running my own lab in five years time, and I said as much. I think this can quickly be turned into a positive saying that this is an exciting time where you can see what you like and build up skills so that in five years you might have in mind the research themes that you want to develop for when you are going to look for a faculty post.
After the interviews there was what I described to myself as an “awkward mingle lunch”, where members of the faculty and candidates had the chance to mingle over muffins. At first I thought this was a terrible idea and was tempted to run away but actually it turned out to be really fun. Everybody was more relaxed and you could get a little insight into the social atmosphere of the place, see if you think you’d be a good fit.

Good luck!

Ps. I did get offered the post and decided to take it!

Author: Dr Deirdre McClean (@deirdremcclean1)

19/04/2016

School of Natural Sciences Postgraduate Symposium 2016: Part 3/3

Aoibheann Gaughran (@Aoibh_G)

Supervisor: Nicola Marples

Title: How population density influences social mammal ecology: A case study of the European badger.

The local density of a population of social mammals can affect many aspects of its ecology including social structure, mating systems, dispersal behavior, territorial behavior and the dynamics of disease. Scientists and policy-makers need a comprehensive understanding of the local population density as this may dictate the most effective management strategy. The European badger provides a particularly good species to investigate the effects of population density on other density parameters because its density varies by orders of magnitude across its wide geographic range. Further, it acts as a wildlife reservoir for bovine tuberculosis in the UK and Ireland, where it is subject to control operations. Currently, a haphazard classification of local population densities hampers a clear understanding of the badger’s ecology, leading to inappropriate management systems. We have conducted a meta-analysis to investigate the relationships between social group size, territory size, and group density and population density in badgers. We demonstrate that population density fundamentally alters badger ecology, affecting the interactions both within and between social groups. We also propose a classification system for densities of the European badger which highlight important ecological differences between populations across the density spectrum. Our findings provide a more cohesive picture of the species’ ecology across its range, facilitating appropriate targeting of disease management and conservation regimes.

Michelle McKeon-Bennett

Supervisor:Trevor Hodkinson

Title: Characterisation of endophytic microbes within Sphagnum magellanicum from Clara Bog, County Offaly, Ireland: Implications for enclosed environment hydroponic systems in Space.

This work investigates potential mutualistic relationships between endophytic microbes and species of native Sphagnum moss sampled from Clara Bog, County Offaly, Ireland. The application of the ion-exchange ability of Sphagnum moss to water remediation and recourse recovery within an enclosed hydroponic system has been investigated by the author at NASAs Space Life Science Laboratory, Kennedy Space Centre, Florida. While this research indicated that Sphagnum could be utilized in this manner, it resulted in yet more questions, specifically in relation to microbial interactions and growth mechanisms within the Sphagna:plant test bed.

It is postulated that endophytic microbes growing mutualistically within S. magellanicum may be responsible for (a) anti-algae and anti-microbe effects within the hydroponic system and (b) increased nutraceutical content within the associated salad crop. Microbial DNA isolated from 100ug samples of S. magellanicum, was extracted and used to identify microbial endophytes using standard barcoding primers. Genetic fingerprinting is being utilised to type the endophytes. Isolation and culturing protocols from Sphagnum plants have been developed and applied for the characterisation of microbial species during hydroponic systems using S. magellanicum as a growth medium. Further investigation of mutualism between identified endophytes and a cultivar of Lactuca sativa known as ‘Lollo Rosso’ is ongoing.

Alex O’Cinneide

Supervisor: Anna Davies & Martin Sokol

Title: The effectiveness of renewable energy policies in encouraging renewable energy generation.

Over the last twenty years the EU and its individual countries have been engaged in implementing policies to increase the use of renewable energy (RE) as a generation source. Motivations for this support of RE generation include, but are not limited to, concerns over climate change and pollution, national security risks associated with fossil fuels, and a wish to increase the competitive position of RE in markets which have been traditionally dominated by carbon based power. The issue of climate change and renewable power’s role in addressing this complex challenge has, in particular, been brought into sharper focus following agreement on emissions pledges from all the EU countries, and a new target of keeping global warming below 1.5C in December 2015 in Paris at COP 21; targets which will require a material response by policy makers throughout the EU. An understanding of what policies have been most effective in increasing RE is therefore critically important in designing new schemes, a comprehensive analysis of which has not been completed to date. I am therefore conducting a comparative analysis of the effectiveness of RE policies in encouraging RE generation (solar and wind, which given their advantages in cost and deployment have been the dominate focus of policy) across the EU from 1995 to 2015, with a primary focus on four countries of contrasting contexts, Ireland, UK, Italy and Portugal. While several studies have attempted to determine the effectiveness of various policies in various countries, these have been limited in scope and have not attempted to account for the variety of policy design features or individual country, market and key actor characteristics that influence policy strength. Adopting an energy transitions theoretical framework, this research would constitute the first study undertaken to determine how policy has effected the growth of renewables across Europe.

Anne Dubéarnès

Supervisor: John Parnell & Trevor Hodkinson

Title: Systematics of the genus Embelia Burm.f. (Primulaceae – Myrsinoideae)

Within the Primulaceae family, the Myrsinoideae form a highly variable tropical group, ranging from climbers and shrubs to trees, and characterised by the presence of dark dots on the leaves and fruits. This subfamily contains over 1300 species, divided into approximately 40 genera. Many of these genera are in need of taxonomic revision, as their limits are poorly defined and sometimes rely on ambiguous characters. Among these genera is Embelia, a genus of climbing shrubs distributed mostly in South and South-East Asia, tropical Africa and Madagascar. Embelia displays extensive morphological variation – especially regarding the position, shape, size and merosity of the inflorescences and flowers. It is distinguished from other Myrsinoideae only by the climbing habit, and the relationship with morphologically similar genera has not been critically evaluated yet. The last monograph of Embelia by Mez (1902), recognised eight subgenera and 92 species, but the total number of species is currently estimated at 150-200, and the subgenera used by Mez must be assessed and refined. My project aims to combine morphological and molecular data in order to test the monophyly of Embelia and to provide a taxonomic framework of the subgenera.

Eoin Mac Réamoinn

Supervisor:Cliona O’Farrelly & Paula Murphy

Title: Toll-Like Receptor Gene Expression During Early Murine Embryonic Development.

Toll-like receptors (TLRs) are renowned for their fundamental roles in immunological surveillance and response initiation. While TLR proteins in invertebrate species, such as Drosophila, carry out functions in the immune system and in “building” the body plan in the embryo, such non-immune functions have not been thoroughly investigated in mammals. Although TLR genes have duplicated independently in these lineages, and may therefore have diverged in aspects of their functionality, limited studies have recently reported the expression of TLRs in the developing mammalian embryo (Kaul et al., 2012). We report a systematic study of Tlr gene expression in early to mid-gestational murine embryos using whole-mount RNA in situ hybridization and 3D imaging (using Optical Project Tomography), the combination of which has allowed us to record the precise tissues and stages at which these genes become expressed. We have found that the expression of these receptors is particularly enriched within the central nervous system with many Tlrs displaying complementary expression patterns in developing neural tissues, as is the case with Tlrs -1, -5, -6, and -7 in the neural tube at embryonic day 10.5. These findings are in line with experimental data showing that Tlrs -2, -3, and -4 can influence neural progenitor cell proliferation and self-renewal (as reviewed in Barak et al., 2014). In addition to the expression data we have generated, whole-transciptome data is being mined to build a comprehensive picture of Tlr activity during embryogenesis and will aid in the building of specific hypotheses for functional testing.

19/04/2016

School of Natural Science Postgraduate Symposium 2016: Part 2/3

Aoife Delaney (@Ifa_Dee)

Supervisor: Jane Stout

Title: Do principals of cross congruence apply in a naturally disturbed habitat?

Cross congruence is a measure of the degree to which diversity (number or composition of species) of different taxa follow broadly similar patterns in response to environmental conditions. In situations where cross congruence is strong, measuring the diversity of a single taxon can provide information regarding overall diversity, and this has led to the development of indicator taxa. Indicator taxa may be used to indicate general patterns of biological diversity or environmental conditions, often with the inference that where the environmental conditions are favourable for one taxon, other target taxa will benefit. The use of indicator taxa has obvious economic appeal, but cross congruence has been shown to vary greatly in different studies. Habitat heterogeneity and environmental stress can reduce the correlation of diversity among different taxonomic groups.

Within the EU, states which have signed up to the Habitats Directive (Council Directive 92/43/EEC) monitor the condition of habitats of conservation concern (Annex I habitats) using standard methods and report their results to the European Commission. Indicator species are used as part of this habitat assessment. Dune slacks, an EU Annex I habitat, are temporary ponds in sand dunes which can persist for long periods, many having been formed as part of the initial dune-building phase. Despite being stable physical features, they experience both environmental stress (annual flooding and desiccation) and temporal habitat heterogeneity, and this raises questions: do principals of cross-congruence apply here, and are indicator species effective? This study compared patterns of diversity among three different taxonomic groups, to test whether cross congruence was observed. Communities of plants, snails and water beetles in twenty-four dune slacks in Ireland were compared using diversity indices and ordination techniques. Dune slacks were assessed on the basis of the indicator species used in reporting to the European Commission, and the biological assemblages of sites which passed and failed the assessment were compared. The results of this research will help to evaluate current monitoring techniques which are in use throughout the EU and guide monitoring approaches for dune slacks in Ireland.

Qiang Yang (Marvin) (@MarvinQiangYang )

Supervisor: Ian Donahue & Andrew Jackson

Title: Stronger perturbations increase the complexity of ecological stability

The stability of ecosystems determines the sustainability of the biological resource and services that nature offers us, and an understanding of mechanisms and drivers of ecological stability has vast implications for the sustainability and management of natural resources as well as the protection and restoration of ecosystems. Much effort has been contributed to understanding the factor that determines the stability of biological communities. A challenging aspect of stability is its many components, including asymptotic stability, resilience, resistance, robustness, persistence, variability and so on, but most of the previous research failed to analyse ecological stability from an comprehensive angle and we know remarkably little about the mechanisms underpinning relationships among components of stability. Therefore, focus on single stability elements may cause an underestimate of the “real stability” of ecosystems. Here in our research, by simulating the dynamics of 13 four-species food webs following perturbations varying in strength, we show that stronger perturbations decouple the relationship between stability components, i.e. that the efficacy of the single stability element in representing the general character of ecological stability becomes lower under strong perturbations. It is therefore necessary to investigate ecosystem stability from multiple angles, especially under strong disturbance frequently shown in real nature. The decoupling effect of perturbations on the multidimensionality of ecological stability is universal across most of the 14 food-web motifs in our research, implying a similar pattern in more complex large ecological networks.

Alewynne McGeever (@AlwynneMcGeever)

Supervisor: Fraser Mitchell

Title: Population dynamics of Pinus and Ulmus in Europe during the Holocene.

This work investigates and compares the population dynamics of Pinus and Ulmus in Europe, during the Holocene, at varying temporal and spatial scales, by using recently developed and novel modelling methods. The first component characterises the European-wide post glacial rise and mid-Holocene decline experienced by both genera. Pollen data was extracted from 330 sites on the European Pollen Database (EPD). The depth of rise and decline events for each genus in each site core was defined by applying a spline curve, to remove stochastic noise from the pollen data, and identifying the range of depths along which the pollen values increased or decreased.

The R package Bchron was used to calibrate radiocarbon dates and produce an age-depth model for each site, using stochastic linear interpolation and Monte Carlo methods. The age-depth model data was applied to the event depth range to produce a probability distribution of when the rise and decline events occurred.

The second component characterises Ulmus and Pinus when they were abundant on the European landscape. Depth and magnitude data of maximum pollen values for both genera were gathered from the EPD. The age-depth models were used to determine the age of the maximum pollen value depths.

These data were then plotted on maps and empirical Bayesian kriging was used to interpolate the spatial and temporal dynamics of these population events in the two tree genera. This work, therefore, presents novel techniques to quantifying tree population dynamics, and also provides insight into the specific dynamics of two major tree genera in Europe.

Dongwei Zhao

Supervisor: John Parnell & Trevor Hodkinson

Title: Phylogenetics of Camellia (Theaceae) in Indochinese Peninsula

Tea, camellias and oil camellias from the genus Camellia L. (Theaceae) are commercially highly important. About one third of all known Camellia species occur in the Indochinese Peninsula, of which half are endemic. Many new names of Camellia are still being described from this area, which may suggest that it was previously under-collected. Almost no work, however, has focused on the phylogenetics of Camellia in this area. This project aims to address these issues using morphological and molecular approaches. Morphological studies, consisting of a comparison and description of various macro-characters of specimens and palynological analyses, will be undertaken to clarify the boundaries of species in this notoriously variable genus. DNA markers derived from nuclear and chloroplast genomes will be selected to generate molecular sequence data, which will be used to reconstruct a robust phylogenetic tree. A new classification of this genus could then be proposed based on both morphological and molecular data. Species that have potential to supply new traits to the cultivars of tea, camellias and oil camellias could also be identified.

Conor Owens (@conorhpwns )

Supervisor: Fraser Mitchell & Jane Stout

Title: Biodiversity in willow evapotranspiration systems for wastewater treatment

Constructed wetlands are increasingly seen in Ireland and abroad as a solution to the on-site treatment of wastewater from domestic and other sources in rural areas. They are likely permanent features in our landscape that will proliferate into the future. Willow evapotranspiration systems are a subtype suitable for application in areas with low permeability subsoils. These systems are often promoted as having a beneficial role with respect to biodiversity but this has not been rigorously evaluated. This project aims to assess the plant and invertebrate biodiversity of these systems and the contribution they make to the biodiversity of the wider landscape. The factors driving biodiversity in these systems are being investigated and thus this project will provide management recommendations to maximise this biodiversity. This project involves cross discipline collaboration, drawing on expertise from both the TCD School of Natural Sciences and the TCD School of Engineering.

19/04/2016

School of Natural Sciences Postgraduate Symposium 2016: Part 1/3

School of Natural Sciences Postgraduate Symposium 2016: Part 1/3

#zoobotpgsymp, not an infection transmitted by botflies, but the hashtag of the annual Botany-Zoology postgraduate symposium, hosted by the School of Natural Sciences, which took place on the 14th of April.

This year’s symposium hosted 15 student speakers over 2 sessions of talks as well as two pleniaries delivered by our guest speakers: Dr Nina Alphey (University of Oxford, Imperial College London) and Dr Rob Thomas (University of Cardiff).

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!

Darren O’Connell (@oconned5)

Supervisors: Nicola Marples & David Kelly

Title: Ecological character displacement as a driver of diversification

Since Darwin, competition has been recognised as an important factor driving diversification. Competition is energetically expensive and unstable, so direct competition is rarely observed. One way in which species can avoid competition is ecological character displacement. This is where differences between similar species are accentuated when they co-occur but are lost or minimised when they do not overlap.

We suspect this process may have occurred in our study system of south-east Sulawesi, Indonesia. Two closely related and similarly sized species of kingfisher occur in this region, one resident and one migratory. On the Sulawesi mainland and larger (continental) islands they spatially segregate by habitat and resource partitioning. On the smaller islands of the Wakatobi Archipelago there is less habitat diversity and we do not see evidence of either habitat or resource partitioning. We do see a shift in morphology of one of the competing species, the resident Collared Kingfisher (Todiramphus chloris). The Wakatobi population is larger (wing and bill) than mainland populations. The change in habitat structure on the Wakatobi Archipelago bringing these species into closer contact may have promoted this divergence in morphology to alleviate potential competition.

Preliminary genetic work shows divergence between Collared Kingfisher populations of the Wakatobi and Sulawesi mainland, indicating the taxonomy of these populations requires further assessment.

Sukontip Sirimongkol

Supervisor: John Parnell

Title: Morphological characters of Henckelia Spreng (Gesneriaceae)

The genus Henckelia is one of the most complicated genera in the family Gesneriaceae. Recent molecular phylogenetic studies on Chirita and Henckelia are presented. These have separated Chirita from other genera such as Henckelia, Damrongia, Microchirita, Liebigia and Primulina. Some members Henckelia have been moved to other genera including Codonoboea, Didissandra, Didymocarpus, Lindernia and Loxocarpus resulting in a reduction in the number of Henckelia species to 57. Defining morphological characters for Henckelia allowing separation from these other genera are as yet unclear but will be derived from materials collected on fieldwork. In addition, for these morphological studies, specimens lent from Aarhus University Herbarium (AAU), University of Aberdeen (ABD), The Natural History Museum (BM), The Forest Herbarium (BKF), Bangkok Herbarium (BK), Royal Botanic Garden Edinburgh (E), Royal Botanic Gardens (K), Kunming Institute of Botany (KUN), The National Herbarium Nederland (L), Singapore Botanic Gardens (SING) will be used. The final thesis will therefore be in part molecular but with palynological, ecological, morphological and biogeographic data. This will allow for a revision of Henckelia in Thailand and Indo-China including Myanmar and Southern China.

Dermott McMorrough (@derm_mcm)

Supervisor: Andrew Jackson

Title: Now you see me: Examining the variation in time perception

Sight is one of our most valuable senses: constantly feeding us information about our environment, allowing us to evaluate potential mates, and perhaps most importantly: enabling us to find food. In the animal kingdom, a number of strategies are deployed as individuals and groups go about finding the food necessary for moving, growing, and ultimately passing on ones genes.

The way in which animals and humans acquire, process, and act upon visual information is a highly evolved, intricate process played out over minuscule time scales. In the time it takes for a predator to realise that its prey is about to change direction, or for an expert batsman to notice the spin on an approaching baseball, it is often too late to act. Our knowledge of temporal variation in this key trait lag in comparison with our understanding of spatial acuity.

Using a combination of simulation and psychometric techniques, I aim to tease apart the relationship between information acquisition over discreet temporal scales and the evolutionary consequences for both animal and human systems.

Anindita Lahiri

Supervisor: Trevor Hodkinson, Gerry Douglas, Brian Murphy & Colin Kelleher

Title: Characterizing candidate disease resistance loci in ash (Fraxinus) and an assessment of ash fungal endophyte strain variation in Ireland

Ash is very useful and abundant tree found throughout Europe, which is now threatened considerably because of a disease called ash dieback. It is caused by a fungal pathogen known as Hymenoscyphus fraxineus Baral. It can damage plants irrespective of their age group but young plants are more susceptible to the disease. Ash dieback starts from the midrib of the leaves and travels through the midrib to the stem part of the plant where the fungal mycelia blocks the xylem and phloem vessels and the plant dies because of lack of water and nutrients. This project is currently undertaking a comprehensive study of the leaf fungal endophytes of healthy plants to characterize their microbiome. We have cultured endophytes in a malt extract agar media and isolated them on the same media by sub-culturing. We are currently amplifying nuclear ribosomal bar coding DNA regions and sequencing them to identify the fungal isolates. We will then test the biocontrol potential of some of these against the disease pathogen.

Maureen Williams (@MoDubs11)

Supervisor: Ian Donohue & Celia Holland

Title: Does parasitism interact with warming to modify energy flow in ecosystems?

Gammerid amphipods are key components of aquatic ecosystems around the globe, acting as important detritivores and frequently dominating benthic assemblages in both rivers and lakes. Their ability to process detritus and return nutrients to the ecosystem may, however, be undermined by infection with behaviour-modifying acanthocephalan parasites. Moreover, as gammerids are ectothermic, the impact of parasitic infection could also vary with temperature. We explore whether parasitism and warming interact to modify energy flow in ecosystems by comparing individual energy budgets for Gammarus duebeni that were infected with the common acanthocephalan parasite Polymorphus minutus, with those of uninfected individuals of similar size across a broad range of temperatures.

29/02/2016

The Evolution and Laboratory of the Technician.

First in a series of posts on life after an undergraduate degree, Alison Boyce gives an account of the life of a scientific technician.

Science, engineering, and computing departments in universities employ technicians. Anyone working or studying in these areas will have dealt with a technician at some point but most will be unaware of a technician’s route into the position and their full role in education and research.

Technical posts are varied e.g. laboratory, workshop, computer. Funding for technical support is afforded by the Higher Education Authority (HEA) to provide assistance in undergraduate teaching. This is the primary role of technical officers (TOs) after which the Head of Discipline or Chief Technical Officer (CTO) decide further duties.

History

Until the early 1990s individuals joined the university as trainee technicians. Many came through the ranks starting as laboratory attendants, a position which still exists. Trainee technicians would spend one day a week over four years working towards a City and Guilds’ qualification. At this time the occupation was mostly hands on with little theoretical work. Many started young by today’s standards (starting at 14 years old was not uncommon), and they continued to study well past diploma level. Changing the nature of the role so much that nowadays almost all technical officers have primary degrees and come with a more academic view of the position.

In 2008, it was agreed that incoming technical officers must hold at least a primary degree in order to work at Trinity College Dublin. Those looking for promotion to Senior TO would require a Master’s and to CTO, a PhD. Those already in the system would not be penalised, local knowledge and experience are recognised equivalents and rightly so. This agreement gave rise to the job title changing from technician to technical officer reflecting the removal of the apprenticeship system. Many still use the old name but it doesn’t cause offence. These qualifications represent minimum requirements. TOs constantly train, learning new technologies and procedures. It is difficult to resist the temptation of further study when you work in an educational environment.

From graduate to TO

Gaining experience in medical, industrial, or other educational laboratories is most important. Further study in areas general to laboratory work are also advantageous e.g. first aid, web design, or statistics. Sometimes researchers move into a technical role temporarily and find they enjoy it so stay on. Applying to a discipline with some relationship to your qualifications makes sense; a physicist may not enjoy working in a biological lab. Having come though the university system many graduates would be familiar with teaching laboratories and their departments. Seeing a place for yourself in the future of a discipline is vital for career progression as it is seldom you will see a TO moving from one department to another. It should be possible to adapt the role to your skills or study to meet those required for promotion.

OLYMPUS DIGITAL CAMERA — BioLab Teaching Facilities

Day to day

All labs/disciplines differ but certain core responsibilities fall to the technical staff at some point. Running practicals is the biggest responsibility during term time with design and development out of term. Some departments in science and engineering have lab and field based classes. Various modules require field sampling in preparation for the practical. Getting out on the road can be very satisfying even if you are at the mercy of nature!

If you consider what it takes to run a home you’ll have an idea of what a TO does to maintain a lab/department. Ordering supplies and equipment. When something breaks, repair it or have it mended in a cost effective way. Logging, maintaining and installing equipment, health and safety information and implementation, chemical stock control, running outreach programmes, planning and managing building refurbishment, organising social events, updating the discipline’s web pages, assisting undergraduate student projects and much more.

These are just the basic duties and do not describe the essence of technical work at university level. Firstly it is to guide, instruct, and assist in scientific matters. An analytical and practical mind is necessary. You must have a willingness to facilitate the design and execution of projects in teaching and research. If you are eager to help and learn, it’s the perfect job for you. The information base for many materials and methods is the technical staff. Local knowledge and an ability work in consultation with other departments is often key to completing a project. Ideally, when a researcher leaves the university, their skills should pass to a TO keeping those abilities in-house. Imparting them to the next generation.

If you’re very lucky, you’ll be in a discipline that encourages you to take part in research and further study. It’s wise to check where a discipline or school stands before considering work in that area. Career opportunities open up in such disciplines. CTO Specialist is a promotion given to someone with expertise of a specialist nature e.g. IT, histology. Experimental Officer is a post created to further research in a discipline and often requires some teaching.

Overall, the position is what you make of it. If you strive to improve and adapt, you’ll find it immensely rewarding. Many practical classes repeat annually but on a daily basis you could be doing anything, anywhere. Being a technical officer is stimulating and constantly changing, keeping your brain and body active. You won’t be sitting for too long when you’re surrounded by young adults in need of advice and equipment. The relationship is symbiotic, your knowledge and their enthusiasm eventually gets any problem sorted.

Author: Alison Boyce, a.boyce[at]tcd[dot]ie

Alison Boyce has worked as a technical officer at Trinity College Dublin for over 20 years. In that time, she has acted as a master-puppeteer in seeing countless undergraduate projects through to completion. Her in-depth knowledge of technical, theoretical, and practical aspects of natural sciences has made her one of the most influential figures in the history of this department.

The editorial team thanks her for taking the time to write this piece.

24/02/2016

The expanding tropics

It was a spring day in April 2004 when Qiang Fu first noticed the anomoly in the data. On either side of the equator – in a belt strecthing from 15 to 45 degrees latitude – the lower atmosphere was warming more than anywhere else on the planet. Fu, a professor at the University of Washington in Seattle, was stumped.

It wasn’t until a year later that Fu realized what he had discovered: evidence of a rapid expansion of the tropics, the region that encircles Earth’s waist like a green belt. The heart of the tropics is lush, but the northern and southern edges are dry. And these parched borders are growing — expanding into the subtropics and pushing them toward the poles.

The expansion of the tropics is the subject of my latest feature, which appears in a recently published edition of Nature. You can read the full feature online at Nature.com: http://www.nature.com/news/the-mystery-of-the-expanding-tropics-1.19271 (behind a paywall). But here, I’ll give you a taste of what it’s about.

In the past ten years – since Fu first published his discovery in the journal Science – scientists have been turned their attention to this subject in a big way – there have been lots of scientific papers, theories and measurements – yet it’s had surprisingly little coverage by the media.

I’d thought about writing on this topic for a while and the time seemed right when I noticed that a bunch of 50 or so scientists were meeting last summer in New Mexico to trash this topic out. The meeting itself wasn’t open to the media, which was unfortunate, but I‘ve since managed to talk to a lot of the people who gathered for five days in that hot conference room in Santa Fe last summer.

I wanted to know answers to the same questions as those scientists, and those conversations would form the basis of my article. I’ve been writing about climate change for more than ten years now, and so I’m used to a lot of uncertainty in science. It was good preparation for writing this piece! On tropical expansion, still so many questions remain unanswered, such as how fast is it happening, what’s causing it and where are the future boundaries of the tropics likely to be? And importantly, why should we care?

Well, you’ll have to read the feature to get an answer to all of those questions, but I’ll answer a couple of them for you here.

How fast is it happening? Estimates range from less than half a degree of latitude per decade to several degrees of latitude per decade over the last few decades. At the more extreme end, that’s like moving London to the latitude of Rome over the course of a century. Pretty big deal. But it’s worth pointing out that some of the more recent estimates have been more moderate; they’re still bad news for cities such as San Diego, though, that would experience a big impact even with a one degree latitude shift in the edge of the tropics.

As to why we should care, well there are lots of reasons: aside from the potential water crisis for major cities such as San Diego, Perth and Santiago. tropical expansion could wreak havoc for some of the world’s most fertile fishing grounds, global grain production could shrink and biodiversity, especially at the southern tips of the African and Australian continents, (and they are astoundingly diverse) will suffer.

Now, if you’re interested in geeking out on all the details (and, in my view, reading the real story, which is about what is happening way up in the atmosphere near the Equator), check out the full story on Nature: http://www.nature.com/news/the-mystery-of-the-expanding-tropics-1.19271

author: Olive Heffernan (@O_Heffernan)

image: Amy Toensing/National Geographic Creative

23/02/201623/02/2016

The up-goer five: Explaining research using the “ten hundred” most used words.

At today’s NERD club, we tried our hand at explain our research using the up-goer five, which limited our available vocabulary to the “ten-hundred” most common words (thousand isn’t one of them).

After some brief hesitation, the 9 of us present found out that despite being quite challenging, this can be an incredibly fun and useful activity when it comes to explaining our often jargon-filled research to the public. While this system is rigid, and a tad extreme with words such as “plant” and “science” unavailable, it forced us to find alternative ways of explaining what we do.

Here’s what we came up with:

Prof. Yvonne Buckley

Original version

Decision makers and land managers are increasingly required to manage landscapes for multiple purposes and benefits. However, despite progress in the development of frameworks linking natural capital to the provision of ecosystem services and human benefits there remains little guidance for how management interventions can improve ecosystem service provision. As ecosystem services cannot be directly influenced, interventions need to be directed towards natural capital stocks. We provide a framework that explicitly links natural capital stocks to ecosystem service provision and identify manageable attributes of natural capital stocks as the critical intervention point. A structured decision making process based on our framing of the ecosystem services concept can facilitate its application on the ground.

Simple version

How to manage the living things that help us to live and enjoy life
People need many different things like food and wood from the land and I am interested in helping them to manage their land to get lots of good things from it. People have come up with ways of finding out the relationship between living things and the good things like food but it is still hard to find out how to manage the land for what we want. This is because when we make living things different it is hard to tell what will happen to the good things we want. We think the best way of getting out of this problem is to understand how changing where living things are and how many of them there are changes the food and other good things that we want. We help by giving people a plan for how to manage living things that will give us more of the good things we want from the land. This plan will help people to talk about what they want from the land and how to get it.

Olive Heffernan

The world is getting warmer, much warmer and quickly. It’s hot outside, in the air and in the water, even deep down in the water. Ice is becoming water, land is getting drier, so in some places its too wet and in others its too dry. People are having a bad time in lots of places. Animals are sad too. We know all of this because of the hard work of people’s brains.

What can be done?

We can drive less. We can eat fewer moving, living things. We can wear more clothes and not make our houses hot. Or we can do nothing. And wait until it is much hotter. Then we can try to change the world by putting things in space that will block the sun out. Or we can put stuff in the sky to make it cooler. If we do none of these things we might end up in the water, in hot, hot water.

Dr Kevin Healy

Two legged animal eating animals were around for 160,000,000 years but are not anymore. We do not really know what they ate. Some were as small as a dog while others were as big as a bus so they would have needed more food. One type of food that they might have eaten was already dead food. We know animals today eat food they found that was already dead so animals that are not around may have also eaten dead food. But did the big animals that are no longer around eat more or less dead food than the small animals? We made computers games to show that actually both big and small animals are very bad at eating dead things, while animals in the middle are much better at eating dead things. This was true even if we changed how far they could see, how much dead food was there, how many other animal eating animals were around and how much food they needed. We show that dead things might have been important to animals no longer around and that how big you are might still be important to how much dead stuff animals eat both today and in the past.

Luca Coscieme

“If I have everything I need, to do whatever I need to, I am happy. Just to say, if I have food I eat and I am happy. If I don’t have enough I have to eat less, or take food from somewhere else. If I take it from somewhere else, maybe another person will not have it for his own.

To do food I need land. The problem is that after I use land to do food this land gets bad and is not beautiful anymore. But if I have a lot of money, I can buy land and food from somewhere else and keep my land beautiful and clean.

If people can buy the land and the food they need, there can be a person with more money than you that buys all the things you need, and you can’t eat and live. So, it is important to control what people do with their money. It is important to check that no one is taking food or using land that is needed for another person to live.

People with no food get angry and one day they will come where people with money live and take back their land and their food.

I am studying a way to control if people with money is taking food and land from other persons that really need it (more than these people with money).

We can stop that by checking if these people really need these things and if they can find these things where they live. If they can, they have to use them, instead of going somewhere else to make less beautiful the land of other people.

Maureen Williams

Mean animals that live in other animals and how they make the other animals do weird things when its hot

Mean animals that live in other animals and then hurt the other animals are in many places. The animals I study all live in water that does not run. The mean animals sometimes make the house animals do things they would not do most of the time. When the house animals do strange things, this can make everyone else in the whole water group do things different to how they usually do and power from food can go to different places. When the water gets hot, everyone in the water does things not how they do them in cold water. I study how the mean animals and the house animals do things when the water is hot and cold and how this makes everyone in the water different. I also study how all the animals doing different things can make the power from food go different places and can change who eats who and how often. I study these things in the water outside and in small water inside.

Aoibheann Gaughran

How large a group of animals is can change how they act. It is important to know how big or small a group of animals are so we can understand how they play with one another and live in their home. Small night time animals with black and white faces are important to study because they get a cold that they can pass on to bigger black and white animals that live in fields eating green stuff to make the white stuff we put in our coffee. We carried out a study of papers that looked at the grouping of small black and white faced animals, how many of them lived together, how big their homes were and how many there were in total. We showed that how many animals there are in an area, changes how they act, their relationships with one another and with other animals that may not be their family or friends. All of this means we can better understand how these animals pass their colds onto one another. We have come up with a group of names that you can use to quickly and easily tell other people many animals there are in an area and how it makes this group different to other groups. We hope that our study will help people who want to save the small black and white animals as well as those people who want to do away with the colds that the animals get in a much better way than they do now.

Dermott McMorrough

I want to know how the brain understands what it sees in the world. When we see the world through our eyes, they send this to the brain telling it what they saw. The way the brain understands this is important because when the brain talks to the eyes, the pictures can be slow or might not get to the eyes at all. When this happens in people, they think they have a friend when they do not. They are talking to themselves.

We try to understand how the eyes talk to the brain by making simple games on a computer that make animals play with each other with an angry animal chasing a smaller animal. We set up roads between the cells in the brain and then make the brain bigger to see is the angry animal better at chasing the smaller animal in the computer game.

We try to understand this by looking into the animal brain while it plays around in interesting worlds on the computer. By changing the number of roads in their brains before and after the games, animals change what they catch, we hope to learn more about the brains power to understand these games.

This study will make new games of animal moving by bringing good ideas from old people in white clothes to the field of moving studies. Doing so will allow us to answer simple questions about the relationship between bodies of angry animals and their food and to add for the first time why food matters in such relationships. These relationships explain how animals talk with the world around them, and are at the heart of our entire idea of world.

Alain Finn

We study how and why trees and other green living things live and grow where they do. To do this we have to go to where the green living things live and look at them and what other things are living beside them. Green living things need to live in the ground, the ground is different all over the world and some things can live in some places and not others. We try to understand why this is by changing what’s in the ground and seeing what type and how many of each thing continues to live there.

Green things what live in the ground can also change themselves to fit the type of ground, rain or sun they get every day. They can change many things such as how big or small they grow or how thick their leaves are but quite often to make a good change to one part of their body they must also make a bad change to another. We try to understand what causes these changes by looking at one green thing that lives all over the world and seeing what changes are made and where the things with those changes are living.

Attempting to describe population ecology

If you’re interested, ESA’s new sci comm section has some useful tools for science communication: https://advancingecocomm.wordpress.com/

With thanks to the members of NERD club. You can find them on twitter at @y_buckley, @O_Heffernan, @healyke, @lucacoscieme, @MoDubs11, @Aoibh_G, @derm_mcm, @finchyIRL

INSPIRED BY XKCD. (THE IMAGE IS FROM #386.)
CREATED BY THEO SANDERSON. HOW DOES IT WORK?