School of Natural Sciences Postgraduate Symposium: Part 4/4

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On the 15th and 16th April we had one of my favourite events at Trinity College Dublin: the 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 amazing plenary talks from Dr Nick Isaac (CEH) and Professor Jennifer McElwain (UCD). 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!

 

Paul Egan: A growing problem − invasive species distribution modelling of Rhododendron ponticum and the implications for conservation.

The invasive alien Rhododendron ponticum is a widely naturalised and problematic weed throughout Ireland, Britain and areas of NW continental Europe. Using invasive species distribution modelling (iSDM) at a fine (2 km) spatial resolution, we examined the bioclimatic and landscape factors which govern the distributional pattern of R. poniticum across the Atlantic biogeographical region compared to its native range in Iberia and the Black Sea region. Good model performance allowed successful prediction of known areas of intense invasion. Model predictions of habitat suitability can help indicate the challenges for local irradication of R. ponticum and therefore help prioritize conservation efforts. Paradoxically, iSDMs generated from the invasive range also provides much needed assessment of the species’ severely restricted native range, where R. ponticum is presently classified as endangered.

Ruby Prickett [@RubyPrickett]: Geographical, ecological and genetic characterisation of perennial biomass grasses. 

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.

Shane McGuinness [@S_Mc_G]: Tourists, farmers and agri-industry: the political ecology of human-wildlife conflict on the margins of a Rwandan protected area. *Highly commended*

As human populations grow, protected areas are put under increasing threat from resource extraction and associated loss of ecosystem services. Furthermore, improved conservation and protection has led to growing faunal populations within these, increasing interactions with neighbouring human populations and reducing support for conservation actions. This is particularly acute where communities bordering protected areas are subsistence farmers. This paper addressed conflict on the margins of Volcanoes National Park, northern Rwanda, through a mixed methods political ecology perspective. Lying in the Albertine Rift Biodiversity Hotspot, it harbours endemic species of primate (mountain gorilla, golden monkey) and significant yet understudied biodiversity, but is bordered by one of the most densely populated regions of mainland Africa. Given the tourism value of this national park and the value of its surrounding land for export-driven agri-industry, the concerns of park-adjacent communities require specific consideration.

Sven Batke: Past hurricanes in predicting present diversity and richness patterns in Cusuco National Park, Honduras. *Best talk 2/2*

High energy weather events are often expected to play a substantial role in biotic community dynamics and large scale diversity patterns but their contribution is hard to prove. I am going to present an overview on how to generate hurricane exposure data at a mesoclimate level for a specific region. Moreover, I am going to present some results that highlight the link between exposure vulnerability and observed tree damage and the potential effect hurricane winds might have on canopy epiphyte diversity patterns.

Vishnu Mohanan [@vmohanan]: Characterisation of lignin and cellulose genes in biomass and energy crops. Sadly Vishnu missed the symposium but we still have his abstract…

Dwindling fossil fuel reserves requires us to look for other sources of energy and emerging bioenergy grasses provides us with an alternative such as Miscanthus, maize, switchgrass and several woody bamboos. Bamboos (subfamily Bambusoideae) have evolved a woody character via enhancement of the lignocellulosic component of vascular tissue, especially vessels. Reeds (e.g. Arundo, Phragmites, subfamily Arundinoideae) and Panicoideae (e.g. Saccharum, Miscanthus, Panicum) have also evolved this trait. It is not known if they have achieved this via alternative biosynthetic paths/genes. Our aim is to first investigate the evolution of genes known to be important for woodiness in grasses (cellulose synthase genes, Cesl, is one such gene family). Secondly, we aim to investigate the effects of woodiness on grass evolution to see if woodiness was a significant key innovation for speciation in the groups that have evolved it.

School of Natural Sciences Postgraduate Symposium: Part 3/4

lifespanOn the 15th and 16th April we had one of my favourite events at Trinity College Dublin: the 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 amazing plenary talks from Dr Nick Isaac (CEH) and Professor Jennifer McElwain (UCD). 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!

 

Karen Loxton [@LoxtonKaren]: Parasite lost: Helminth parasites in the invasive bank vole in Ireland.

Invasive species are a major cause of biodiversity decline throughout the world. Determining why some species become invasive when introduced to a new environment is therefore of great importance. One hypotheses is that invasives escape their native parasites and are ‘released’ from the effects of parasitism. This project looked at the intestinal helminth parasites of the invasive bank vole to determine if it is less parasitised than in its native ranges.

Kevin Healy [@healyke]: Digging how you wing it! Extrinsic mortality and longevity in volant and fossorial endotherms. *Highly commended*

Longevity is a fundamental life history trait that exhibits considerable variation among species. While longevity strongly correlates with body size many species live either far longer, or indeed shorter, than expected. Classical life history theory predicts that species that experience high extrinsic mortality will, on average, evolve shorter lifespans. We tested using phylogenetic comparative methods in birds and mammals whether species that either possess abilities or live in environments that reduce predation display longer lifespans. Our results showed that as predicted traits such as volancy, fossoriality and foraging in arboreal environments are associated with long-lived species.

Louise Esmonde: Plant selection for use in a submerged macrophyte vegetation (SAV) wetland under temperate conditions.

Constructed wetlands are seen as a sustainable and low carbon alternative to conventional wastewater treatment solutions. Submerged Aquatic Vegetation (SAV) wetlands utilize the ability of submerged macrophytes to remove nutrients and metals from the water phase to treat wastewater. This study uses the relative growth rates (RGR) of a number of submerged macrophyte species as an aid in selecting the best species for use in a SAV wetland. So far the RGR of the submerged macrophyte species Myriophyllum spicatum, Elodea canadensis and Ceratophyllum demersum have been measured. RGR was found to be in the order: E. canadensis > M. spicatum for planted specimens and M. spicatum > E. canadensis > C. demersum for unplanted specimens. Research is on-going into the treatment potential of these species in terms of nutrient and metal removal from wastewaters.

Melinda Lyons: Petrified plants – the ecology of lime-rich springs

Petrifying springs are intriguing ecological and hydrogeological features with extreme chemical conditions in which specialised plant species thrive.  They deposit ‘tufa’, a porous rock, on the ground surface and on plants where lime-rich spring water emerges.  Recent measurements of tufa accumulation show surprisingly rapid growth rates. This distinctive habitat (a priority habitat in Annex I of the Habitats Directive) is being investigated in Ireland for the first time.  Analysis of relevé data indicates that different subtypes occur depending on topographical settings.  Some examples are of particularly high conservation value, most notably those on the Benbulbin Range of Counties Sligo and Leitrim.  The habitat is vulnerable to changes in water flow and quality, land use practices and visitor pressures.

Hanan Elshelmani: MicroRNA profiling in serum of Age-Related Macular Degeneration patients

Age-related macular degeneration (AMD) is a common condition causing a progressive visual impairment, leading to irreversible blindness. This condition is characterised by loss of central vision attributed to degenerative and neovascular changes that occur in the neural retina and the underlying choroid. In what we believe to be the first study of its kind, here we aimed to establish if circulating miRNAs may exist which are associated with AMD and so may have relevance as novel test for rapid screening, early diagnosis; disease sub-typing; and/or treatment selection for AMD. Results: Unsupervised hierarchical clustering (performed using dChip software) indicated that AMD specimens have a different miRNA profile compared to that of healthy controls. Overall 157, 207, 190 miRNAs were detected in control, neovascular and atrophic respectively. 56 and 11 miRNAs, respectively, were found to be detectable at significantly higher levels in serum specimens from neovascular and atrophic patients compared to control sera. Interestingly, only 5 differentially-expressed miRNAs overlapped between atrophic and neovascular patient groups; suggesting biomarker specificity for different types of this condition.

Patricia Coughlan: The phylogenetics of paclitaxel biosynthesis genes in Taxus baccata, Taxus hybrids and allies

Taxus baccata, more commonly known as the Irish Yew, is a natural producer of Paclitaxel. Bristol Myers Squibb developed an effective anti-cancer drug from Paclitaxel and gave it the trade name Taxol. Taxol is used to treat ovarian, breast and lung cancer. This project will develop molecular primers to amplify and study the genes involved in the Taxol biosynthetic pathway, and take a phylogenetic approach to discover which genes are more important for paclitaxel production. More specifically, it will discover variation in these genes between Taxus baccata and Taxus hybrids such as Taxus xmedia.

Earth day

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Monday 22nd April was Earth Day. In schools and offices all around the world people organised events to highlight the importance of the Earth and the harm that climate change, deforestation, and other human impacts are causing.

As an ecologist and someone who cares about conservation I should welcome Earth Day and its relative, Earth Hour, with open arms. Shouldn’t’ I? Maybe, but I really can’t. In fact, I find these sorts of events incredibly frustrating. Implicit within them is the idea that if we spend one day really caring then we can spend the other 364½ how we like.  I know that this is not the intention but I fear it is the reality.

Earth Day is popular with companies trying to improve their ‘green’ image, and it is here I have a big problem. I have no issue with companies trying to improve their green credentials, but improving their image and improving their credentials are not the same thing. How ‘green’ is a company who decides to spend Earth Day extoling the benefits of re-using cups at the coffee machine when the next day they send staff on a ‘training course’ that just happens to be in a hotel in Portugal? Who cares if you encourage everyone to print double-sided if you then require that 1,000-page file to be photocopied five times and then sent to offices all around the country (yes, I am drawing on past experience in these examples!).

I understand that Earth Day, and similar initiatives, try to encourage people to make small changes that are of little consequence in themselves but multiply over many people to make large differences. People are encouraged to turn off lights, the TV, their computer, and so on, when they’re not being used for long periods. The most commonly given reason for doing this is to ‘save you money’. After all, we live in a capitalistic society where money drives many of our decisions and if we can use money to drive lower energy consumption then everyone wins, surely?

Well, no. The problem comes from the rebound effect. If you save money on your heating bill most people don’t just say ‘yippee, I’ve saved money on my heating bill’, they say ‘yippee, I’ll put those savings into the holiday fund’ or similar. So the money saved on heating goes towards a flight to a tropical paradise where you stay in a five-star hotel for a week and lounge on the beach. This doesn’t exactly help the environment.

And this is where my biggest problem ultimately lies. No matter how hard we try to reduce our energy use, whether it’s through small behavioural changes or making things more energy efficient, the rebound effect will get us every time. I don’t know what the solution is but I think that this is something that really needs to be discussed publicly.

Sometimes the causes and effects of climate change can seem so overwhelming that people (myself included) want to give up, believing there’s nothing they can do. Unfortunately, there’s some truth in that. But one thing we can do is realise that it is overall effects that we need to consider, not individual ones. It’s not a very sexy message or one that is easy to sell, but unless it becomes the focus of the discussion then Earth Day is going to be nothing more than a wasted PR exercise. And that’s a real shame.

Author

Sarah Hearne: hearnes[at]tcd.ie

Photo credit

http://thinkloud65.files.wordpress.com/2011/01/children_holding_hands_around_the_world1.gif

School of Natural Sciences Postgraduate Symposium: Part 2/4

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On the 15th and 16th April we had one of my favourite events at Trinity College Dublin: the 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 amazing plenary talks from Dr Nick Isaac (CEH) and Professor Jennifer McElwain (UCD). 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!

 

Danielle McLaughlin: BMP signalling disruption in the foregut of the Adriamycin mouse model of Oesophageal Atresia/Tracheo-Oesophageal fistula.

1/3500 neonates are born annually with Oesophageal Atresia/Tracheo-Oesophageal Fistula(OA/TOF), a birth defect of unknown cause, where the oesophagus fails to properly form and connect with the stomach. Despite corrective surgery, afflicted children have long-term health problems. Oesophagus and trachea arise from embryonic foregut. We use an animal model with OA/TOF-like foregut malformations, the Adriamycin Mouse Model(AMM), to investigate the developmental origins of these malformations. An important embryonic organising structure, the notochord, is abnormal in shape, position and molecular characteristics in AMM embryos. Current work focuses on Bone Morphogenic Protein signalling, analysing downstream events and showing very specific disturbances in AMM notochord and foregut.

Donna Hawthorne: What role did fire play in the Irish uplands, from the early Holocene to the present day, and how should fire be best managed in the future?

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, especially in upland areas. Past climatic oscillations have been studied at 10 sites throughout Ireland in an attempt to understand the current climatic changes which may mirror future patterns in climate. This coupled with the palaeo-reconstructed landscape character and fire regime at each of these upland sites, 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, as well as the historical record from a number of sites in Killarney National Park. 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 second year of a four year PhD programme and preliminary results will be presented.

Eileen Diskin: The f word. *Highly commended*

Antibiotic resistant bacteria are bacteria that can survive exposure to the antibiotics designed to render them harmless. You’ve probably heard them mentioned in the news; MRSA is frequently cited as an example of the threat they pose to human health. In this presentation, I will give an overview of my research on environmental reservoirs of antibiotic resistance. In sharing a selection of my results, I will address several questions: What does my approach have to offer? What challenges have I overcome in my research, and what opportunities have arisen as a result? I will conclude by considering what the next steps are, both in my project specifically and in this research area more generally.

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.

Erin Jo Tiedeken [@EJTiedeken]: The buff-tailed bumblebee Bombus terrestris has poor acuity for the detection of toxins in nectar. *Highly commended*

Bees feed exclusively on nectar and pollen to obtain carbohydrates and proteins necessary for survival.  Paradoxically, these plant products often contain toxic secondary compounds usually associated with defence against herbivores.  Although these compounds commonly occur at low concentrations they may still have significant effects on pollinator behaviour and health. The aim of this study was to determine whether a generalist bumblebee, Bombus terrestris, can detect naturally-occurring concentrations of potentially toxic compounds in floral nectar. We found the detection thresholds for five plant compounds: quinine, caffeine, nicotine, amygdalin, and grayanotoxin, all of which are found in the nectar of plants pollinated by Bombus species.  In paired choice experiments, individuals were offered both a sucrose solution and a sucrose solution containing a putative ‘toxin’. The detection threshold was determined when bees significantly preferred the sucrose solution to the solution containing the secondary compound.  The detection threshold depended on the compound, but in all cases was above the naturally-occurring concentration range found in floral nectar.  The inability of bumblebees, an important group of pollinators, to detect toxins in floral nectar suggests this plant trait may be maintained in plant populations if it confers any benefit to the plant.

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 impacts 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, an experiment was established in large outdoor mesocosms and the effects of water level fluctuations and nutrient enrichment, both separately and together were quantified.

School of Natural Sciences Postgraduate Symposium: Part 1/4

Postgraduate students from Trinity College Dublin's School of Natural Sciences
Postgraduate students from Trinity College Dublin’s School of Natural Sciences

On the 15th and 16th April we had one of my favourite events at Trinity College Dublin: the 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 amazing plenary talks from Dr Nick Isaac (CEH) and Professor Jennifer McElwain (UCD). 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!

 

Rebecca Rolfe [@rolfera]: Identification of mechanosensitive genes during skeletal development: alteration of genes associated with cell signalling pathways.

Mechanical stimulation is important for correct formation of the skeleton. Mutant mouse embryos that develop with no skeletal muscle have altered mechanical stimulation resulting in specific defects in ossification and joint formation. 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 cytoskeletal architecture. In particular, multiple components of the Wnt signalling pathway are affected. Further analysis will examine the mechanisms by which mechanical stimulation influences gene expression and differentiation, findings that are relevant to controlling differentiation in stem cell based regenerative therapies.

Adam Kane [@P1zPalu]: Scrounging Scavengers: Vultures acquire information on carcass location from scavenging eagles.

Vultures have an ecological role as obligate scavengers. In addition to being unable to kill prey for themselves we suggest that they are dependent on other species to locate food. Our analyses of bird arrival times at carcasses show that vultures join a carcass after discovery by raptors more often than expected by chance. We develop a game-theoretic model showing that such an interspecific producer-scrounger game is evolutionary stable when vultures are dominant to raptors in agonistic interactions over food. This hierarchy was confirmed at the carcass. Vulture populations are declining so our findings have implications for the conservation of the group.

Sarah Hearne [@SarahVHearne]: Intrinsic and extrinsic factors shape global marine diversity.

Intensifying anthropogenic pressures on ecosystems on a global scale have lead to an increased focus on the relationships between biodiversity and stability. Many studies of biodiversity have focussed on changes in diversity measures over relatively short timescales. However, there are also long-term changes in biodiversity which have been revealed through the fossil record. My project is examining global marine invertebrate diversity throughout the Phanerozoic Period (540my to present) to determine the causes of the cycles of extinction and origination over this time period. Using a new technique, convergent cross mapping, it has been shown that extinction and origination are both driven by diversity and each other, while extinction is also causally affected by temperature and origination by sea level.

Aoife O’Rourke: Spring foraging resources and the behaviour of pollinating insects IN grey dune ecosystems.

Grey dunes are a priority habitat under the EU Habitat Directive. They often contain creeping willow (Salix repens L., Salicaceae), which is suggested to be an important early season resource for bees and other obligate flower visitors. However, there is a paucity of empirical evidence to support this claim. We examine the springtime activity of obligate flower visitors in the grey dune ecosystem in relation to nectar sugar concentration and composition, relative abundance (%) of essential amino acids in pollen, and the abundance of floral units of S. repens and co-flowering plants in the environment. We also investigate the effect of S. repens presence on the abundance and species richness of solitary bees, bumblebees and hoverflies. Insect focal observation, pan-trapping and chemical analyses techniques were used to explore our research questions. Results will be presented and discussed in the context of managing habitat to increase resource availability for pollinators during spring.

Deirdre McClean [@deirdremcclean1]: The world in a bottle: Investigating stability and social transactions in microbial communities. *Best talk 1/2*

Understanding how perturbations affect the long term stability and dynamics of different systems has been a core challenge for ecological research. Identifying the mechanisms by which communities respond to and recover from different perturbations is of vital importance for assessing the impacts of anthropogenic pressures on the environment. Long term, multi-generational field studies are typically impractical, costly and confounded by a host of other ecological variables that need to be accounted for. Logistically feasible model systems are therefore needed in order to test more generalized ecological and evolutionary theory. Here we use experimental microcosms to examine the interactions among food web structure, habitat modification and social interactions in order to determine how these might moderate the effects of perturbations on stability.

Brian McGuinness: Escallonia spp. fungal pathogens. Sadly Brian missed the symposium but we still have his abstract…

A fungal disease affecting plants from the genus Escallonia has become a significant problem for both the nursery industry and for gardeners who use it as an ornamental boundary hedging. Development of lesions generally starts on older leaves throughout the plant usually causing some degree of defoliation ranging from mild to severe and sometimes resulting in plant death. We show how susceptibility of Escallonia to leaf spot disease varies across species and infra-specific taxa by in-situ assessment. No 100% genetic match currently exists for the organism causing the leaf spotting which is the same organism affecting plants in the U.K. Next steps include generating a full taxonomic description based on morphology and conducting next generation sequencing to identify any population differences that may exist.

Hide and seek with a T-Rex in a drawer

Natalie Cooper and Sive Finlay already posted on this blog about the amazing old stuff you can find in a Natural History Museum (here and here). Palaeo collections are also special, I spent one week in the Smithsonian Institution Paleobiology collections to measure some Eocene American primate teeth and I was amazed by the quality of their collections. But the nice thing about Palaeo collections is that when you’re looking for a particular specimen, you always come across wonders you didn’t expect.

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Rows of drawers…
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…Containing loads of boxes…
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…Each one containing tiny fossils, like this Tinimomys molar.
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But it’s not just tiny primate teeth !
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Some random mammoth skull…
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…Can be found near paleo-shark teeth…
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…With some weird Helicoprion spiral teeth!
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Oh and yes, not to mention the dinosaurs such as this hadrosaurid skull…
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…Or this sauropod one.
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And I even found, hiding in a drawer… a T-Rex!

 

Author

Thomas Guillerme: guillert[at]tcd.ie

Photo credit

Thomas Guillerme, with the kind permision of Michael K. Brett-Surman.

 

Disney Ecology

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In light of the current stresses of exam season, I have been contemplating my parallel educational history. Of equal, if not superior, importance to any stage of my conventional academic life, I have had a Disney education. If I visit medieval castles or forts rich in feudal history I can’t help but mentally locate Rapunzel’s tower and contemplate the prince’s access route. My Greek mythological references are entirely based upon Disney’s Hercules and any mention of Rudyard Kipling is incomplete without at least one verse of the Bare Necessities. Zoological education is no exception. Early Disney films were rather loosely based on real zoological principles – I don’t remember Snow White using any Pavlovian theory to behaviourally condition her furry friends to help with the housework. Similarly, Mary Poppins serenaded an American robin from her London home because studio executives thought the sight of a European robin would be too confusing for their target audience. However, some recent Disney tomes are more grounded in realistic ecology. Disney was my first introduction to fundamental ecological and behavioural concepts as varied as breeding coalitions, mutualistic relationships and inter-specific communication.

Responsible for introducing Swahili phrases to a generation of Timon and Pumbaa fans, the Lion King is a Disney classic, both as a film and more recently as a highly popular stage musical (which is coming to Dublin soon – even if you don’t normally like musicals you must go to this show for the most incredible stagecraft you will ever see). The film marked one of the first times that animators made a specific effort to study their animal subjects to make their movements and behaviours as realistic as possible. Prior to the release of this film, my four-year old self didn’t know that male lions, often brothers, form coalitions to take over prides or that female lions take a cooperative, crèche approach to raising their offspring. Cooperative behaviour in lions continues to spark interest and research to understand why lions are unique among big cats in exhibiting these social tendencies. Of course, some creative licence remained in Disney’s depiction of their feline heroes – the voice of Darth Vader is sadly absent from the Serengeti and male lions don’t lead a troupe of goose-stepping hyenas in a song of revolution. Similarly, rather than a “king and queen”, there’s an equal dominance status within male members of a coalition and within adult females in a pride (unfortunately socially equal characters don’t lend themselves easily to a re-telling of Hamlet). Despite the sprinkle of Disney magic however, the basic ecological premise of Simba’s pride remains grounded in fact.

My ecological horizons were further expanded by Finding Nemo’s depiction of the mutualistic relationship between clownfish and the anemones they call home. It’s a deceptively simple relationship – the anemone’s sting provides the fish with a predator-free habitat while Nemo and his friends help keep the anemone free from parasites. However, many of the finer details underlying this interaction continue to spark research interest (and I’m obviously not the only one to have experienced a parallel Disney education). Nemo has provided evidence that mutualistic interactions tend towards a nested structure. More recently, the way clownfish move their fins has been identified as helping to increase anemones’ oxygen consumption at night – although, hampered by a malformed fin, I wonder whether Nemo’s personal anemone is gasping for breath a bit more than the other anemones? Furthermore, Finding Nemo did not neglect my geographical education – I now know that to get from the Great Barrier Reef to Sydney it’s just a short ride on the East Australia Current – and if I meet a turtle on the way, just call him “Dude”, Mr Dude is his father.

Thanks to Disney, Nemo’s pal Dory is another star of every aquarium. Forgetful but lovable, Dory was my first introduction to the realms of interspecific communication. While Dory speaks whale, it appears that some whales can learn to talk back. A captive beluga whale in San Diego seems to modify its call to mimic human speech. Neither of these examples are true interspecific communication; Dory’s valiant efforts to converse were unsuccessful and the Californian beluga’s “human” vocalisations appear to be relicts of an ability to mimic other whale species.  In both cases, information is not passing between fish and whale or whale and human. Though who knows, perhaps Finding Nemo 3 will be a story of the quest to discover the Rosetta Stone for interpreting whale speech…

So through the talking animals, improbable alliances (why a meerkat and warthog??) and heart-warming moral tales, look out for the ecology in your next Disney film. Combining their subliminal ecological messages with the excellent work of the Disney conservation fund hopefully many more generations will experience a Disney ecological education.

Author

Sive Finlay: sfinlay[at]tcd.ie

Photo credit

wikimedia commons

Finding a PhD

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Undergraduate and Masters students often come to me for advice about how to find a PhD position. I know quite a few students read this blog so I thought I’d share the advice here. Hopefully some of it is helpful! Note this is aimed at people in the UK and Irish system who often go straight from undergraduate to a PhD (or do a brief one year Masters course in between the two). But many points are relevant to the US system too.

1) First make sure you definitely want to do a PhD!

This is really important and I think it’s something that very few of us ever bother to do. The thesis whisperer has some amazing advice on this, and many other subjects related to PhDs, so I won’t repeat too much here.  (See http://thesiswhisperer.com/2011/11/07/should-i-do-a-phd/)

Doing a PhD can be an amazing experience, but it can also be extremely frustrating. Often it’s amazing and frustrating at the same time! You will work long hours for several years with very few rewards and low pay. Then once you finish your PhD things get even trickier – there’s no job security until you reach the Lecturer/Assistant Professor level which generally won’t happen until you’re at least 30, and getting that lecturer’s job is extremely difficult as there are far more qualified PhD students than there are postdoc jobs and lecturer jobs. So to succeed you need to work really hard and also have good luck. It’s good to aim high, but it’s also worth having an alternative career plan in mind for if the whole academia thing falls through. So before you start the long road of potential academic misery, make sure you have a really clear reason WHY you want to do a PhD. If it’s because you love research and can’t imagine doing anything else then great! If it’s because you need one for your chosen career (within or outside academia), again great! But if it’s because you don’t really know what else to do after graduating, or because you want to be a student for a few more years, then I’d recommend researching other options.

2) Advertised PhDs.
These PhDs generally already have funding and a planned research project. You just need to apply. Applications are usually fairly simple, just a CV and cover letter plus a couple of references (usually two). For the cover letter, make sure you describe exactly how you meet the criteria in the job description. Check out our earlier blog posts for help with CV writing. For referees try to include academic referees. Your project supervisor would be a good person to ask, followed by the head of department or your tutor. If the position is in aquatic ecology and you did particularly well in your aquatic ecology module you could ask the lecturer who taught you. Make sure you ask people before you put them down as references.

PhDs are advertised in many places including:

Twitter (with #phd or #jobs)
www.findaphd.com
ECOLOG Archives
Evoldir
University websites

Twitter can be particularly useful for this, as lecturers often tweet about positions in their lab and retweet adverts from other lecturers.

3) Non-advertised PhDs.

Not all PhD positions are advertised. Sometimes this is just because the person taking on students already has someone in mind or a good pool of undergraduate students to choose from. More often though this is because although the lecturer is perfectly happy to have a new PhD student they don’t have any funding. In these circumstances you need to apply for your own funding.

There are a couple of options when it comes to funding. The simplest are “personal” awards or studentships. These are PhD scholarships given to individual students based on various criteria – usually the quality of the student and of the proposed project. The other option is that a supervisor may include PhD student funding on a larger grant they are applying for. In this case the responsibility for the application rests with the supervisor. For personal awards the responsibility rests with you.

To apply for your own funding you first need to find a possible supervisor. You should already have an idea of the kind of project you’d like to work on, so you can use the internet to search for supervisors who might fit your interests. Ask around your current lecturers to see if they know of anyone suitable. You can narrow the search by also thinking about the place you’d like to study at. Once you’ve identified a possible supervisor, send them a brief email with your qualifications (attach your CV), what you’d like to work on, why you’d like to work with them and ask if there would be any opportunities in their group. Also mention that you’d be happy to apply for funding (if you have a funding body in mind mention this too). Don’t do this as a bulk email; make sure it’s tailored to the person in question. Also make sure it’s brief; most people today read emails on mobile phones so long emails are annoying.

If they say yes then you can work with them to prepare a proposal. Don’t get discouraged if you don’t get replies or if you get lots of negative replies. It’s not personal, it’s just that people are busy and some already have as many PhD students as they can handle!

One quick tip on choosing a supervisor (again thesiswhisperer has lots of advice for this): don’t just focus on the senior people. It’s exciting to work with a famous scientist, but more often than not they are extremely busy and their groups are hard to get into. More junior people are often given money for a PhD student or two when they start a new job. They also tend to have more time.

4) Where to apply for funding.

The best thing to do is to talk to your potential supervisor about funding options. There are fewer and fewer options these days but each university usually has some kind of scheme, and scholarly societies often give out scholarships. What you are eligible for will depend on the project, your nationality and the country you wish to do your PhD in. For example, EU citizens can get funding from Marie Curie/European Commission if you do a PhD outside of your home country (and in the EU). Students of any nationality can apply for funding from the Irish Research Council to do a PhD in Ireland. Students of any nationality can also apply for a Trinity Postgraduate Scholarship or Ussher Scholarship from Trinity College Dublin if they wish to study at TCD.

5) DO NOT accept a PhD with little or no funding.

Some people are so keen to do a PhD they’ll accept one with little or no funding. This is a terrible idea (unless you’re independently wealthy!). You will need to pay fees (at TCD these are currently nearly €6000 a year) and need money to live on. Many people try to manage this with a part time job, but if you’re working you’re not doing your PhD, which should be a full time job in itself. And remember for every extra year doing your PhD you need to pay fees. This doesn’t even consider where the money for lab materials, conference travel or equipment is going to come from. So make sure you check the status of the funding before you say yes!

6) Qualifications needed for PhD positions.

If you only have an undergraduate degree then you need a 2.1 or 1st class degree. Remember you’ll be competing with lots of people when you apply so this is just a guide. You can get a PhD with a 2.1 BUT if all the other applicants have 1st class degrees you will struggle. I personally would prefer a student with a 1st for their project and a 2.1 overall, to a student with a 2.1 for their project but a 1st overall.

If you have a Masters then you may get a PhD with a grade lower than a 2.1 but only if you got a good grade on your Masters (preferably a Distinction). Again, your mark for the project component is the most important.

If your qualifications are unusual make sure you explain them. Also make sure you explain them if you are applying to a foreign university which may use a different system. Percentage marks often help here. If you know where you ranked in your class include this information too. If applying for positions in the UK, Irish students should highlight the fact that Irish degrees are 4 years long thus almost the equivalent of a degree and a Masters in in UK.

7) Should I do a Masters or work experience?

Masters courses can be great but they are also expensive and may be of limited benefit in some cases. If you don’t feel ready for a PhD, or are unsure you want to commit to a PhD, a Masters may be more sensible than jumping straight in to a PhD. Also if your grades in undergrad were not very impressive, doing a Masters and getting a Distinction or Merit can override these issues. However, if you’re certain you want a PhD and your project and overall grades were good at undergrad there’s no reason you shouldn’t apply for PhDs straight away. One solution might be to apply for Masters courses and then pull out if you get a PhD (check your contract so you don’t end up losing any money). Masters in Research (MRes) courses may be a particularly good idea as they involve several research projects so allow you to decide if you really like research or not. MSc courses also include taught elements, so these are good if you want to learn more about a specialised topic. These also end with a long research project.

If you want to get a field or conservation based PhD, then work experience may be a better option than doing a Masters. This may still be expensive as most of these positions are unpaid, but then you have the option of volunteering for some of the time and then working to support yourself. Work experience can be Research Assistant positions at universities, internships at conservation charities etc. The Institute of Zoology take interns every year, as do the IUCN. There are field projects on meerkats and baboons run out of Cambridge University that take volunteers each year. Also search ECOLOG and EvolDir (see links in 2 above) for other field assistant positions. Alternatively, if you have a potential supervisor in mind you could email them and offer your services. Or offer to help at a local university so you can live at home and save money. Research Assistant jobs are a great way to learn about PhDs and research from PhD students and researchers you interact with, however, you have to be prepared to work independently as people often don’t have much time to supervise interns.

That’s my advice! Feel free to add alternative advice if you have any. And good luck finding a PhD!

Author

Natalie Cooper

nhcooper123

ncooper[at]tcd.ie

Photo credit

PhD comics

Icefish: The coolest fish on the planet

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I love fish. Not (just) to eat, but to study and learn about and at times just marvel at their beauty. They are arguably the most diverse vertebrate group (and easily arguable if you take the cladistic view that all vertebrates are, at heart, just highly modified fish). But even focusing solely on actinopterygians (ray-finned fish) every aquatic niche is filled by one species or another, from the poles to the equator, from the high Tibetan plateau to the depths of the ocean where sunlight is a distant memory. If there’s water chances are there’s fish.

My particular passion is for deep-sea and polar fish. They have, in my opinion, some of the weirdest adaptations to their environment and I’ve reached a point (right around the time a fish with a transparent head was filmed in the wild!!) where nothing they can do can surprise me.

Despite my jaded outlook I like to keep an eye out for interesting news stories and the other day I stumbled across a story in the Independent about a ‘mysterious fish with clear blood’. I read the story with increasing disappointment as I realised the fish was mysterious only to the reporter, but it provides a perfect opportunity to share the wonders of icefish with a wider audience.

Icefish (Channichthyidae) live in the Southern Ocean. They are a family in the suborder Notothenioidei, a group found in the Antarctic and sub-Antarctic, and have been a love of mine for almost a decade. Notothenioids live in water which reaches sub-zero temperatures, but where their softer, lower-latitude relatives would freeze instantly, they swim merrily on. They can do this due to adaptations, one shared by most Notothenioids and one unique to icefish.

The first adaptation is, in every sense of the word, the coolest I know – they have evolved antifreeze! Antifreeze glycoproteins to be exact. These AFGPs inhibit the growth of ice crystals and prevent the blood and tissues from freezing.

The second adaptation, found only in icefish, has resulted from the interplay of two properties: at low temperatures fluids become viscous and large molecules, such as haemoglobin, increase this viscosity further still; and oxygen solubility increases as water temperature decreases. Icefish have exploited this second property to counter the first. Haemoglobin is an oxygen carrier, but at low temperatures it becomes more of a hindrance than a help. Icefish have a leathery skin instead of scales, allowing oxygen to be transported across their skin as well as their gills, and the high oxygen concentration in the water means that the haemoglobin can be lost with little reduction in oxygen capacity which is exactly what they have done. It helps that these fish aren’t exactly active, preferring to wait for prey to come their way than actively seek it out, but even so I think there are few other animals that could lose haemoglobin and still be alive, let alone live with few negative consequences.

The most striking consequence of this loss is that icefish have white flesh and gills. Normally gills are  one of the reddest parts of a fish due to the need for blood to collect oxygen as water passes over them. But in icefish their gills are white; freakily so.

Normal fish gill (Thunnus fallai)
Normal fish gill (Thunnus fallai)
Icefish gill (Champsocephalus esox)
Icefish gill (Champsocephalus esox)

 

The news story, originally from AFP and posted almost verbatim on several websites, was extraordinarily hyperbolic. It gave the impression that haemoglobin- and scale-loss were unique to this species. Yet, as I’ve said, haemoglobin loss is found in all members of the icefish family and scale loss is found in many species.

The real story is that they have managed to get the species to spawn in captivity, which is a fantastic achievement as anyone who knows anything about closed life-cycle aquaculture will know. Unfortunately it seems that this legitimate success is not sufficiently newsworthy and so a false story has been created. The upside I get to talk about one of my favourite fish so I guess it’s not all bad news!

Author

Sarah Hearne: hearnes[at]tcd.ie

Photo credit

Sarah Hearne

Top tips for science networking!

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Science is a business like any other, and it’s hard to get things done if you don’t know anyone outside of your own department. Other scientists will review your papers and grants, invite you to give talks and hopefully employ you in the future. So the more people you know, the easier it gets. Conference season is just around the corner so I thought I’d continue my hints and tips series by talking about networking at conferences.

Step 1: Finding someone to network with…

Find someone you know and get them to introduce you to everyone they know. This person may be your supervisor, but postdocs and other PhD students can be just as helpful. Make sure you return the favour then everyone will know plenty of people! If you know several people, spend time with each of them meeting all their friends and maximizing the number of new people you meet.

It’s pretty rare to go to conference where you don’t know anyone beforehand. This is much harder than option 1 because you constantly have to make the effort to talk to new people which is pretty exhausting. In these situations try asking your supervisor beforehand if they can remotely introduce you to at least one person there. Then follow them around until you make new friends!

Go to conferences with easily achievable networking goals, for example choose one big name in your field and make sure you have a conversation with them, even if it’s short. However, don’t be that person who goes to conferences with a list of “important” people they want to meet and spends the whole time pestering the big names and ignoring everyone else. The people with the time and energy to start exciting new collaborations are usually students or postdocs, and these are also the people you’ll be meeting at conferences for the rest of your career. So make sure you network with them too!

At huge conferences like ESA it’s often hard to casually network because everyone has already scheduled meetings for every lunch break and evening before they arrive. If you really want to meet with someone drop them an email beforehand and see if you can arrange a quick meeting. Make sure you’re really specific about the meeting place, and don’t be too upset if they don’t show up, they were probably intercepted on the way!

Use social media! Twitter is a great way to arrange tweetups at conferences, and some societies also have Facebook pages where events are advertised. I haven’t tried this yet but I’m very excited about trying it at Evolution and ESEB this year.

Go to all the drinks receptions you can, but skip the conference dinner. This is just my opinion, but I’ve never done any good networking at a conference dinner. They can be fun, but usually they are at the end of the conference so everyone is hanging out with their friends and not really in the mood to talk about work. They are also expensive and the food is often awful. I usually go for dinner with some friends instead and we usually meet other people who aren’t at the conference dinner so we get to make new friends that way!

Step 2: OK so I’m chatting to a new person, what do I say?

I think you should always aim to have a person walk away from a conversation knowing the following pieces of information: your name, your institution and roughly what you work on. Aim to do the same with everyone you meet. If you meet someone particularly relevant to your research interests make a note of this before you forget.

Before going to a conference make sure you have a series of “elevator pitches” prepared. These should be the 1, 5 and 10 minute versions of what you’re currently interested in or working on. If you’re looking for jobs you should also prepare a quick outline of what you’d like to do in the future and the ideal place you’d like to work.

Be interested and interesting. Being interested just involves asking the other person about their work. Everyone likes to talk about their current pet project, and in general these are interesting so you don’t have to fake it! Ask questions where appropriate and be enthusiastic even if you couldn’t care less. If appropriate refer back to their talk/poster or recent papers. Being interesting is harder but again being enthusiastic helps. Talk about your work or the talks you’ve enjoyed at the conference or current areas in science that fascinate you. Hopefully after a somewhat artificial start to a conversation you’ll find yourself in a real and enjoyable chat.

Provided you get in a tiny bit of information about what you’re working on, you don’t have to talk about your work the whole time. Feel free to bemoan peer review, or the funding crisis or the bizarre nature of your structured PhD program. These are great conversational topics as everyone has an opinion and they affect all scientists. Also don’t worry about talking about normal topics – family, hobbies etc. Even the big names have lives outside of academia.

Step 3: Damage control (or OMG I can’t believe I just said that…)

One or two beers are your friends! Alcohol is a great way to reduce inhibitions and help you to chat to people you’d be too terrified to approach when sober. Three or more beers (depending on your alcohol tolerance) are not your friends. If your inhibitions are reduced to the point of dancing on the table people may not remember what you work on. Though they will remember your name…

To be fair, conferences often do involve a lot of drinking and it’s naïve to think you can avoid this entirely. People come to conferences to see old friends and enjoy themselves as well as for work so this should be respected. I think the rule of thumb for alcohol at conferences is to try and hang around with people at the same level of inebriation. Don’t be the drunk group in the quiet bar surrounded by sober people. Also remember that you need to get up the next day and go to lots of talks, so being hungover is not a good idea. Know your limits and never feel pressured into drinking if you don’t want to.

Don’t worry about making a fool of yourself. I’m the champion of this and somehow I still got a job. My classics (all while completely sober) include (1) being put in charge of cake at a meeting in London Zoo and promptly falling over and throwing all the cakes on the floor in front of the director; (2) missing my mouth while talking to a big name at Evolution and pouring coffee all down myself; (3) accidentally wearing a dress you could see my underwear through when meeting the Duke of Edinburgh; (4) complaining that an eminent scientist who published a lot of similar papers would probably publish their shopping list if they could – then realizing the person I was talking to was the scientist’s co-author; (5) insisting that ducks weren’t birds in front of an ornithologist (there’s a logical reasoning behind this but they didn’t stay to hear it); (6) trying to tap someone on the shoulder and accidentally stroking them instead etc. Most of these incidents are not remembered by anyone but my colleagues, and I don’t think they have influenced my career. So if you do say or do something ridiculous, don’t let it scare you away from talking to people in the future!

Those are my top tips; I hope some of them are helpful! I should point out that I don’t actually follow most of them, but I do try my best! Feel free to add more tips in the comments!

Author

Natalie Cooper

nhcooper123

ncooper[at]tcd.ie

Photo credit

wikimedia commons