Category: Seminars

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Seminar series highlights: Nathalie Pettorelli and John Hutchinson

space monitoring

As mentioned previously on the blog, Andrew Jackson and I started a new module this year called “Research Comprehension”. The module revolves around our Evolutionary Biology and Ecology seminar series and the continuous assessment for the module is in the form of blog posts discussing these seminars. We posted a selection of these earlier in the term, but now that the students have had their final degree marks we wanted to post the blogs with the best marks. This means there are more blog posts for some seminars than for others, though we’ve avoided reposting anything we’ve posted previously. We hope you enjoy reading them, and of course congratulations to all the students of the class of 2014! – Natalie

Here’s Sam Preston’s take on Dr. Nathalie Pettorelli’s seminar, “Monitoring biodiversity from space: a wealth of opportunities” and Gina McLoughlin’s views on Professor John Hutchinson‘s seminar, “Six-toed elephants and knobbly-kneed birds! Case studies in the evolution of limb sesamoid bones.”

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Three New Reasons I Want a Satellite

Sam Preston

Despite the best efforts of Google spying on my house and Lee Tamahori making Die Another Day, I still think satellites are awesome. Who among us can honestly say that man-made objects floating in space aren’t straight up cool? And that’s without even considering what we use them for. Where would we be without the internet, or GPS? Probably outdoors, and lost.
But satellites have utility that extends beyond the realm of kittens in top hats, as Dr. Nathalie Pettorelli from the London Zoological Society knows. She gave a memorable seminar on the use of satellites in biological research, single handedly doubling the number of items on my “Reasons I Want a Satellite” list.

1. Vegetation Surveys
The point of owning a satellite – apart from the prestige and party scene – is being able to do cool stuff with it. Unfortunately, most satellites don’t have the kind of firepower necessary to ransom the Earth, but they do have cameras, and there are a lot of uses for a camera in space. For the botanically-minded, vegetation surveys are one possibility.
Working out what trees and how many are in a particular place can be time consuming. You have to go out, pick survey plots, count and identify trees, often in very remote locations miles from the nearest western toilet. Not when you survey via satellite.
To conduct a satellite survey you simply wait until your satellite is overhead, then take pictures. The scale of these pictures can vary from a few tens of centimetres to metres, and once you have them you’ve saved yourself a lot of time, money, and effort. Then you can use your satellite images to spot illegal logging of rainforest, or examine how storms affect mangroves. Best of all, your camera isn’t restricted to what your eye sees. By examining the relative amounts of red and near infrared light reflected from the Earth’s surface, you can determine the “greenness” of vegetation, assess its seasonality, and judge its composition, all of which is vital for finding habitat for reintroduction programs.

2. Multi-Scale Ecology
Two of the seminars we’ve enjoyed have been about ecological scales. Unfortunately, it’s often difficult to obtain data on the largest scales, so unless you’re willing to put in obscene amounts of work and time, you’re not going to get any meaningful information. That is, unless you have a satellite.
Once again satellites trump doing things by hand. They can survey large areas much more quickly and many times more than even the most dedicated research team, and depending on what you’re looking for can provide highly valuable information. Want to assess eutrophication of freshwater? Check out the “greenness” of the lake’s phytoplankton. Want to determine the clarity of the water? Use lasers emission and work out the absorbance rate. If the phenomenon you want to study affects light absorption or reflection in any way, then satellites should be up to the task.

3. Counting Penguins
By now you’ve noticed the theme of my satellite-based projects. When it involves very large – or just difficult to reach – areas, then you can probably do it faster by satellite. But satellite projects aren’t just limited to plants and ecosystems. They can be just as useful for surveying animals over large, hard to reach areas, and there are few areas as large or hard to reach as Antarctica.
If you’ve ever wondered how many penguins are at the south pole, you’re not the only one. We’ve all pondered the number of well dressed birds that manage to carve out a stylish existence on the ice. One research team, however, decided to do something about it, and – you guessed it – they did it with satellites.
The idea is brilliant in its simplicity: take photos of penguin guano from space. Yes, that’s right: millions of euros of equipment used to photograph poo. From space. That has just the bizarre and disgusting ring to it that marks a good zoological study. Outlandish as it may sound, using this method the team discovered 10 new penguin colonies in Antarctica! What’s more, using satellites operating at a finer scale, other researchers were even able to estimate the sizes of penguin colonies!
To sum up, satellites and biological research go hand in hand. No longer is space the privileged realm of the physicist looking down on the (erroneously) perceived softer scientists. Zoologists, botanists, and ecologists have carved out a territory in orbit. There are a lot of questions we’ve yet to face, but the answers are out there.

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Walking on Tenderfoot

Gina McLoughlin

Being an avid follower of a blog called What’s in John’s Freezer naturally I was extremely excited when Professor John Hutchinson from the Royal Veterinary College, London came to give us a seminar. He gave a very interesting and entertaining talk on 6-toed elephants and knobbly-kneed birds: Case studies in the evolution of limb sesamoid bones. Hutchinson explained to us about his recent research into the tiny sesamoid bones, such as the patella, that are found in the limbs of many animals. Sesamoid bones are small “bits” of bone that are generally located in a tendon or near a joint (Sarin et. al., 1999). Their function is not fully understood but it is hypothesized that they may play a role in changing the direction of muscle forces in a limb or may play a role in protecting the tendons.

A very interesting case of such sesamoid bones, which Hutchinson talked about, is found in elephant feet. Elephants, like humans have 5 toes but unlike humans they stand on their tiptoes and have a hoof-like sole. They have a fat pad at the heel of their foot, which acts as a cushion and supports the toes. It is here, buried deep in the fat tissue that the pre-digit bones are found. Hutchinson explained they are like a 6th toe that can be found in both the front and the back feet. The bones are known as the prepollux and prehallux and they connect to the real toes just under where our thumb is (Hutchinson et. al., 2011). They are cartilaginous for most of the elephant’s life, but do eventually ossify when the elephant gets older. Again, the function of these sesamoid bones in the elephant is not fully understood although Hutchinson proposed they could be used as levers for extra support due to the weight of the elephants. Another hypothesis is that instead of developing a single hoof, like in a horse, the elephants use this pre-digit to distribute their weight more evenly on each foot (Hutchinson et. al., 2011). However, these pre-digits have been observed in other animals and have different functions than what they have in the elephant. Most surprisingly to me was that they are found in pandas. Here, they are used for grasping bamboos while eating, kind of like a false thumb. Their 5 fingers close over the false thumb, which has evolved by enlarging the radial sesamoid and functions as an opposable thumb (Endo et. al., 1999).

A thought provoking point that Hutchinson made in his seminar was how do such small bones cause big problems in animals. These bones can cause such big problems that it almost makes big animals appear very fragile. For example, elephants in zoo need to have their feet very well looked after to prevent them from going lame. Hutchinson explained that if an elephant goes lame due to a sesamoid bone problem it is more than likely that the elephant will be dead in approximately 5 years time, as it is very hard to fix and they are in a lot of pain. Likewise, giraffes need a lot of hoof-care to prevent their sesamoid bones from dissolving completely. This would cause the giraffe to go lame and prevent them from thriving.

A more common animal example of a sesamoid injury that I find very interesting, and an area where more research needs to be carried out, is in horses. The sesamoid bones from which most injuries occur are located in the lower limb, at the back of the fetlock joints in the both the fore and hind limbs (Figure 1). In horses it is hypothesized that these bones are used as a pulley for the suspensory ligament as it passes over the back of the fetlock joint. They are very important in the mechanical functioning of the fetlock joint. Horses in competitive sports, such as show jumping and racing frequently suffer from sesamoiditis (Spike-Pierce & Bramlage, 2003). This is commonly caused by heavy loading on the limbs and over-flexion of the fetlock joint, which can result in the sesamoid ligament tearing. This extra pressure can lead to increased internal bone stress, which may lead to a fracture of the sesamoid bones. Faulty blood flow to the bone can be a result of this damage and demineralization of the bone can occur.

Figure 1: Labeled diagram of an equine lower limb showing the fetlock joint and sesmoid bones.
Figure 1: Labeled diagram of an equine lower limb showing the fetlock joint and sesmoid bones.

Thankfully, most cases of sesamoiditis can be treated with anti-inflammatory medicine, cold therapy and support strapping or bandaging. However, in more serious cases where a fracture has occurred the horse may never return to the top of their sport due to the damage (Kamm et. al., 2011). Once a sesamoid bone is damaged they are very difficult to cure because every time the animal walks they put more pressure on the bone, preventing it from healing.

By the end of the seminar I was amazed that such small bones could be so interesting. I would never have though that these tiny bones could be the cause of such big problems not only in competitive horses, but also in large animals such as elephants. Overall, I really enjoyed Hutchinson’s talk. I thought he was a very good speaker and I would now possibly consider doing some research in this area myself.

 

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

B.terrestris

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

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

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

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

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

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

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

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

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

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

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

*Highly commended

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

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

*Best talk 1/2

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

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

Kevin Healy: The evolution of potent venom in snakes*

*Highly commended

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

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

*Best talk 2/2

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

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

Image Source: Wikicommons

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

Rhododendron

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

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

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

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

Alwynne McGeever: The quantification of tree population dynamics*

*Highly commended

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

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

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

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

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

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

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

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

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

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

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

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

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

Image Source: Wikicommons

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School of Natural Sciences Postgraduate Symposium 2014: Part2/4

Trex

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

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

Aoife Delaney: Eco-hydrology of humid dune slacks*

*Highly commended

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

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

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

*Highly commended

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

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

*Highly commended

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

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

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

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

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

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

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

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

Adam Kane: Ontogenetic dietary partitioning in Tyrannosaurus rex*

*Highly commended

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

Image Source: Wikicommons

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School of Natural Sciences Postgraduate Symposium 2014: Part1/4

tcd logo

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

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

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

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

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

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

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

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

*Highly commended

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

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

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

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

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

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

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

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

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

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Seminar Series: Nathalie Pettorelli, Institute of Zoology, London

space monitoring

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

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

Space, the final frontier for ecology?

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

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

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

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

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

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

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

Author: Sharon Matthews

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Evidence of Global Change is Sky High

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

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

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

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

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

Author: Sinead Barrett

 

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Seminar Series: Redouan Bshary, Université de Neuchâtel

cleaning station

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

This week, views from Cormac Murphy and Gillian Johnston on Redouan Bshary’s seminar “Marine cleaning mutualism; from game theory to endocrinology and cognition”.

To clean or not to clean that is the question

With an average size of around seven and a half centimetre I would never have considered the  blue streak cleaner wrasse, Labroides dimidiatus, to be a particularly intimidating animal. Yet over the course of 50 minutes I heard them compared to 4 of the most villainous and screaming entities I know; Niccolo Machiavelli, the Mafia, the global market and a four year old child (anyone surprised by this last entry has probably never had to take care of children).

Cleaner wrasse gain much off their food by eating off the bodies of larger client fish that visit their cleaning stations. This would seem to be a mutually beneficial arrangement, the wrasses have their food come to them and the client fish have their exoparasites removed. But the cleaner fish face some problems. While there are local clients that guarantee a meal, visitor fish passing through the area (who are bigger than the locals 80% of the time) are not as willing to wait in line to be cleaned and will move on. The cleaner client relationship is strained by the cleaners’ preference for the mucus the fish makes rather than the exoparasites. But taking the yummy mucus requires biting the client fish, who may retaliate and will definitely leave the cleaning station after such an encounter. The matter of obtaining food from the most readily available sources and/or of the highest nutritional content is of special importance to the wrasse. Once a wrasse has gained a certain amount of body mass it becomes a male and may take over a harem of smaller females, giving it a greater chance of bearing more offspring. This is something to strive for, but for the wrasse that are already males they don’t want one of their harem to become one of their competitors.  The males will attempt to cheat before the larger females can deprive them of the nutritious mucus and will retaliate against the larger females if they cause the clients to jolt and leave. Dr. Redouan Bshary of the Université de Neuchâtel, Switzerland, is interested in how these little fish deal with the dilemmas they are faced with in their struggle to acquisition food for power and their aggressive gender politics.

An example of Dr. Bshary’s examinations of the cleaner’s feeding strategies focused on their response to visitors. This was tested by placing the fish in a tank with two plates of food, a green one representing the local client and a pink one representing the visitor. If the fish ate off the pink plate, both plates would remain and the fish would get all the food. However, if the fish ate from the green plate first the pink plate would be taken away, simulating how a visitor fish moves on if it doesn’t get cleaned on the first approach. This task was deceptively difficult, as unlike classical conditioning i.e. Pavlov’s dogs, the fish get a reward whichever plate they go for, the behavioural learning lies in realisation that one option will result in a future benefit (both food plates remaining) in addition to the immediate reward. The majority of adults tested learned to go for the green plate first within 100 trials. Juvenile cleaners could not grasp the lesson with the exception of one individual, though it turned out that particular juvenile was just very fond of pink and when the experiment was repeated with the colours reversed it was just as lost as its peers. The adult cleaners’ ability to modify their behaviours based on previous trial experiences are impressive when you consider that the fish outperformed both great apes and human children under four years old that were given the same task.

This is just a snapshot of Dr. Bshary’s work on the behaviour of cleaner fish which brings up interesting and controversial questions about the intelligence of these animals and the conditions under which more complex forms of cognition might develop. Does the cleaner’s besting of our infants suggest they have a higher level of cognition or, more likely in my opinion, are their actions the result of interacting evolved rules of thumbs? Studies like this show us that animal behaviour can be far more complex than it may originally appear.

Author: Cormac Murphy

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You Should Never Bite the Fish That Cleans You!

On Friday the sixth of December, Redouan Bshary came to Trinity College to deliver what turned out to be a lively talk accompanied by engaging slides that summed up the last ten years of his work! Along to his talk, he brought an abundance of enthusiasm, leaving us all in a jolly mood to start our weekends. Aside from the upbeat approach to his talk, other aspects captured the audience’s attention as well. The aim of Bshary’s work turned out to be very interesting and was a very appropriate topic to discuss with a group of zoology enthusiasts.

The aim of Bshary’s research was to discover whether it is easier for cleaner fish to use size over any other characteristic in order to distinguish between resident and visitor fish. Visitor fish tend to be bigger and this can help cleaner fish to make quick decisions, which can improve their fitness instead of wasting time, allowing visitor fish to move elsewhere.

Cleaner fish provide a service to larger fish that consists of removing dead skin and parasites from their bodies and in some cases, removing particles from their teeth. The ability for them to quickly distinguish between visitor and resident fish in order to provide this service is very important, so the fish invest a lot of time in trying to learn this skill. If the cleaner fish make the mistake of feeding from the resident fish first, by the time they move on to the visitor fish, it will have moved elsewhere, giving other cleaner fish the opportunity to feed from it. This reduces the amount of food available to the cleaner fish.

Bshary tested the efficiency with which cleaner fish can learn this skill of feeding on the visitor fish first. He set up his experiment using a cleaner fish placed in a tank with two plates of food, each plate being a different colour. One plate represented the visitor fish, the other represented the resident fish. He allowed the cleaner fish to feed from whichever plate it desired. If the cleaner fish chose to feed from the ‘visitor’ plate first, it would then be allowed to feed from the ‘resident’ plate afterwards. However, if the fish selected the ‘resident’ plate first, by the time it was finished, Bshary would have removed the ‘visitor’ plate. Bshary repeated this experiment for 100 trials in order to establish how quickly the fish learned to associate feeding from the ‘visitor’ plate first with the availability of more food.

During his talk, he presented his results on graphs and explained their significance. His study found that, on average, adult cleaner fish could learn to do this after fifty trials, with juvenile fish taking significantly longer. He then slightly modified the technique for this study and tested it on other species. He found that humans were capable of learning this, but not until they were at least four years old. He found that chimps were slightly better at it but still not at all as efficient as the cleaner fish. He concluded that this is quite a difficult skill to learn so the fish must be in someway adapted for this task. It is obviously useful to them so perhaps this adaption has evolved to increase their fitness by obtaining higher amounts of food. The ability to learn this task so quickly has established that cleaner fish have quite a high cognitive ability.

Given that there is intense competition in the reefs where the cleaner fish are found, it is important that they invest effort in distinguishing correctly between visitor fish and resident fish.

Using size as a proxy, cleaner fish correctly identify visitor fish 87.5% of the time but this obviously is not good enough as the fish then spend time learning to properly distinguish, allowing them to be correct 99% of the time.

Bshary emphasised the important roles that cleaner fish play in the well-being of larger fish and vice versa. Trust is very important between the two, especially when cleaner fish will often venture into the mouths of larger fish to clean their teeth. Honesty is essential for these dynamics to work and so larger fish will open their mouths as an honest commitment signal, reassuring the cleaner fish that this is a safe way of getting food. Should the larger fish try to eat the cleaner fish, upon closing its mouth, the water will be expelled out, bringing the cleaner fish with it. Before Bshary’s talk, I had often seen examples of smaller fish in the mouths of larger fish and wondered how they could be so trusting, this informed me that really they were not in danger at all.

Overall, Bshary’s talk was engaging and provided answers to questions that I had asked myself in the past. If it were up to me, he would certainly be a welcome speaker at Trinity College again.

Author: Gillian Johnston

Image Source: Wikimedia commons

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Seminar Series: Kendra Cheruvelil, Michigan State University/Queen’s University Belfast

landscape limnology

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

This week, views from Kate Purcell and Andrea Murray-Byrne on Kendra Cheruvelil’s seminar “Understanding multi-scaled relationships between terrestrial and aquatic ecosystems”. (See Kendra’s blog about her trip to TCD).

The Power of Knowledge

As the old saying goes: “knowledge is power”. As scientists, a comprehensive understanding of that which we are studying is the key in enabling us to implement our research in a practical manner. From the perspective of an ecologist, compiling a large dataset can be costly – both in time and money. However the benefits of having a centralized dataset can be invaluable. Dr Kendra Spence Cheruvelil, an associate professor at the Michigan State University, has carried out extensive work on lakes in Michigan. Her work highlights the importance of compiling knowledge into shared datasets.

Cheruvelil recently gave a seminar in Trinity College on her work on Michigan lakes. Cheruvelil explained how data on the lakes in Michigan from governmental departments is not standardized. The data can therefore be used to draw incorrect inferences about the lakes in question. This example highlights the need to have a collaborative database where such information can be shared.

As well as explaining the need for a complete, standardized dataset, Cheruvelil demonstrated the importance of understanding the regional spatial scale when extrapolating information to make inferences about lake systems. Cheruvelil and colleagues stated the importance of fully understanding systems from the local to the continental scale. According to Cheruvelil, in order to make correct inferences we need conceptual models of relationships across scales, large datasets, and robust modeling approaches to deal with these data.

Cheruvelil and colleagues studied 2,319 US lakes in 800,000 km2. Using two variables – total phosphorus and alkalinity – they found that there was a high level of among-region variation in lakes. The found that the amount of regional variation present depends on what you look at, and as spatial extent gets bigger so too does regional variation. The amount of regional variation therefore depends on the spatial extent, the response variable of interest (with total phosphorus < alkalinity) and the regionalized framework.

Why is knowing what drives ecosystem processes in lakes important? Cheruvelil made the point that having these data allows for interactions between local and regional scale variables to be accounted for. Inferences can then be made about these variables and how they may drive ecosystem processes in other lakes with less data. The landscape features driving lakes are multi-scaled (local and regional), both hydro-geomorphic and anthropogenic, difficult to disentangle and different according to the response variable of interest.

Cheruvelil’s research is important, especially from a management point of view. It shows the importance of using both local and regional scales when making inferences about any ecological system, including lake systems. Making better and more informed inferences about the driving factors behind the lakes are especially important as we’re in an era facing large-scale climate change.

Author: Kate Purcell

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Paint by numbers: using inferences as a guide to paint the bigger picture

Limnology is the study of inland waters, including lakes, rivers, streams and wetlands. Dr Kendra Cheruvelil is a landscape limnologist currently carrying out research on a huge dataset of lakes in the US. She began her talk by discussing the implications of this kind of work. Her research attempts to integrate freshwater and terrestrial landscapes. As she pointed out – the map of an area you choose to show depicts exactly what you want someone to see. She illustrated this point by showing different land use maps for the state of Michigan. Michigan looks like quite a dry place when you only include lakes on the map, but when streams and wetlands are also included the picture of the freshwater ecosystem is very different!

Cheruvelil compiled a huge multi-scaled (local and regional) and multi-themed (like geology and land use) dataset from existing databases.  These databases came from different organizations and in total she ended up with data on 2319 US lakes in a 800,000km2 area. This huge dataset was necessary for her equally big questions. Firstly she asked how much among-region variation is there, and secondly she wanted to know what the likely causes of this variation (if any) were.

Because ecosystem variation is driven by things like hydrology, geomorphology, as well as anthropogenic and atmospheric factors, on different temporal scales like decadal or seasonal, and different spatial scales like local or regional, the research area can be quite messy in your head (at least it was in mine!) but Cheruvelil broke it down nicely and made it a lot more digestible.

Two variables she chose to look at were total phosphorus and alkalinity. These were chosen as they can indicate stressors: total phosphorus as it can show eutrophication, and alkalinity as it can indicate acidification. They also provide a nice contrast as total phosphorus is considered to be important on a small scale, whereas alkalinity is broader as it has to do with geological features. Using hierarchical models to test the data (which I won’t dwell on because it’s a little above my head!), Cheruvelil found that a high proportion of variation is regional, for example about 75% of the variation in alkalinity was regional. This did, however, vary depending on which regionalization framework she used, but she picked a hybrid model that encompassed both freshwater and terrestrial factors, so despite the different results depending on the framework I think she gave good reasons for picking the one she eventually used.

As far as her second question – the likely causes of this among region variation – she tested the data with conditional hierarchical models (which again I won’t go into, but neither did she which was for the better I think!). Results here suggested that a few regional variables explained a high proportion of the regional variation. However, she was careful not to jump to conclusions that these variables were driving among region variation, and she clearly explained that there are most likely some confounding variables which are hard to disentangle using her methods.

Okay, so you want to study all these lakes and see if they vary among regions – but why? Why on earth is this important? These are valid questions that you may be asking yourself – and questions Cheruvelil was prepared for. She explained how making inferences from a sample lake is important when considering the bigger picture, for example when going from a local level of an individual lake and its watershed to the regional level of grouped lakes within a similar geographical region, to finally all the way up to a continental scale. The void she is filling with her research is the regional level – building models that will allow future researchers to extrapolate from their study lake and infer things at broader scales to see the bigger picture. This is important as most studies on ecosystems will be on a single lake, and I think the take home message was that findings at the local scale may or may not apply to other lakes, depending on how similar they are and if they are in similar regions.

Author: Andrea Murray-Byrne

Image Source: Landscape limnology research group http://www.fw.msu.edu/~llrg/

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Seminar Series: Fiona Doohan, University College Dublin

wheat field

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

This week, views from Gina McLoughlin and Joanna Mullen on Fiona Doohan’s seminar, “Plant-Microbe interactions – the good, the bad and the ugly”

GM Crops Don’t Kill

Genetically modified (GM) crops, are crops that have been modified using genetic engineering techniques to introduce certain qualities, or traits into a plant where they did not occur naturally. Usually, the genes for the desirable trait are taken from one plant and inserted into the genome of another strain of that plant. However, because of this engineering many people think that GM crops pose a serious health hazard and there seems to be a lot of tension around the topic of GM crops. This tension is mostly stemming from big companies, like Monsanto, that have nasty practice records and design GM crops for patents and profits instead of solving food problems.

However, there are many researchers out there that are working on GM crops to try and solve food problems and ensure there is enough food to feed the world’s growing population. Dr Fiona Doohan is a senior lecturer in the School of Biology and Environmental Science, UCD and she has been doing research on food security. The work that she presented to us in her lecture focused on how to enhance disease resistance in cereal crops. For her research she specifically looked at the disease Fusarium head blight (FHB) in wheat. Wheat is the second largest source of calories, after maize, yet it is produced in only a small percent of the world. FHB is a huge problem for farmers as it causes serious yield loss, which they cannot afford. It cost about €9 million per year in order to control FHB with inconsistent fungicides, so Doohan and her team are looking at a better alternative to protect these crops.

Deoxynivalenol (DON) is a mycotoxin that commonly causes the damage associated with this disease. DON is toxic to humans, animals and plants (Rocha et al., 2005) and it is very important that it doesn’t get into the food chain. DON also aids the spread of the disease in wheat heads and increases the severity of the symptoms of FHB (Bai et al., 2001). It causes bleaching of the wheat heads, alters membrane structures and causes cell death. DON also inhibits seed germination, shoot and root growth, root generation and protein synthesis (Rocha et al., 2005). Some wheat strains are resistant to DON and the genes that cause this resistance are being identified (Walter et al., 2008).

Doohan and her team wanted to look at different strains of wheat and how they reacted to DON. They put two strains of wheat up against each other, Remus and CM82036, to try to find the mechanism that allows DON resistance. Remus is the strain that is used in cultivation because it has more desirable qualities than the CM82036 strain but it is susceptible to DON. Analysis of the results was performed using DDRT-PCR and microarrays and a list of genes that could possibly be involved in DON resistance were obtained. One of the genes in this list was an orphan gene. This is a gene that had no significant homology to any known genes and it has also never been described before. Doohan and her team are doing further research into this orphan gene and hopefully it will be a lead to adding resistance to the Remus strain.

Doohan’s work may be essential to human survival if the population keeps rising and people need to start trusting research and open their minds to GM crops. Research has found that there are no adverse affects to using GM crops and they are no more unsafe than crops modified using conventional improvement techniques. They pose no additional risk to human health or to the environment. GM crops have many benefits that people overlook; they require fewer chemicals to protect them, like pest-resistant cotton. GM crops can also benefit farmers as they are more reliable and resistant to stress. Some farmers are so eager to use these crops they have had to be pirated in, for example Bt cotton was pirated into India. GM crops are also safer and more precise than mutagenesis techniques.

However, I don’t think that this evidence and these benefits are enough to change the negative opinion that society has on GM crops. I think people need to be shown that scientists, like Doohan, are now producing GM crops for the public’s benefit.  I am of the opinion that we need to change the negative attitude toward GM crops that the big companies have created and, unfortunately, this may take a very long time and a lot of effort in order to convince the consumers. It makes sense that, in order to feed 9.5 billion people on the land area that we have to grow food, with limited water, pesticides and fertilizer, and with the hugely changing climate, we need to be looking at alternative ways for human survival. Maybe GM crops are the answer.

Author: Gina McLoughlin

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Are we just clutching at straws or is there grain of hope in the battle to save our crops from destruction?

Food, we can’t live without it, we can’t live on it if it’s diseased. This is the motivation behind the work of Fiona Doohan and her team in U.C.D, who are striving to improve the security of the world’s food supply by improving the resistance of cereals such as wheat and barley to the many diseases that currently threaten their very existence. During her seminar on Friday the 22nd of November in Trinity’s Botany Lecture theatre, she outlined the main areas on which her work focuses. At the heart of which is research dedicated to plant disease control and stress resistance, as well as the potential influences of climate change and adaptation to disease.

Currently approximately 2332 million tonnes of cereals are used worldwide each year and they are considered to be a universal staple food in the diet of humans, making Fiona’s research all the more important.

During her talk she discussed one of the main diseases of interest to her group, “Fusarium Head Bight Disease” (FHB). This is a fungal disease affecting crops of Wheat and Barley, causing visible bleaching of the infected cereals early after infection.

The real trouble with this fungus however is that it produces a mycotoxin known as deoxynivalenol (DON) which leads to significantly reduced yields of the crop, and importantly can have toxic effects for animals and humans and as such infected crops are not allowed enter the food market, resulting in significant loss to revenue for farmers.

The big problem when attempting to control and prevent FHB is that fungicides have proven to have little effect on controlling it.

One of the big steps forward in tackling this fungus was the discovery of the significance the role of DON plays in spreading and maintaining the infection. Research has shown that if the DON toxin is knocked out early on the infection will be reduced and the bleaching symptoms do not develop. Also, without the DON toxin, there will be no adverse toxic effects for humans and animals thus removing the food safety concern.

Interestingly not all wheat is susceptible to FHB and DON; some exotic wheats are naturally resistant to the toxin and fungal disease. This has led to researchers asking what are the mechanisms and genes that lead to potential resistance to DON/FHB. Using gene expression studies to isolate possible genes associated with DON resistance, Doohan’s team have discovered several genes which they believe to be of interest, most noticeably one particular orphan gene.

Orphan genes are genes which are restricted to a certain lineage. They are particularly important in stress resistance, but are often ignored. It is on the role this orphan gene plays in DON resistance that Doohan’s team have centred their research efforts. Noting the importance not to tissue specificity per say but it’s specificity to DON, the orphan gene will not have an effect on mutant strains of DON. However, when artificially expressed in a non-exotic strain of wheat that would normally express DON when infected, the orphan gene has been shown to inhibit the expression of DON thus inhibiting the development of FHB.

Though these results are very encouraging, the true significance of this discovery and whether it can be applied practically to the production of crops is still waiting to be tested. Unfortunately due to strict European laws the first tests on genetically modified, field planted crops are likely to have to take place in the U.S.A. However Doohan’s research does offer a glimmer of hope in the rather bleak fungus covered problem FHB and it’s (g)rain of terror on stalks of wheat all over Europe.

Author: Joanna Mullen

Image Source: Wikimedia commons

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Seminar series: Tom Ezard, University of Southampton

Forams

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

This week; views from Sarah Byrne and Sean Meehan on Tom Ezard’s seminar, Birth, death and macroevolutionary consequences.

Splitting Hares – easier said than done?

In a recent talk given by Tom Ezard, a research fellow and evolutionary ecologist, the definition of a species was examined and challenged. While defining a species may seem a simple task for just about anybody and in particular a room full of people with a biology background, the actual definition can be harder to understand when thinking about fossil or species’ records and gaps across time. Ezard highlights that a dynamic approach is needed when discussing speciation and the definition of a species. Claiming that you shouldn’t define a species at one particular moment in time, he details that large gaps in the fossil record make it very difficult to have a fully complete picture about speciation events. In other words, making inferences about speciation events from a certain snapshot in time could overlook the dynamic process of change that occurs over time and give us inaccurate theories about the macroevolution of species.

Following on from the definition of a species, Ezard was interested in the fossil record and how it can give us information about the species record and also, more importantly, about diversity. He was interested in finding out where these gaps in the fossil record had occurred and what impacts they could possibly have. In graphs he provided, it was clear that there was a difference between data over time with more species surges found in recent data in comparison with the past, indicating the number of species has increased over time. However, it’s a little misleading because as time develops we learn more about how to indentify species of have better techniques to do so, it is therefore unclear as to whether or not there has been a big increase in species.

To better explain some complicated parts of the speciation theory, Ezard used a baseball analogy which I was thankful for, showing a picture of various baseballs over time. Ezard explained how techniques improve over time and how the original was very different to the new and modern ball. All of the baseballs of various different ages, textures and shapes remained part of one game (or one species) and that there was no split into a new game (or new species). He stressed that this continuation was very important in understanding macroevolution and when identifying species, that it was vital to look at gaps in the lineage. This brings us back to the fact that the fossil record needs to be examined further and the question of what is meant by a species may need to be redefined. Ezards definition of a species as ‘a single line of descent, a sequence of populations evolving separately from others seems closer to the real definition than previously thought.

Speciation was also a key factor of Ezard’s talk and he was interested in identifying budding speciation events while still being able to identify their ancestors. Two main types of speciation and evolution were discussed in the talk, one type; anagenesis refers to a change along a branch of a phylogeny or the evolution of a gradual change within a species over time. This theory was backed by Darwin and eventually leads to a speciation event. In contrast, cladogenesis, where a population stays stable until a big speciation event happens suddenly and then a splitting occurs between species that ensures they can then not reproduce with each other.

The split can be caused by either biotic or abiotic factors with disagreements regularly occurring between geologists and modern evolutionary biologists over whether the biotic factors (such as competition) or the abiotic factors (such as climate) are the main key drivers affecting species ecology and diversification. So, what is the main driver affecting species ecology and in turn speciation and diversification? Ezard was interested in finding this out.

Using observational studies, algorithmic processes and a multivariate complex approach, Ezard was able to account for ecological differences between species. Lotka’s equation gave an estimate of birth and death models that detailed speciation probability and extinction risk. Species respond differently to global drivers of change and these differences have macroevolutionary consequences. The Red Queen Hypothesis mentioned above, a biotic factor that describes how predator and prey are continually adapting to out-do each other affects species much more so than climate does, and in comparison, climate, an abiotic factor has much more of an effect on extinction.

So, it seems that a combination of both factors are important although they affect both speciation and extinction at different rates. Ezard indicated that, in order to understand diversity, it was first necessary to understand the biotic factors that impact the split and to then devise a model to draw these two areas together. Ezard’s enthusiastic and engaging approach clearly showed his passion for the subject and the interesting topic left me with a lot to think about it.

Author: Sarah Byrne

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Lumpers and Splitters: Apparently they’re not varieties of potato

What is a species? This question seems so fundamental to biology that surely the experts have answered it by now, right? Wrong. Defining a species is a difficult thing, and each new definition seems to come up short in certain criteria. For example Ernst Mayr’s widely used definition of a species: “groups of actually or potentially interbreeding natural populations, which are reproductively isolated from other such groups” completely disregards species which reproduce asexually. For this reason I like Simpson’s evolutionary concept for defining a species and this is precisely what Tom Ezard uses for his work on macroevolutionary dynamics. This concept holds that each species represents a single line of descent; it begins with a speciation event and terminates with extinction. Ezard used the evolution of the baseball to demonstrate this concept. Although the modern baseball is considerably different from its original ancestor, it is still a baseball and there have been no ‘speciation’ events or splits in the lineage to form a new type of ball.

It was Darwin who first coined the term ‘lumpers and splitters’. Lumpers are those biologists who tend to ‘lump’ many ‘species’ in together as one. The splitters are those biologists who like to make as many ‘species’ as possible. In his 1945 work ‘The Principles of Classification and a Classification of Mammals’ George G. Simpson notes rather sardonically: “splitters make very small units – their critics say that if they can tell two animals apart, they place them in different genera … and if they cannot tell them apart, they place them in different species. … Lumpers make large units – their critics say that if a carnivore is neither a dog nor a bear, they call it a cat.” So we can see that this problem is an old one, and that Simpson’s evolutionary concept is very useful for defining species in macroevolutionary studies.

In order to study macroevolutionary dynamics one needs a fairly detailed picture of a clade’s development, and not many organisms provide a suitable fossil record for a detailed study. Fortunately Ezard and his team found the perfect organisms for this purpose; the Foraminifera. These creatures are marine dwelling amoeboid protists. When they die they sink to the bottom and leave behind their calcium shells or tests. They are deposited and preserved on the sea floor and in the right conditions over time can form stratified layers of fossils which give a very complete picture of their evolution over time. Also,the stable isotope ratios of oxygen in the shells can be used to reconstruct palaeo-climatic conditions. These attributes make them incredibly useful in the study of macroevolutionary dynamics.

So, what are the driving forces of speciation? Is there one factor which influences this process above all the others? This is what Ezard and his team set out to investigate. The foraminifera had an interesting story to tell. It was found that incipient species diversify the fastest. This was found to be primarily due to biotic factors or ‘Red Queen’ factors. As a clade grows older it was found that diversification slows due to diversity dependence. However, it was found that extinction is primarily influenced by climatic or Court Jester factors. These findings are important in order to grasp a general understanding of macroevolutionary dynamics. It means that impacts of diversity and climatic fluctuations are not felt uniformly across a phylogeny.  More simply put, it means that the extent of the effect of biotic and abiotic factors on a clade depend on how old it is.

In summary, what Ezard and his team found was that there is no dominant macroevolutionary force, but that, a combination of biotic and abiotic variables drive speciation and extinction. They also found that species’ ecologies are important driving forces in these processes.

Author: Sean Meehan

Image Source: Wikicommons