ecology Archives - Page 5 of 10

05/03/201424/02/2014

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

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

03/03/201424/02/2014

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

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

26/02/201423/02/2014

School of Natural Sciences Postgraduate Symposium 2014: Part2/4

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

18/12/201327/11/2013

Seminar series: David Angeler, Swedish University of Agricultural Sciences

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 Somantha Killion-Connolly and Joe Bliss on David Angeler’s seminar, Ecological complexity: a torture or nurture for management and conservation?

Panarchy – Sense or nonsense?

Scientists have been told for many years now to lift their heads from their microscopes, look up and take in the bigger picture. Well the picture has gotten even bigger and more complex according to the hypothesis of panarchy (Gunderson & Holling, 2002). In a recent seminar by Dr. David Angeler of the Swedish University of Agricultural Sciences, Dr. Angeler attempted to communicate this approach as the way forward in ecosystem management. If you were to do a search of the internet for the definition of panarchy, don’t expect a nice simple concise definition, as this controversial approach takes a bit of explanation. Ecologists have been providing evidence for decades showing that ecological systems are far more complex than imagined. Panarchy attempts to provide a conceptual framework for characterising the interactions between ecological and human systems in order to manage them in a sustainable manner.

Panarchy seeks to find common ground between economic, social and ecological theories. This seems like a big ask and paradoxically the way it seeks to achieve this is, using Dr. Angeler’s analogy, to break up the big picture into smaller pieces to make a jigsaw puzzle. Where the hypothesis begins to make a lot of sense is that is requires you to take not only a top –down, as was traditionally used, but a bottom up approach also. Ecologists have traditionally investigated ecological communities and how they have changed spatially and temporally. Dr. Angeler proposes to instead look the big ecological picture in terms of scales. We should not only be looking at how organisms at different scales are affected by biotic and abiotic variables in time and space, but also the interactions between scales. Therefore, according to panarchy, ecological systems consist of scale specific structures and processes that change and interact as you advance through the scales. The further spatial dimensions are increased, the slower the processes are in the environment and vice versa.

Where the theory begins to get more complicated is when you need to view an ecosystem and its constituents as undergoing a continuous cycle of change, with four defined stages. The stages are referred to as the exploitation stage (rapid expansion in an open niche), conservation stage (accumulation of energy and a period of stability where the carrying capacity is reached), the release stage (period of rapid decline due to changes in pressures) and the re-organisation stage (period of natural selection from the pressures of the release stage).

Dr. Angeler in his research on the invertebrates in freshwater lakes of Sweden (Angeler et al., 2013) has shown how the theory is empirically testable using multivariate time series modelling. This method is based on a redundancy analysis and adapts a spatial method to time series analysis. Using this long term data set collected by his University, Angeler’s aim was to track changes in the species community and gain an understanding into what are the vulnerabilities of these vertebrate communities to changes in their environment. The practical goal of this work is to prevent a system from reaching its tipping point. The results of this study suggested that studying processes that happen on a temporal scale which are un-related to general environmental changes has strong management and conservational potential. Personally, I think the main concepts of panarchy do make sense but its application and the analysis required is far from simple and it really is a difficult idea to communicate.

Author: Somantha Killion-Connolly

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Multivariate Time Series Modelling Explained
I think the language of science often hinders the communication of ideas and restricts them to a narrow audience of specialists. I attended a talk given David G. Angeler presenting his research on Ecological Complexity using Multivariate Time Series Modelling and the Panarchy concept to study the condition of a number of Swedish lakes. I found it difficult to even understand what the research was about so, I have been inspired to write this blog and explain part of this complex topic, in simple language which I hope will be graspable for a wider scientific audience.

Let us start be first breaking down the term “multivariate time series modelling” and studying its parts. Multivariate means more than two variable quantities. In this context of studying ecological complexity, these variable quantities include the number of organisms of a particular species or species group as well as abiotic factors such as mineral concentrations and water temperature. Time series modelling involves plotting data at uniformly spaced time intervals. So multivariate time series modelling is plotting multiple variables against time.

The benefit of plotting multiple variables such as multiple abiotic factors and a species population’s numbers on a specific time scale is that it allows you to find correlations between factors. For example, if we take the population numbers of a plankton species which were sampled once a month in a lake we can plot the population number over a year and see how the population fluctuates. Our plankton may show fluctuations up and down over the year. To investigate whether any of the abiotic factors influenced the fluctuations in our plankton numbers we can plot how the abiotic factors fluctuated over the same time span and see if any of them correlate with the fluctuations of the plankton. If any of the abiotic factors fluctuate with the same rhythm as the population then we might suspect this in an important factor influencing the population. However this doesn’t rule out the possibility that the abiotic factor itself varies with the population number but is not the cause of the fluctuation, correlation does not prove causation, but this can then be investigated by experimentation.

Another important benefit of using multivariate time series modelling, which Angeler used when studying the ecology of his lake, is that it allows us to see correlation at different time scales. For example plankton may fluctuate up and down in a regular pattern in response to annual variation in day length. But on a longer time scale, say over 20 years, there may be a trend of increasing population numbers due to a large scale effect such as climate change.

Looking at ecological variation using multivariate time series modelling allows us to assess how organisms are responding to different conditions on small and large time scales. Angeler hopes to use these data to assess the health of ecosystems and to understand how they will be able to handle changing conditions such a global warming. He suggests that management may be able to aid ecosystems facing this large scale change by affecting them in ways which act on smaller scales.

Author: Joe Bliss

Image Source: Wikicommons

02/12/201301/12/2013

Join us!

It’s that time of year again at EcoEvo@TCD where we start looking for people to apply for Irish Research Council fellowships to come and join us as postdocs or PhD students. These awards are open to anyone, regardless of nationality. Details can be found here(PhD funding) and here (postdoc funding).

But why would you want to join us? I can talk (type?) at length about this but maybe the best people to ask are the students and postdocs we already have working here. So here are their comments instead!

Thomas Guillerme @TGuillerme

Supervisor: Natalie Cooper (Zoology)

As a French student, starting a PhD in this department was made really easy by the people working here. Not only the academic work and projects are really exciting, but also the social part of the department makes work really easy going and fun.

Deirdre McClean @deirdremclean1

Supervisor: Ian Donohue (Zoology)

I can’t recommend the zoology department enough as a place to do a PhD! This is largely due to the great diversity of projects going on and the close relationships between staff and students. Collaboration is greatly encouraged and there is so much opportunity for this through NERD club, tea breaks and pub trips! We have a really nice mix of empirical and theoretical projects meaning that we get really different and interesting perspectives on our work, which I think has been great in my development as a scientist. Being in a small department has a lot of advantages and it means I always find so much support from my supervisor, other PhD students and other staff. Because of the friendly atmosphere and the variety of research groups and backgrounds, lunchtimes, tea breaks and pub visits provide great opportunities for getting input on your work, coming up with new ideas and having debates! There is also a lot of opportunity for teaching, outreach and collaborating with other groups/departments. The campus here is beautiful and right in the centre of town so it’s a really nice place to work and socialize too!

Shane Mc Guinness @S_Mc_G

Supervisor: Anna Davies (Geography)

Without the support, funding and independence provided by IRC funding, my amibitions to study endangered species conservation and human development in Africa would not have been realised. In addition, the increasing integration of the School of Natural Sciences makes this a truly interdisciplinary environment to work in.

Karen Loxton @LoxtonKaren

Supervisor: Celia Holland (Zoology)

From fantastic supervisors to technicians who seem able to solve any problem, the Zoology Dept. has been an amazing place to study for a PhD. Staff are generous with their time and expertise and the seminars and EcoEvo group are a great way to keep up to date with research outside your own. The diversity of projects within the department ensures that pub conversations are always an opportunity to learn something new and interesting.

Kevin Healy @healyke

Supervisor: Andrew Jackson (Zoology)

So far I have really enjoyed doing my PhD in the Zoology department, mostly this is due to the fact that we get the opportunity to work on loads of cool collaboration projects (right now I’m working on a T.rex paper due to a bet in the pub on who could have a dinosaur paper first) but also because there is a very relaxed social vibe to the department as well. I think my development as a scientist over the last two years is also really down to the amount of support from not just my supervisor but all the other members of staff, whether its from our NERD club meetings, going to conferences or just a lively debate at lunch. It also helps that the department is right in the middle of Dublin so there’s plenty of pubs to continue work after 5!

Sive Finlay @SiveFinlay

Supervisor: Natalie Cooper (Zoology)

The Zoology Department is a lovely home for a PhD student. There is a very relaxed, friendly atmosphere with plenty of opportunities to mix with and learn from staff, postdocs and fellow students. We’re a relatively small department but that is definitely to our advantage because you get to know people from diverse research backgrounds and you’re not lost in the anonymity of being yet another student in a large research lab. In the past few years there’s been increased collaboration and integration across the School of Natural Sciences through our NERD club meetings, postdoc talks, weekly seminars from invited speakers and via the EcoEvo blog, all of which are great for getting out of the bubble of being stuck in your own project. There are also plenty of opportunities to get involved in teaching, collaborative projects, fun outreach events and of course a healthy amount of socialising… What’s more, Trinity is a great university with a beautiful campus in the centre of the city – not a bad place to work!

Seán Kelly @seankelly999

Supervisors: Nicola Marples and Dave Kelly (Zoology)

The Zoology Department and the School of Natural Sciences are full of friendly and welcoming students and staff from a great variety of backgrounds. I never fail to find support or advice on my PhD project when it’s needed, whether from my supervisors, other staff or students. The diversity of expertise within the department is a real asset; one that is readily available to you. Integration within and between the various departments is ever increasing and collaboration is greatly encouraged. Lunchtime conversations often turn into lively debates and sometimes lead to new collaborative projects. There’s ample opportunity for teaching experience, group learning and social outreach, as well as socialising, of course.

Sarah Hearne @SarahVHearne

Supervisor: Ian Donohue (Zoology)

I was nervous moving to a new university to study a new field of biology, but I shouldn’t have been. The department is incredibly friendly and welcoming and there is a great spirit of collaboration. This isn’t a place to hide away for three years, it’s a place where discussions are had or ideas spawned over a pint in the pub or during a lunch break. People share their successes and commiserate over failures. Some great science is done as well!

Adam Kane @P1zPalu

Supervisor: Andrew Jackson (Zoology)

The Zoology department has a great group of scientists who are interested in each other’s research which makes for excellent collaborative opportunities. The best advertisement I can give for it is that I don’t dread getting out of bed on a Monday morning.

Katherine Webster

Supervisor: Ian Donohue (Zoology)

Being part of the dynamic and interactive EcoEvo group in the School of Natural Sciences has greatly enhanced my experience at Trinity as a postdoc. From the students to faculty, you gain valuable feedback into your own research while learning about new ideas that expand your own perspectives. Being in Dublin and walking the hallowed grounds of Trinity College certainly adds to the experience!

If you’re interested and have a member of staff with appropriate research interests in mind, please get in touch! Contacts and research profiles of staff can be found here. Note that, unfortunately, the application success rate is fairly low and the applications themselves take a bit of effort to fill in for both the applicant and the academic who supports the application. Because of this we won’t be able to support every person that contacts us. But we promise to be realistic about your chances of getting funding. This is judged on your CV, the project, and the fit of the project to the chosen supervisor. The call opens in November and the deadline is January.

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

Image: Wikimedia commons

27/11/201326/11/2013

Blog-tastic!

Andrew Jackson and I started a new module this year called “Research Comprehension”. The aim of the module is simple: to help students to develop the ability to understand and interpret research from a broad range of scientific areas, and then to develop opinions about this research and how it fits into the “big picture”. In our opinion, this is perhaps the most important thing an undergraduate can get out of their degree, because no matter what you do when you graduate, in most jobs you will be expected to read, understand and interpret data. Often this will be in a subject you are unfamiliar with, or use unfamiliar methods or study organisms. So being able to understand this information is key!

The module revolves around the Evolutionary Biology and Ecology seminar series in the School of Natural Sciences, so the topics are broad and cover whole organism biology, molecular biology, genetics, plants, and animals etc. Students attend the seminar on a Friday and read some papers sent on by the speaker. There is then a tutorial on a Monday with a member of staff who has interests in the area of the seminar. This gives everyone a chance to clear up any confusion and to discuss what they liked (and disliked) about the seminar. The continuous assessment for the module is in the form of the blog posts we will post here. Thus the module also aims to improve the students’ abilities to communicate all kinds of scientific research to a general audience, a skill that is currently in great demand.

From next Wednesday onwards we will select a few blog posts to put onto EcoEvo@TCD. These may not necessarily be the posts that get the best grades, but they’ve been chosen to reflect the diversity of angles the students have taken to communicate the parts of the seminar they found most interested. Overall we’ve been extremely impressed with the quality of their blog posts, so we hope you enjoy reading them!

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

Image Source: Jorge Cham, www.phdcomics.com

08/11/201307/11/2013

Trophy Hunters

Antler collection at Harvard's Museum of Comparative Zoology — Antler collection at Harvard’s Museum of Comparative Zoology

It may be an inconvenient truth in these conservation-focused times but we owe a debt of gratitude to the trophy hunters; the army officers and colonial-types who killed animals for sport and prestige. Without their considerable efforts, the vaults of natural history museums would be devoid of the skeletons and skins which form the bases of both exhibitions and many PhD and MSc. theses. Of course, were it not for the over-zealous efforts of hunters perhaps many charismatic animal species wouldn’t be so endangered now but let’s focus on the positives here…

Naturally, if you’re a hunter looking for a prize, bigger is usually better. It’s far more impressive to have a stag or bear’s head mounted on your wall than a hedgehog or shrew – although I would like to hear the embellished stories which might arise from tales of killing your first hedgehog! Similarly, if you are a taxidermist or museum collections manager in many ways it is easier to prepare and preserve large rather than small mammal specimens.

These collection trends are all well and good if you’re interested in the charismatic species. I, however, am studying the little shrewy-type things; hedgehogs, moles, shrews, golden moles and tenrecs – fascinating species but not prized possessions for your trophy case. Even in some of the world’s largest natural history museums it’s difficult to find intact skulls and skeletons of some of these creatures. Combined with the inherent delicate nature of these animals (some tenrecs’ limbs are tiny!) compiling a complete morphometric data set of the groups remains challenging.

Tenrec limbs with a pen for scale; teeny tiny tenrecs!

For the museum collections of these little critters that do exist; I am eternally grateful to the progenitors of carefully handwritten labels accompanying the skulls and skeletons on which my PhD research depends. Adventurers such as Major Forsyth, G.K., Creighton, and C.J., Raxworthy who donated specimens from their tropical voyages deserve special thanks in any research which arises from their collective efforts. However, I am also grateful to the back-yard naturalists, the people who collected and preserved the seemingly ordinary, every-day species of common shrews and hedgehogs which are no less important to ecological and evolutionary research than their exotic counterparts. I benefitted greatly from their collective efforts during my recent trip to Chicago’s Field Museum.

Whether naturalists or trophy hunters, the individuals immortalised by museum specimen labels couldn’t possibly have envisaged all of the diverse future research which would be based on their prized collections. It’s an important reminder that, despite the inherent appeal of flagship species, the lesser-spotted or common-something-or-others are just as deserving of our attention and study. Even if you don’t have the equipment or inclination to start posting skeletal remains of common species to your local natural history museum, there are still plenty of ways of contributing to the study of “ordinary” wildlife. Don’t be dazzled by the allure of large-animal trophy hunting and remember that, when it comes to understanding the natural world, bigger is not always better.

Author:

Sive Finlay: sfinlay[at]tcd.ie

@SiveFinlay

Photo Credits

Sive Finlay

11/10/201305/04/2019

Big is better!

Reflections on geeking it up at Intecol 2013 by Jane Stout

Having not been to a 2000+ delegate, multi-session, international conference for several years, I was a bit nervous in the run up to INTECOL2013 “Into the next 100 years: advancing ecology and making it count” – would it be possible to see all the talks, read all the posters and meet all the people I planned to? (Answer: no). Would I remember everyone and would anyone remember me from past meetings? (Answer: some yes, some no – thank goodness for name tags). Could I follow in the footsteps of Katie Taylor, the last girl from Bray to take the stage at the London ExCeL Arena, and take the Olympic gold? (Answer: no; note to self: must try harder). But I needn’t have worried – INTECOL 2013 was excellent: it was well organised, the quality of the science was top-notch, the sun shone, and the whole thing was very inspiring and humbling. Continue reading “Big is better!”

20/09/201317/09/2013

The ‘Natural’ World

What images come to mind when you think of a field ecologist? Do you see what I see? I see someone, probably in khaki shorts and a broad-brimmed hat, walking through thick rainforest, listening to the calls of birds, waving off insects determined to find a patch of skin to bite, and smelling the exotic aromas of plants and animals living, dying and decaying.

You may well be thinking that this is an idealised image of a field ecologist and while it may have been true 50 years ago, it’s harder to imagine now. After all, every day we hear about habitat destruction and how mankind is damaging the natural environment. But I’d like to propose that even 50 years, or 100 years, or even 1000 years ago mankind was having an impact on the environment and this idea of the ‘natural’ world really needs rethinking.

Take, as an Irish example, the Burren. I visited this area for the first time a few weeks ago and was stunned by the rugged beauty of the place. It was sparsely populated, only a few sheep and cows (and the occasional donkey) provided evidence of any human presence in places; how much more ‘natural’ could one get? Plenty more, it turns out, as the entire landscape is the result of human impacts.

The entire area is littered with signs of prehistoric people, the most striking of which was the 5,000 year old Poulnabrone portal tomb. This tomb dominates a limestone pavement with a view that stretches for miles across to the sea. Yet reading the information boards it quickly became apparent that this was not the landscape in which the tomb was constructed. At that time the area was heavily forested with small clearings made by people to farm and build their homes. The tomb would most probably have been largely hidden from all but those who knew its location. Yet over the next few thousand years people cut down more and more trees to make use of the timber and to clear the way for more farmland. However, the trees were the only thing holding the thin soil in place and with the loss of the trees, the soil soon followed, until all that was left were patches of vegetation and entire hillsides of exposed limestone bedrock. That stunning ‘natural’ landscape is the result of ancient habitat destruction!

A similar story can be told across much of the world. New Zealand, adopted home of the hobbits, with its fields and rolling hills, was once almost entirely forest. Yet when the Maori reached the islands around a thousand years ago they proceeded to reduce the forest cover by almost half, and the European settlers reduced it by half again. In addition, the loss of so many endemic species also led to changes in the structure of the remaining forests, though precisely how is still being debated.

It’s the same the word over. Take, as a final example, Australia. The sixth largest country, the world’s largest island, yet it has only 0.33% of the world’s population. Surely humans can’t have had much of an impact there? Well, yes they can, particularly if you think that they are at least partly responsible for the loss of the megafauna. For more details on that I highly recommend Tim Flannery’s 1994 book ‘The Future Eaters’, with the teaser that I never knew that dung was so important to a properly functioning ecosystem! But even ignoring that, Aborigines had a long and close association with the land, heavily modifying environments through activities including the use of controlled burning.

I could go on (and on, and on) for every habitat on almost every continent, but it would get rather monotonous. My point is that when we look at the ‘natural’ word we rarely see something that’s never been touched by man however far into the ‘wilds’ we go. The ‘natural’ world has been modified, sometimes subtly, sometimes dramatically, for thousands of years as countless generations have struggled to survive and prosper. Ecology, however much we like to think otherwise, always involves a human component. Sometimes the humans who made the impacts have long gone and the landscapes have become so normal and ‘natural’ its hard to think there was a time they were ever different. But if we are to understand the world we need to understand the historic impacts we have had, not just on climate, not just in towns and cities, but also on the ‘natural’ world.

Author

Sarah Hearne: hearnes[at]tcd.ie

@SarahVHearne

Image sources

Sarah Hearne

Ewers et al. (2006) Biological Conservation 113:312-325

19/06/2013

The world dyed by algae

Photograph by Brian Skerry, National Geographic — Seamount, Cortes Bank

The term “algae” does not refer to a single taxonomic group but instead comprises a diverse array of species, from prokaryotic cyanobacteria to many types of unicellular and multicellular eukaryotes. It’s well known that algae make great contributions to sustaining the diversity and productivity of our natural world. It has been estimated that the number of algae species could range from 30,000 to more than 1 million. So it’s not surprising to find that algae, so high in diversity and abundance, have significantly altered the appearance of our planet.

Just as plants add colour to our terrestrial world, algae are responsible for the diverse colours of many aquatic systems. Without the existence of macroalgae, most marine zones would be barren places and we would miss the beauty of park-like intertidal zones and magnificent marine forests comprised of gigantic algae such as the Giant kelp (Macrocystis pyrifera). In the shallow zone of rivers and lakes, attached filamentous macroalgae can flourish when the pressure of competition from aquatic plants is low, making the river and lake much greener than it would be otherwise. Microalgae also play their own role in dyeing the environment. In marine areas with high concentrations of phytoplankton, the existence of large amounts of chlorophyll absorbs the red and blue portions of the light spectrum and reflects green light. Therefore, sea water in these regions is not blue but appears as different shades; from blue-green to green. Attached microalgae, such as some benthic diatom species, can easily occupy diverse substrates, such as stones and aquatic plants, and decorate that substrate with their own colour. Despite their tiny volumes, only several μm in length or diameter, the adherent strength of these algae is quite strong and it is not easy to remove them from the substrate (as I found out when helping Lindsay with her field experiments!).

Some people might say they prefer multicoloured coral reefs to algae. However, even the beautiful colours of coral reefs depend on Symbiodinium, one group of dinoflagellate algae which live in a symbiotic relationship with coral polyps. However, this relationship is not absolutely stable and severe environmental stress can sometimes weaken the symbiotic bond. Increased sea water temperatures and ocean acidification can cause coral polyps to expel their algae. As a consequence, the corals lose both their color and any phototrophic capabilities and eventually become boringly white; a process termed coral bleaching.

Algae are also responsible for the beautiful colours of some sea slug species. In contrast to the harmonious symbioses between algae and corals, some sea slugs directly consume algae and use the algae’s pigment to produce remarkable body colors which can either be apatetic or aposematic in their functions.

Sometimes, however, algal colouration is not always welcome. Blooms of intensively growing algae can produce very ugly and unpleasant colours. Cyanobacterial blooms are one of the most common environmental problems in freshwater systems including eutrophic lakes, reservoirs and the backwater zone of rivers. During bloom periods, lake surfaces can be partly or fully occupied by cyanobacterial cells, creating an unappealing dark blue-green colour.

A cyanobacterial bloom in Chao Hu, the fifth largest freshwater lake in China

Other algal groups, such as some dinoflagellates, are commonly found in marine blooms. The colours of algal blooms in marine systems are more diverse depending on the type and density of bloom species. However, one kind of bloom, Noctiluca scintillans, is especially unattractive. Proliferation of this species creates a bloody red colour remarkably similar to the one described in Exodus, which may be one of the earliest recorded instances of a red tide (“… and all the waters that were in the river turned to blood. And the fish that were in the river died, and the water stank …”).

A Noctiluca scintillans bloom off the coast of eastern Australia — A *Noctiluca scintillans* bloom off the coast of eastern Australia

Author

Qiang Yang: qiang.00.yang[at]gmail.com

Photo credits

Brian Skerry, National Geographic

Wikimedia commons

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