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Research Funding Provided by: Australian Government
Research Funding Provided by
Australian Government

Australian Research Council

Environmental Futures Network
Environmental Futures Network
The University of Adelaide
North Terrace Campus
Darling Building
South Australia 5005

Phone: +61 8 8303 3952
Facsimile: +61 8 8303 4364

Early Career Researcher Programs (ECRs) Round 4 Progress Reports

[back to Round 1 or Round 2 or Round 3 or Round 5 reports]

Project title: Assessing climate impacts on biodiversity: training workshop on bioclimatic modelling
CI(s)/Institution: Elvira Ploczanska, Postdoctorial Fellow, CSIRO Marine and Atmospheric Research Tasmania ($15,000)

Workshop

Now open: A two-day teaching workshop, 'Species' Distribution Modelling Methods for Biologists
University of Queensland: 15&16th November 2007

Download promotional Flyer here
Places are limited to number of PCs available, so please be early to RSVP
Course Fee: Free to ECRs Members from contributing institutions
Non members: $400
Interested people should reply directly to elvira.poloczanska@csiro.au by 10th October, 2007

Participants will be selected by relevance to their research and priority will be given to those who are from EFN contributing organisations. Refer to participating organisations here

Download registration form here

Aims/background:

This project that will take advantage of the visit of international and Australian experts to Brisbane to teach a two-day training workshop on bioclimatic modelling. This course will be useful to ECRs from a range of disciplines such as marine and freshwater ecology, plant ecologists and animal conservation and will introduce Australian ECRs to bioclimatic modelling and thus increase Australia's capacity to predict impacts of climate change on Australian marine, terrestrial and freshwater biodiversity.

As recognition of the potential consequences of climate change for biodiversity increases, the necessity for accurate predictions of impacts is increasing. Bioclimatic modeling can quickly provide much-needed valuable information to anticipate biological loss and to guide research, even where knowledge of underlying ecological processes is lacking. Bioclimatic models correlate a species' current distribution with selected climatic variables to identify the 'climate envelope' for the species. The models can then be used to predict future potential distributions of species using climate change scenario data or to hindcast distributions using historical climate data. This approach provides a useful first approximation of key drivers of species distributions over large spatial scales, and can be applied even when detailed mechanistic understanding of underlying biology and ecology is lacking. There are a suite of bioclimatic modelling approaches including generalised linear models, classification trees, generalised additive models, random forest predictors, artificial neural networks and genetic algorithms for rule-set prediction1,2. The increasing number of bioclimatic models being produced for Northern Hemisphere terrestrial species that successfully simulate current species distributions indicates these models are very effective in evaluating climate drivers.

Project:

The course will be aimed at ECRs with some knowledge of bioclimatic modelling: this will not be a prerequisite, we expect computational proficiency. It is intended that the workshop be held at the University of Queensland. This will be a 'hands-on' course to teach ECRs how to apply these techniques, as well as underlying theory, concentrating on several modelling approaches (to be decided by tutors). The workshop will be free to ECRs from EFN organisations. Participants will be selected on the basis of relevance to their research and membership of the Environmental Futures Network.


Project title: Understanding recent evolutionary history of Australian Biota: "Phylogeography and Coalescence Workshop"
CI(s)/Institution: CI(s)/Institution: Alexandra Pavlova, Monash University, Joanna Sumner, Australian National University & Museum Victoria & Daniel Murphy, Royal Botanic Gardens, Melbourne and University of Melbourne ($15,000)

Aims/Background

The workshop brought together national and international experts in regional and comparative phylogeography and coalescence methods. The workshop aimed to equip early career researchers in Australia with essential theoretical and methodological skills in phylogeographic analyses and coalescence methods. In addition, it aimed to encourage collaboration between like-minded researchers working on evolutionary history, population genetics and conservation of the Australian biota. Invited talks were focused on conceptual issues of comparative phylogeographic research, new methodological advances and directions the field is taking.

Presentations
Dr. Paul Sunnucks, Monash University.
Paul presented a background to coalescence and phylogeographic analyses, demonstrated strengths and weaknesses of Nested Clade Analysis (NCA) and statistical phylogeography, and using multiple examples from microbiogeographic study in Tallagandra State Forest, introduced approaches to comparative phylogeographic studies. Paul also discussed different temporal scales and choice of appropriate genetic markers and addressed questions that were sent in by participants prior to the beginning of the workshop.

Dr. Stuart Baird, l'Institut National de Recherche Agronomique, France
Stuart's presentations covered the theory behind coalescence methods and analyses, which were followed up in his computer workshop. He also discussed recent innovations in the analysis of georeferenced field data (including his own development of software) and model-based inference for sampling strategies.

Dr. Margaret Byrne, Department of Environment and Conservation, WA
Margaret Byrne broadened the taxonomic coverage of the workshop by giving a presentation about the current state and challenges of research specific to plant phylogeography, including the recent development of DNA sequence markers.
Dr. Luciano Beheregaray, Macquarie University
Luciano reviewed the taxonomic coverage of phylogeographic studies, presented the concept of study design, sampling strategies and resulting phylogeographic outcomes, using examples to highlight difficulties, achievements and conservation implications. He gave numerous examples of phylogeographic studies in different biogeographic settings, which included tropical rainforest, temperate coastal and volcanic island scenarios..

Dr. Ryan Garrick, Virginia Commonwealth University, USA
Ryan presented multiple approaches to comparative phylogeography, testing congruence and integrating inferences. He discussed sensitivity and power of statistical phylogeographic methods, and gave an overview of MESQUITE, which was followed up by computer session.

Computer workshops (facilitated by Filipe Santos, l'Institut National de Recherche Agronomique, France)
Dr Stuart Baird ran sessions on: Geneland http://www.inapg.inra.fr/ens_rech/mathinfo/personnel/guillot/Geneland.html#Introduction
Graphical interface for Geneland http://www.inapg.inra.fr/ens_rech/mathinfo/personnel/guillot/GenelandGUI.html and
Dancing tree (software for coalescent analysis of gene trees, a demonstration version was provided for workshop participants)

Dr Ryan Garrick ran a computer workshop on the program Mesquite 1.12 http://mesquiteproject.org/mesquite/mesquite.html

Attendees: The workshop was attended by 4 Senior Academics, 13 ECRs, and 20 PhD Candidates

Outomes

The workshop successfully created a forum for the exchange of ideas, methodologies, and results, whilst stressing the need for further conceptual development. The participants were given plenty of opportunity for discussion and asking questions to the presenters in both formal and informal settings.

The directions in comparative phylogeography are based around the fact that populations are neither panmictic nor in uniform habitat. Thus, there is a growing appreciation of the importance of having spatially-explicit analyses - notably coalescence. The uptake of coalescent approaches and software that enables us to use these approaches has been very important.

The main conclusions:

  1. Comparative phylogeography aims to discover commonality or differences in responses of different organisms to the same environmental histories, and, thus, to improve understanding of processes of speciation and the underpinnings of biodiversity distribution. The determination whether there is concordance (or not) in location of areas is important in management recommendations, and counters the uncertainties of single species studies.
  2. It seems possible in the near future to obtain affordable genome sequencing for non-model species. We should aim to design efficient marker sets to extract information from different temporal scales of analysis.
  3. Phylogeographic results and inferences can be improved by taking geographic coordinates and habitat suitability into account when reconstructing coalescent histories. The software programs Geneland and Dancing Trees provide an opportunity to achieve this goal.
  4. Observed genetic (and phylogeographic) structure results from a combination of repeated climatic impacts and stochastic processes. Statistical phylogeography is an objective test of hypotheses and a way to seek processes behind the patterns, but it is currently limited by computing power. Statistical phylogeographic methods often assume simple histories, which make them difficult to apply. On the other hand, Nested Clade Analysis is an empirical, but non-statistical way of inferring historical processes and relative timing of events. Therefore, integrative approaches using multiple analyses are needed.
  5. Even apparently (qualitatively) congruent phylogeographies could have resulted from different historical processes. Direct (observed spatial-genetic patterns) and indirect (hypothesized alternative scenarios) comparative phylogeographic approaches are now available to distinguish between concerted and species-specific responses and to test congruence over time. The use of multiple markers is essential.

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Project title: Bioavailability of organically bound iron to phytoplankton of the Southern Ocean, visit to Dr Veronique Schoemann's lab, Belgium
CI(s)/Institution: Christel Hassler, CSIRO Atmospheric & Marine Research ($1,500)

Aims/background:

International research programs, such as CLIVAR GEOTRACES and SOLAS recognise the ocean's critical role in regulating the Earth's climate system. During the last 15 years it has been demonstrated by microcosm experiments and large scale in-situ Fe fertilisation experiments that iron controls primary productivity, as well as the planktonic community structure in more than 40% of the oceans (High-Nutrient, Low-Chlorophyll areas - HNLC). In this respect, global climate models suggest the HNLC Southern Ocean (SO) as being the ultimate sink for atmospheric CO2 over the next 100 years. For these reasons, the parameterisation of iron bioavailability in biogeochemical and climate models is of great importance. Indeed, data allowing an accurate modelling of iron bioavailability in the oceans is missing. Since dissolved inorganic iron concentrations are insufficient to sustain the growth of planktonic organisms and most of iron is complexed with organic ligands (> 99.5 %), the bioavailability of organic iron to phytoplankton of HNLC regions is a critical parameter. Whereas work with natural phytoplankton is environmentally relevant, it provides little information on the processes controlling the bioavailability of organic iron. Mechanistic understanding of iron bioavailability should be first assessed at the species level before one proceeds interpretation of the phytoplankton dynamics in response to iron in the oceans.

Project:

The collaboration with Dr. Véronique Schoemann started during the SAZ-SENSE voyage (2006-2007) where we measured the ability of natural phytoplankton of the SO to access variable forms of organically bound iron. This research visit to Dr. V. Schoemann at the Laboratory of Ecology of Aquatic Systems (Université Libre de Bruxelles, Belgium) allowed to continue our collaborative work using 4 monocultural strains isolated from the SO, representing the major phytoplankton groups (diatoms and prymnesiophytes) present (see Figure 1). Their ability to access 7 environmentally relevant organic forms of iron (siderophores, heme ligands, polysaccharides) was measured via radiolabeled iron bioaccumulation experiments. Results from those laboratory experiments will be compared with those obtained during SAZ-SENSE.
During this research visit we also worked on collaborative publication from the results obtained during the SAZ-SENSE voyage and Dr. C.S. Hassler presented her results on the use of cyanobacterial iron-dependent bioreporters in freshwaters at the Université Libre de Bruxelles. Finally, Dr. C.S. Hassler was introduced to laboratory techniques employed to enumerate aquatic bacteria, autotroph and mixotroph phytoplankton, and protozoan.

Top figure: image of selected phytoplankon from the Southern Ocean. Diatoms are (A) Chaetoceros sp. CS 624 (scale bar is 10?m), (B) Thalassiosira antarctica Comber (scale bar is 10?m)< (C) Fragilariopsis kerguelensis forming chain (scale bar is 50mm, both in Bright field and with DAPI staining). Heptophytes is Phaeocystis antarctica (D) present as single cells and colonies (scale bar 100?m, images in bright field and epifluorescence)


Outcomes:

Dr. CS Hassler learnt different techniques to enumerate bacteria, phytoplankton and protozoa from marine samples. In addition, opportunity was taken to work on manuscripts related from data obtained during the SAZ-SENSE voyage. Finally, Drs. C Hassler and V. Schoemann continue their collaborative work on the role of biologically produced organic ligands to sustain iron bioavailability. Preliminary results shows that different phytoplankton from the Southern Ocean are able to access differently iron bound to organic ligands. In fact, some ligands were found to increase significantly iron bioavailability, which is against prediction using thermodynamic chemistry. The polysaccharides (dextran), porphyrin (protoporphyrin IX) and the cathecolate siderophore (Gallo-catechin) were the organic ligands which promoted the most iron bioavailability. The monosaccharides tested either increased (for the colonial haptophyte Phaeocystis sp.and the chain forming diatom Fragiliariopsis kerguelensis) or had no or little effect on iron bioavailability (single cell diatoms, Chaetoceros sp. and Thalassiossira antarctica). The impact on iron bioavailability could be seen on primary productivity. Therefore, this visit allowed scientific experiments showing that biologically produced/released organic ligands, often overlooked such as saccharides and porphyrins, are critical to maintain iron bioavailability and primary productivity in the Southern Ocean. These results will be published in a peer-review journal.

Project title: Systematics and biogeography of a Oxyscelio and related genera of parasitic wasps(Hymenoptera: Scelionidae) with special reference to the Australasian fauna; visit Dr John Heraty’s lab, University of California
CI(s)/Institution: Sally Thompson, University of Adelaide, School of Earth & Environmental Sciences ($1,500)

 

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Project title: Travel funding to obtain training from museum curators and experts in the field of geology, geomorphology and ecoloyg of the Pilbara region, Australia
CI(s)/Institution: Mitzy Pepper, Australian National Univesity

 

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Travel funds to attend workshops in analytical techniques to identify drivers of disease and to investigate mechanisms of disease resistance in corals (USA).
CI(s)/Institution: Cathie Page, James Cook Univesity ($1,800)

 

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