Early Career Researcher Programs (ECRs) Round 4 Progress Reports
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| 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)
A two-day teaching workshop, 'Species' Distribution Modelling Methods
University of Queensland: 15&16th November 2007
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 firstname.lastname@example.org
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
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.
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
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)
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.
|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,
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
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
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
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
Attendees: The workshop was attended by 4 Senior Academics,
13 ECRs, and 20 PhD Candidates
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:
- 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
- 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
- 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.
- 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.
- 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.
| 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)
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.
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 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)
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 Heratys lab,
University of California
CI(s)/Institution: Sally Thompson, University of Adelaide,
School of Earth & Environmental Sciences ($1,500)
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
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