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Early Career Researcher Programs (ECRs) Round 1 Reports
[To Round 2 or Round
3 or Round 4 or Round
5 reports here]
1. Project title: Coevolution
of the Cotesia flavipes complex and their polydnaviruses: toward
the effective control of stemborers in Australia.
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CI(s)/Institution: CI(s)/Institution: Kate Muirhead,
University of Adelaide, School of Earth & Environmental Sciences ($3,500)
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Aims/Background
Kate visited Dr Jim Whitfield's laboratory at the University
of Illinois at Urbana-Champaign and attended the Evolution 2006 Conference
in Stony Brook, New York, to learn about the latest methods and analyses
in the study of coevolution. These skills will be used in her PhD project
to investigate coevolution of the Cotesia flavipes parasitic wasp complex
and their polydnaviruses (PDVs).
Project:
Jim Whitfield is one of the world's leading investigators
on the evolution of endoparasitism in braconid wasps. Travel to his
laboratory for two weeks gave Kate the opportunity to interact and collaborate
with other students and research scientists working on similar species
and to broaden her knowledge on the coevolution of Cotesia and their
PDVs.
At the Coevolution Symposium Kate gave a presentation on her PhD research
into the Cotesia flavipes complex and their polydnaviruses. She received
positive feedback on her presentation and also some useful advice concerning
her project. The conference gave her the opportunity to meet and discuss
her research with a number of scientists using new analysis methods.
Outcomes:
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Kevin Johnson, a leading researcher on coevolution
of birds and lice at the Illinois Natural History Survey, provided
Kate with some coevolution papers discussing current techniques
and showed her how to use the coevolution analyses programs TreeMap
1 & 2, Treefitter and a data-based parsimony method that he
has developed.
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Josephine Rodriguez, a PhD student working on
Cotesia, showed her a method to dissect insect genitalia in preparation
for the SEM, which is an important component of her project for
identification purposes.
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Kate gave a presentation on her work and received
some helpful feedback at a roundtable discussion with Jim Whitfield,
Sydney Cameron and their students on current methods and analyses
being used in ecology and molecular biosystematics.
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Learning about programs used in molecular systematics
and molecular clock analysis, such as SplitsTree and Rates.
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Jim provided samples from his collection that
will be useful for her PhD
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2. Project title: Multidisciplinary
training workshop for the integration of biodiversity modeling, environmental
data, phylogenetic diversity, and carbon accounting
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CI(s)/Institution: CI(s)/Institution: Susan Cameron
and Rob Waterworth, ($15,000)
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Aims/background:
The workshop was held 6-7 June 2006 at the Australia
Museum in Sydney. Ten Early Career Researchers participated, including
the co-PIs. The workshop was held in conjunction with a larger EFN
working group meeting (2010 working group, Faith and Ferrier). Four
'mentors' from the 2010 Working Group attended the ECR workshop.
Project:
As most participants were not familiar with one
another or with the EFN (as stated in the proposal), a large part
of the first day was spent with introductions and brief research
presentations designed to generate group discussion. Dan Faith introduced
the EFN and the 2010 Working Group and Rob Waterworth and Susan
Cameron presented goals for the meeting and questions to consider.
Each participant gave a 20 minute research presentation of their
research as it applied to the workshop themes and discussion followed.
The second day was more focused, with demonstrations and hands-on
training of several biodiversity measuring and monitoring tools,
including the Biodiversity Analysis tool (Dan Rosauer, CSIRO/DEH),
the National Carbon Accounting System (Rob Waterworth, Australian
Greenhouse Organisation), Environmental Diversity software (Faith)
and Generalised Dissimilarity Modelling (Cameron). Several breakout
sessions were conducted on topics such as 'Monitoring biodiversity:
What are we measuring and what does it tell us' and 'integrating
carbon accounting and biodiversity protection'. These discussions
provided the participants with the opportunity to discuss synergies
within their different disciplines and potential research collaborations.
Some synergies identified included :
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Linking biodiversity priority setting with
analysis of environmental change
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Phylogenetic analyses at multiple scales
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Linking climate change, biodiversity and landcover
change
Outcomes:
The workshop met the goals stated in the original
proposal including sharing research ideas across disciplines and
providing links to the 2010 EFN Working Group. All participants
(with exception of Moffett, Kelley, and Armour) also attended the
2010 EFN meeting held over the following two days, 8-9 June 2006
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3. Project title: The adaptive
significance of temperature-dependent sex determination in an Australian
lizard
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CI(s)/Institution: Daniel Warner, University of Sydney
($1,500)
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Background:
Daniel visited Professor Mats Olsson's laboratory at the
University of Wollongong to study the adaptive significance of temperature-dependent
sex determination (TSD) in a lizard from southeast Australia - the jacky
dragon (Amphibolurus muricatus). In many reptile species, an individual's
sex is determined by temperatures experienced by the embryo during development.
The adaptive value of this mechanism has puzzled biologists for decades.
A widely accepted hypothesis (the diffAAerential fitness model) for
the adaptive significance of TSD states that incubation temperature
affects the fitness of male offspring differently from female offspring.
That is, temperatures that produce females are optimal for daughters
and temperatures that produce males are optimal for sons. No rigorous
experimental tests of this hypothesis have been conducted on reptiles.
The objective of his research is to test this hypothesis.
Project:
The funds provided allowed Daniel to travel to the University
of Wollongong to learn and conduct specialized genetic techniques to
determine parentage of the second generation of offspring. From February
to April 2006 he spent time learning and optimizing the techniques.
During this time he initiated DNA extractions from his samples and prepared
a manuscript that describes the microsatellite markers that were developed
specifically for jacky dragons. He also spent time testing the jacky
dragon DNA markers on other lizard species that are being studied in
Mats Olsson's laboratory. Fortunately, these tests indicated that several
of the markers developed for the jacky dragon also work successfully
in several other lizard species. Thus, Daniel's work will directly benefit
future work coming from Mats Olsson's laboratory.
From May to August, he was able to finish all DNA extractions and successfully
genotyped every individual lizard from his project and was very successful
at assigning parents to the second generation of offspring. This allowed
him to determine which individuals were successful at reproducing, thus
enabling him to evaluate if temperatures during incubation have sex-specific
effects on reproductive success.
Outcomes:
The financial support enabled Daniel to acquire new skills
(Optimization of primers for genetic studies, DNA isolation from tissue
samples, PCR, Genotyping, parentage analysis) and has enhanced understanding
of the evolution of TSD. The results suggest that TSD may be maintained
because optimal incubation temperatures differ for sons versus daughters
in a way that fits with predictions from the differential fitness model.
These results provide the first empirical support for the differential
fitness model and thus will make a substantial contribution to the field
of sex determination.
This work also has implications for conservation of species with TSD.
For example, TSD places several reptiles under serious threat from global
climate change because even a modest change in environmental temperatures
can massively shift offspring sex ratios. Results from this study demonstrate
how such temperature changes may affect the fitness of the offspring.
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4. Project title: The origin
and future of the Cophixalus frog diversity of Australia's Wet Tropics
rainforest
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CI(s)/Institution: Conrad Hoskin, University of Queensland
($3,500)
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Aims/background:
The purpose of the research visit was to work with Prof Craig Moritz
and his research group to resolve the systematics and evolution
of the Cophixalus frogs of the Wet Tropics rainforests of north-east
Queensland. This research aims to understand the origin of the exceptional
Cophixalus diversity seen in the rainforest of the Wet Tropics,
through an analysis of diversity at all scales from the genus as
a whole, through lineages within species, and down to divergence
between populations across environmental gradients. This research
is important for elucidating the processes driving diversification
and for understanding the impact of global climate change on Wet
Tropics diversity in the past and present.
Project:
The research visit was conducted at the Museum of Vertebrate Zoology,
which is part of the University of California, Berkeley campus.
Conrad was primarily working with Prof. Craig Moritz (Director of
the Museum of Vertebrate Zoology). Additionally, he was collaborating
on the project with a member of his research group, Mrs Maria Tonione,
and also with Assoc. Prof. Catherine Graham at the State University
of New York, Stony Brook. He also interacted with other members
of Prof. Moritz's research group as well as other researchers in
the Museum of Vertebrate Zoology. Funding was organised through
the School of Integrative Biology at the University of Queensland,
where he recently completed his PhD.
The opportunity arose while at UC Berkeley to assess genetic variation
in a frog parasite of the Wet Tropics. His PhD research was on genetic
and phenotypic variation and secondary contact in the Green-eyed
Tree frog Litoria genimaculata. This frog is parasitised by the
larva of a Diptera of the genus Batrachomyia. He has long been interested
in assessing genetic population structuring in this parasite to
see if it matches that of its host. He was able to achieve this
while at UC Berkeley and successfully sequenced the same mtDNA gene
in the parasite formerly sequenced in the frog. Conrad also had
the opportunity to assess chytridiomycosis prevalence in the frog
hybrid zone studied during his PhD.
Outcomes:
He acquired a number of new skills while at UC Berkeley.
He learnt several new laboratory techniques including a new DNA extraction
method, a new PCR clean-up method, how to run a capillary sequencer,
real-time PCR, and parasite genetic analysis. He also learnt a range
of new techniques for the analysis of genetic data. In particular
he acquired skills in the management and analysis of large genetic
data-sets, how to resolve and score nuclear sequence data, programs
for the analysis of genetic structuring and hybrid zone analysis (Bayesian
Analysis of Population Structure - 'BAPS 4', 'Structure', 'Arlequin',
'NewHybrid'), analyses of environmental divergence between lineages
and environmental niche modelling, and the analysis of chytrid prevalence
data.
The research visit was highly successful in achieving the goal of
understanding evolution of the Wet Tropics Cophixalus frogs, and also
for conducting other research on Wet Tropics frogs. The greatest success
was obtaining a very large and informative genetic data set for the
analysis of phylogeographic structuring and secondary contact between
lineages within Cophixalus ornatus.
The enclosed photo shows a male Cophixalus ornatus calling from the
trunk of a tree. This species is found in the Wet Tropics rainforest
of north Queensland, between Townsville and Cooktown. In the summer
wet season, males (about 23 mm long) climb a couple of metres into
the vegetation and call with a loud bleating call. Populations of
this species consist of five lineages, four of which meet in a complex
hybrid zone that I have been studying.
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5. Project title: Research Visit
to Prof Jim Whitfield's Lab at the University of Illinois
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CI(s)/Institution: Nick Murphy, University of Adelaide,
School of Earth & Environmental Sciences (3,500)
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Aims/background:
The objective of my visit was to synthesize my work
on microgastroid wasp phylogeny with polydnavirus (PDV) studies being
undertaken by Prof Jim Whitfield and to learn new analytical techniques
for the analysis of molecular phylogenetic data.
Project:
The main purpose of this visit was to further enhance
collaboration with Prof Whitfield and improve our current study of
microgastroid phylogeny and PDV evolution. Activities included:
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An exhaustive search of fossil literature for
the dating of microgastroid nodes. This will vastly increase the
nodes for which dates are available.
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A discussion of the relative merits of a number
of analytical methods and computer programs for undertaking molecular
clock analysis. The result of which was to undertake the dating
of the microgastroid nodes using penalized likelihood in the computer
program r8s, which allowed the use of multiple fossil to calibrate
minimum ages for a number of nodes.
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Cutting edge phylogenetic data exploration using
the program Splitstree 4. In particular, Prof Whitfield demonstrated
the use of 'filtered supernetworks' to examine the phylogenetic
signal produced by individual genes, an analytical procedure that
Prof Whitfield has helped to develop along with the Splitstree
author, Daniel Huson.
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Progressed significantly a manuscript entitled
'Phylogeny of the microgastroid complex of subfamilies of braconid
parasitoid wasps (Hymenoptera) based on sequence data from seven
genes, with an improved estimate of the time of origin of the
lineage', which will be submitted for publication before the end
of the year
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Numerous roundtable and informal discussions with
Profs Whitfield and Cameron, and their students, on the current
state of hymenopteran molecular systematics and analytical methods.
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Future opportunities with regards to microgastroid
systematics and phylogenetic analysis were explored.
Outcomes:
This visit enabled Nick to improve his understanding
of analytical techniques associated with molecular clock analysis
and data exploration. He will be able to pass these newly acquired
skills directly on to students who he is teaching. The research visit
has also strengthened the relationship between The University of Adelaide
and The University of Illinois and there is a potential for further
research collaboration.
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6. Project title: Sex Allocation
in Reptiles: Ecology, Evolution, and Conservation
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CI(s)/Institution: Tobias Uller, University of Woolongong
(3,600)
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Aims/background:
The workshop on sex allocation in reptiles brought together
national and international experts in evolutionary ecology, sex determination
and herpetology. The workshop intended to stimulate development of sex
allocation biology using reptilian model systems and to integrate sex
allocation research with recent theoretical and empirical advances in
studies of sex determination. In addition, it aimed to promote collaborations
between universities and research groups with different research of
taxonomic background. This was further facilitated by Australia's leading
role in sex allocation and sex determination research.
Project:
Invited plenary talks focused on broad conceptual issues
and the current state of sex allocation research, whereas additional
speakers were free to present novel empirical work from their own laboratory.
The main areas that were covered were costs and constraints on differential
sex allocation, relationships between sex allocation and sex determination,
and consequences of global climate change for species with temperature-dependent
sex determination.
Main Presentations
Prof. Jan Komdeur Avian sex allocation: mechanisms
and fitness consequences
Prof. Andrew Cockburn Chasing sex allocation in complex vertebrate
societies - are we missing the point/s?
Prof. Arthur Georges Sex determination and sex allocation
Dr Ido Pen Modeling evolutionary transitions between GSD and TSD
Dr Erik Wapstra Sex allocation in squamates: does the story become
clearer with more data?
Dr Tobias Uller Constraints on differential sex allocation
Outcomes:
The workshop successfully managed to create a forum
for exchange of ideas, model systems and results in sex allocation biology
as evident from the positive response from attendees and other colleagues,
both national and international. New collaborations were established
between a number of research groups at different universities, including
University of Groningen (the Netherlands), University of Wollongong,
University of Sydney, University of Canberra and University of Tasmania.
The support for making this meeting a recurring event has been very
strong and future meetings are already being planned. The main conclusions
can be summarized as follows:
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Reptilian model systems provide an excellent opportunity
to test current theoretical models in a way that is not possible
in most other vertebrate systems
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Recent studies in reptilian sex allocation has provided
novel insights into the processes and mechanisms of sex determination
and sex allocation
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Integration of proximate mechanisms of sex determination
and sex allocation will transform the field, both theoretically
and empirically
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Recent results on lizards suggest that our current
understanding of the evolution of sex determination must be revised
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Climate change influences sex ratios at birth in
species with temperature-dependent sex determination and may have
consequences for population demography and population persistence
The workshop resulted in a research synopsis that was
submitted for publication in the leading review journal Trends in Ecology
and Evolution.
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7. Project title: Short course, Enhanced
understanding of shallow lake ecology-interpreting sediment records of
plant remains
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CI(s)/Institution: John Tibby & Jennie Fluin, University
of Adelaide ($9,863)
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Background/Aims:
The "loss" of submerged plants from shallow lakes and estuaries
is one of the most significant human impacts on aquatic ecosystems in
the world. Plant loss frequently results in reduced biodiversity and
the maintenance of phytoplankton dominance that, even with significant
management intervention, is difficult to eliminate. Despite the importance
of this phenomenon, there is considerable debate about the key processes
driving "switches" between plant and phytoplankton dominance.
This short course provided participants with the means to document
such switches using the "record" of plant (and animal) remains
preserved in the sediment. In ideal settings, it will allow researchers
to assess different hypotheses about the causes of such switches (see
Reid et al., 2007, J. Paleolimnology in press).
The five day short course, held in January 2007 and hosted by the University
of Adelaide, was delivered primarily by Drs Carl Sayer and Tom Davidson
of the Environmental Change Research Centre, University College London.
Dr Sayer has recently published a profoundly different theory about
what causes the decline of plants in eutrophic shallow lakes (Jones
and Sayer, 2003, Ecology 84: 2155-2167). He has also shown how studies
of fossil biota can elucidate the nature and causes of changes in aquatic
plants (e.g. Sayer et al., 2006, Env. Sci. Tech. 40: 5269-5275). Dr
Davidson is pioneering new approaches to understanding the history of
lake ecosystems, particularly through the analysis of plant and animal
remains (Davidson et al., 2003, J. Paleolim., 30: 441-449 and Fresh.
Biol., 2005, 50: 1671-1686).
Project:
There were a total of twenty-one workshop participants from University
of Adelaide (13), The Australian National University (1), University
of Canberra (1), Flinders University (1), Macquarie University (1),
Monash Universities (2), University of Tasmania (1) and the Environment
Protection Authority, Victoria (1). These included 17 early career researchers.
The short course focused on applied issues and examined how plant seeds,
leaves and other remains can document changes in aquatic plant composition
and abundance. Lecture topics included:
1. the ecological structuring role of plants in shallow lakes,
2. determining restoration targets using plant remains,
3. production, dispersal and preservation of plant remains.
Practical exercises focused on techniques for sampling, extracting
and identifying plant macrofossils. Where possible, participants studied
their own material. Alternately, they examined core material from a
wetland on the lower River Murray. They also compared the representation
of plant remains in a variety of modern sediment samples to plant abundance
recorded at the time of collection.
Outcomes:
Apart from broadening the knowledge of a number of early career researchers,
the following were important workshop outcomes:
- Discussions held during the course have, in part, facilitated a
joint application from the University of Adelaide, EPA Victoria and
Monash University to Land and Water Australia's 2007 Innovation Call.
If successful, the techniques demonstrated in the course will be used
to understand the (past) response of aquatic plants in Western Victoria
to drought.
- The course allowed several early career researchers to highlight
their work and gain critical feedback from the leaders and other participants.
- Tara Lewis (PhD candidate and ECR Monash) demonstrated her excellent
plant macrofossil database. Resultant discussions focused on the ways
in which others might utilise this database, hence reducing duplication
of effort.
- Reporting of the workshop in the Australian Society for Limnology
newsletter and Quaternary Australasia, will further broaden exposure
to these relatively new approaches.
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