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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 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.
CI(s)/Institution: CI(s)/Institution: Kate Muirhead, University of Adelaide, School of Earth & Environmental Sciences ($3,500)

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:

  1. 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.
  2. 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.
  3. 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.
  4. Learning about programs used in molecular systematics and molecular clock analysis, such as SplitsTree and Rates.
  5. Jim provided samples from his collection that will be useful for her PhD

2. Project title: Multidisciplinary training workshop for the integration of biodiversity modeling, environmental data, phylogenetic diversity, and carbon accounting
CI(s)/Institution: CI(s)/Institution: Susan Cameron and Rob Waterworth, ($15,000)

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 :
  • Linking biodiversity priority setting with analysis of environmental change
  • Phylogenetic analyses at multiple scales
  • 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
CI(s)/Institution: Daniel Warner, University of Sydney ($1,500)

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.


4. Project title: The origin and future of the Cophixalus frog diversity of Australia's Wet Tropics rainforest
CI(s)/Institution: Conrad Hoskin, University of Queensland ($3,500)

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
CI(s)/Institution: Nick Murphy, University of Adelaide, School of Earth & Environmental Sciences (3,500)

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:
  • An exhaustive search of fossil literature for the dating of microgastroid nodes. This will vastly increase the nodes for which dates are available.
  • 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.
  • 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.
  • 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
  • Numerous roundtable and informal discussions with Profs Whitfield and Cameron, and their students, on the current state of hymenopteran molecular systematics and analytical methods.
  • 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.

6. Project title: Sex Allocation in Reptiles: Ecology, Evolution, and Conservation
CI(s)/Institution: Tobias Uller, University of Woolongong (3,600)

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:
  • Reptilian model systems provide an excellent opportunity to test current theoretical models in a way that is not possible in most other vertebrate systems
  • Recent studies in reptilian sex allocation has provided novel insights into the processes and mechanisms of sex determination and sex allocation
  • Integration of proximate mechanisms of sex determination and sex allocation will transform the field, both theoretically and empirically
  • Recent results on lizards suggest that our current understanding of the evolution of sex determination must be revised
  • 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
CI(s)/Institution: John Tibby & Jennie Fluin, University of Adelaide ($9,863)

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:

  1. 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.
  2. The course allowed several early career researchers to highlight their work and gain critical feedback from the leaders and other participants.
  3. 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.
  4. 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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