Field of Study
Organisms	Genetics	Systematics	Ecology	Behaviour	Physiology
Bacteria	Gordon		Gordon
Fungi	Burdon (CSIRO)		Burdon (CSIRO) Ash
Plants	Foley Peakall Young (CSIRO)	Crisp West (CSIRO) Bayer (CSIRO)	Ash Nicotra Cunningham (CSIRO) Groves (CSIRO)		Nicotra
Invertebrates	Rowell Trueman Clarke (CSIRO)	Trueman Rowell Yeates (CSIRO)	Sheppard (CSIRO) Cunningham (CSIRO) Clarke (CSIRO)	Backwell Zeil (RSBS) Cooper	Cooper Wallis
Fishes			Fulton	Fulton
Reptiles & Amphibians		Keogh		Keogh Cooper	Cooper
Birds	Double		Cockburn	Cockburn Magrath
Mammals	Peakall		Foley Wallis	Cockburn	Foley
Humans	Easteal
Phylogenetics methods		Trueman Crisp

Out of the darkness:
Predicting rates of respiration of illuminated leaves

Supervisors: Dr Owen Atkin (RSBS), Adrienne Nicotra (BoZo)

Estimates of leaf respiration (R) profoundly influence our understanding of ecosystem and Earth system functioning, and yet we lack basic information on key determinants of this process. For example, although we know that light inhibits leaf R by up to 80% and that failure to account for light inhibition of leaf R can lead to large over-estimates of daily ecosystem respiration, we lack sufficient experimental data to predict intra- and inter-specific variation in the degree of light inhibition of R. This project will establish whether the degree of light inhibition of leaf R differs systematically among plant species adapted to contrasting habitats, and the quantitative importance of light inhibition of R for leaf-level daily net carbon gain.  The project will provide an opportunity for a student to investigate a question of high ecologically significance relevant to global carbon circulation models.  It will enable the student to become familiar with methods such as CO2 exchange, as well as relating physiological variables with environmental parameters. This project will be conducted in collaboration with Dr Patrick Meir (Univ. Edinburgh, UK), Dr Kevin Griffin (Columbia Univ., USA), Prof Matthew Turnbull (Univ. Canterbury, New Zealand) and Prof Jon Lloyd (Univ. Leeds).

Background required: Ideally, students should have completed Biol2121 - Plants: Genes to environment and be planning on taking Biol3125 - Plants and global climate change

---

How does phosphorus deficiency influence respiratory rates in plant species adapted to contrasting habitats?

Supervisors: Dr Owen Atkin (RSBS), Adrienne Nicotra (BoZo)

Nitrogen (N) and phosphorus (P) are the two most important nutrients affecting plant metabolic capacity. Plant tissue nitrogen concentration ([N]) has been shown to scale with R in both leaves and roots, and this knowledge has been used to parameterize large scale models predicting future rates of CO2 exchange between vegetation and the atmosphere. In contrast, much less is known about the extent to which tissue phosphorus concentration ([P]) influences R in natural environments, or whether the relative abundances of P and N are important in determining R in leaves and roots. In addition, the impact of P deficiency on the temperature response of plant R is unknown, even though it is widely recognized that quantification of the response by R to warming needs to be improved. Phosphorus supply is thought to be limiting in approximately 30% of terrestrial ecosystems; and because of this, together with likely future global shortages of phosphorus and global climatic change over the 21st century, there is an urgent need to quantify how [P] influences plant R. Accordingly, this PhD project will use lab-and field-based experiments to: (1) quantify the influence of P limitation on scaling relationships linking R to [N] in plant species representative of contrasting environments; and, (2) establish how P limitation impacts on the dynamic response of respiration to short- and long-term temperature changes. This project will be conducted in collaboration with Dr Patrick Meir (University of Edinburgh, UK), Prof Matthew Turnbull (University of Canterbury, NZ) and Prof Jon Lloyd (University of Leeds).

Background required: Ideally, students should have completed Biol2121 - Plants: Genes to environment and be planning on taking Biol3125 - Plants and global climate change

---

How long does a plant need experience shade for new leaves to exhibit a shade phenotype?

Supervisors: Dr Owen Atkin (RSBS), Adrienne Nicotra (BoZo)

When grown under low light conditions, many plant species acclimate via dynamic changes in biomass allocation (e.g. via making thinner, broader leaves) and physiology (e.g. increased allocation of nitrogen to pigments that intercept light and reduced investment in Rubisco; reduced rates of respiration). Such changes enable leaves to maximize the rate of photosynthetic carbon uptake and thus maintain growth rates in the shade. In recent years, several studies have also demonstrated that developing leaves cannot sense light directly; rather, they rely on signals from mature leaves. What is not known, however, is how long mature leaves need to be exposed to shade for developing leaves to possess a shade phenotype. We will use combine gas exchange and anatomical studies under controlled conditions to tackle this question.

Background required: Ideally, students should have completed Biol2121 - Plants: Genes to environment and be planning on taking Biol3125 - Plants and global climate change

The projects listed below involve fieldwork in the Northern Territory. Since fiddler crabs are seasonal breeders (October - April), mid-year enrolment is necessary.

Fieldwork will be conducted at Ludmilla Creek in Darwin. During the period of fieldwork, honours students will be based at the Northern Australia Research Unit (NARU) in Darwin.

---

Rare male advantage in Uca vomeris.

In many sports, like boxing and tennis, left-handed competitors have an advantage because they are rare. All contestants (left and right handed) have plenty of experience in facing right-handed opponents, but only left-handers are on familiar ground when the fight is between opposite-handed males. In these fights, the right-hander is faced with an unfamiliar opponent with a slightly different style, giving them an advantage.

In most fiddler crab species, males can have their enlarged claw on the left or the right side, and usually it is 50:50 in the population. In a couple of species, however, males are predominantly right handed, with as few as 1% of the population being left handed. Uca vomeris is one such species. This project looks at whether the left handed males are at a fighting advantage and whether this also translates into a mating advantage.

Fiddler crabs are season breeders, so mid-year enrolment is essential. Fieldwork is conducted in the Northern Territory (September – Christmas) when the entire crab lab moves up to the ANU’s research station in Darwin.

Background required: BIOL3131.

This project would involve:

• Observational work: to determine the proportion of left and right handers and to document the two types of fights.
• Manipulations: catching and releasing left and right handers to see how long it takes for them to get a new burrow, how many fights they have on the way, and what the fights are like.
• Experimental work: pitting left and right-handers against each other in some kind of caged experimental set up.

It may also be possible to look at whether the fighting advantage that left handed males have (if it exists) translates into a mating advantage, possibly because left handed males are able to secure better burrows.

---

Male mate choice in Uca mjoebergi.

In most species, females do not mate indiscriminately, but prefer some males to others. The process of female mate selection, its causes and its consequences have been the subject of heated debate for many years. Less studied, however, are male mate choice and mutual mate choice. In burrow mating fiddler crabs it is generally accepted that females select the males with which they mate. It is unknown whether males are also selective in the females they will accept as mates. Female clutch size increases with female body size in most fiddlers, giving males an advantage if they mate with larger females.

Do males put more effort into courting larger females than smaller ones? (e.g. Do they give more waves or have a faster wave rate? Are they more persistent? Do they move further away from their burrows to court larger females? Are they more likely to reject smaller females?).

In some species, the size of mate-searching females decreases over the duration of the breeding cycle (i.e. larger females mate earlier than smaller females).

Is this true in Uca mjoebergi? Do they also, therefore, release their eggs earlier than smaller females?

Do males wave more vigorously earlier in the breeding cycle (because that's when the larger females are there)? Is there size assortative mating?

Effect of population size on substitution rate

Patterns of both molecular and morphological evolution are likely to be very different in small populations than in large populations. But although the effect of population size on patterns of molecular evolution is a key component of theoretical models, it has been subject to relatively few robust empirical tests. Finding out the nature and the extent of the effect of population size on rates and patterns of molecular evolution is essential not only for the development of molecular evolutionary theory, but also for the increasing application of molecular data in conservation biology and population ecology. This project would involve identifying lineages with consistently low population size (e.g. inbred, geographically restricted or endangered populations) and comparing the rate of genome evolution to related lineages with large population sizes. For more detail on this and other projects please contact the supervisor.

Background required: You should have completed Advanced Genetics or Bioinformatics, or show other evidence of understanding basic principles of DNA sequence analysis. If you are interested in this topic but not sure if your background is appropriate, please feel free to discuss this with me.

---

Does selection balance metabolism, mutation and longevity

There is a great deal of interest in the relationship between metabolism, mutation and life history (particularly longevity). It has been suggested that metabolism is the ultimate driver in evolution because it produces free-oxygen radicals that can damage DNA, limiting the ability of organisms with a high metabolic rate to maintain a body over a long life span. Furthermore, it has recently been suggested that metabolic rate can be used to “calibrate” the rate of molecular evolution in different species. But do organisms that have a lower metabolic expenditure show less sign of DNA damage? One way of answering this question would be to compare rates of molecular evolution in specie that differ in metabolism, or longevity, but are otherwise similar in other aspects of their biology. For more detail on this and other projects please contact the supervisor.

Background required: You should have completed Advanced Genetics or Bioinformatics, or show other evidence of understanding basic principles of DNA sequence analysis. If you are interested in this topic but not sure if your background is appropriate, please feel free to discuss this with me.

---

Replication fidelity and evolution:
copy effects on rate of genome evolution

Although it was once assumed that the rate of molecular evolution would be roughly the same in all related species, it has now become clear that species can differ significantly in the rate at which their genomes evolve. One of the most consistent patterns in tempo and mode of molecular evolution is the generation time effect in vertebrates. The generation time effect assumes that species with shorter generation turnover times will undergo more DNA replications per unit time, and will therefore accumulate more replication errors. While evidence of this effect has been found in mammals, birds, reptiles and fish and invertebrates, relatively little research effort has been directed towards patterns of molecular evolution in plants. This project would involve collating data on lifehistory in plant species and combining this with molecular phylogenetic analysis of DNA sequences to reveal the causes of molecular evolution in plants. For more detail on this and other projects please contact the supervisor.

Background required: You should have completed Advanced Genetics or Bioinformatics, or show other evidence of understanding basic principles of DNA sequence analysis. If you are interested in this topic but not sure if your background is appropriate, please feel free to discuss this with me.

---

Salt-tolerance in plants: a case study in the repeatability and predictability of the evolution of complex traits

Salinity is an ever-increasing problem in agriculture. But despite decades of research, few salt tolerant crop species have been produced. Limited success in breeding salt tolerance is surprising given that resistance mechanisms have evolved in many different plant families. There are more than 1500 different naturally halophytic (salt tolerant) species which employ a variety of different mechanisms for salt resistance. The wide variety of salt tolerant species, and the occurrence of different mechanism, suggest that salt-tolerance has evolved multiple times, in many different ways. This is the paradox of halophyty: there are many mechanisms used and it seems to have evolved many times – if it is so frequently selected for in natural system, then why can we not select for salt tolerance in our crop plants? This project will expand a unique database of all known halophytic angiosperms to include DNA sequence data from Genbank as well as information on salt tolerance mechanisms from the literature for these species and their closest relatives in order to establish whether salt tolerance has, as it appears, evolved more than once, and allowing the number of independent evolutionary origins of salt tolerance to be determined for the first time. For more detail on this and other projects please contact the supervisor.

Background required: You should have completed Advanced Genetics or Bioinformatics, or show other evidence of understanding basic principles of DNA sequence analysis. If you are interested in this topic but not sure if your background is appropriate, please feel free to discuss this with me.

---

Are older species more vulnerable to extinction?

Two recent studies have suggested that older species are more vulnerable to extinction. If these relationships hold more generally, then it might suggest an important cause of extinction risk, and therefore might influence conservation planning. We can test this idea using phylogenetic analysis of lineages that differ in their vulnerability to extinction. We can also investigate why older species should be more vulnerable to extinction using molecular phylogenetic analysis. For more detail on this and other projects please contact the supervisor.

Background required: You should have completed Advanced Genetics or Bioinformatics, or show other evidence of understanding basic principles of DNA sequence analysis. If you are interested in this topic but not sure if your background is appropriate, please feel free to discuss this with me.

---

Molecular Fossils, Purple Oceans and Molecular Dating

Supervisors: Lindell Bromham (BoZo), Jochen Brocks (RSES)

Life in the Precambrian, the time before 542 million years ago, was dominated by bacteria and archaea, organisms that rarely leave diagnostic cellular remains in the fossil record. However, hydrocarbon biomarkers, the molecular fossils of natural products such as lipids and pigments, can yield a wealth of infor­mation about Precambrian ecosystems. Many biomarkers are diagnostic for specific microbial groups such as methanogens, methano­trophs or photo­trophic bacteria and may give infor­mation about ancient biodiversity. A particular biomarker, okenane, discovered in 1.6 billion years old rocks in northern Australia indicates the presence of purple sulfur bacteria (Chromatiaceae) and adds weight to the hypothesis that the oceans may have been vastly anoxic and sulfidic during the mid-Proterozoic (~1.8 to 0.8 billion years ago). However, what were the purple sulfur bacteria like that inhabited this ocean so long ago? In this project, you will use bioinformatic databases to investigate the distribution of the gene that creates the pigment that forms okenane, and use molecular phylogenetic analysis to investigate the origins of the purple sulfur bacteria, in order to reconstruct the ancestral state of ancient purple sulfur bacteria to gain insight into the environment and ecology of the billion-year-old ecosystem.

Background required: BIOL3156 or BIOL3157 would be helpful, as would any experience with analyzing DNA sequences. However, we are happy to discuss the project with students with different backgrounds.

Phylogenetic community ecology

Does phylogenetic relatedness predict which species coexist within communities? Is the structure of species assemblages influenced by phylogeny? In this project, these questions will be tested by compiling databases from published or unpublished ecological surveys and applying computer simulations to test alternative models. The taxon could be mammals, birds, reptiles, plants, or anything for which sufficient data exist. This primarily computer-based project combines phylogenetics with trait evolution and community ecology.

Background required: No strict prerequisites, but a predilection for computers is desirable. Some ability to program would be an advantage, but you will learn the basics of R programming along the way.

---

Modelling extinction risk in mammals

A quarter of mammal species are threatened with extinction: why do some species become threatened while others remain safe? This project will explore this question by using comparative modeling methods to test which aspects of a species’ life history, ecology, or geography predict its ranking on the IUCN Red List. This will involve an initial phase of data collection from the literature, followed by the application of statistical models. There may also be some GIS work involved. The particular geographic region and subset of mammals to focus on will depend on available data.

Background required: No strict prerequisites, but a predilection for computers and a basic familiarity with statistics would be an advantage. A keenness to learn basic programming skills (using the R language) is important.

Honours projects available in locust physiology

The Australian plague locust (Chortoicetes terminifera) is a serious threat to Australian agriculture whenever the appropriate environmental conditions allow for a rapid increase in the population. Various projects are undertaken each year to understand different aspects of the biology of these animals. An Honours student project is available to study either reproduction or fat regulation in the Australian plague locust, to aid in our understanding of the capacity of these animals to build-up numbers so rapidly. The work will involve both whole animal dissections and histological examination. In addition, straight-forward biochemical assays will be used for determining the fat content/reproductive condition in both laboratory and wild-caught specimens. The supervisors will be Paul Cooper of the School of Biology and James Woodman of the Australian Plague Locust Commission (http://www.daff.gov.au/animal-plant-health/locusts). To express your interest or for more information please find our contact details below.

Dr. Paul Cooper - Paul.Cooper@anu.edu.au - (02) 61253069
Dr. James Woodman - James.Woodman@daff.gov.au - (02) 62725075

Geographic variation in common Aotus

Supervisors: Mike Crisp and Lyn Cook

Aotus ericoides is a pea-flowered shrub (family Fabaceae) that is common in heathy communities along the east coast of Australia. It is found all the way from southern Queensland to Tasmania.

It grows in various habitats, eg forest, heathlands and even seasonal swamps, and in these different places, the plant has a different appearance. The problem is whether this just reflects adaptation to a local environment in an otherwise continuously interbreeding, single species, or whether there is really more than one species with subtle ecological and morphological differences between them.

The project would involve sampling of populations in the field, analysis of morphology of specimens, and possibly analysis of DNA samples too. It could also also involve a consideration and testing of species concepts.

---

Templetonia - Speciation and adaptation in the mallee

The dryland mallee communities of southern Australia present some interesting problems in speciation and biogeography. A number of species-groups are widespread in mallee from south-western Australia to south-eastern Australia. Some of these show evidence of cryptic species that are genetically very distinct despite being morphologically near-identical and sympatric (occuring together).

Studying the relationships of such species-groups using molecular and genetic methods may reveal patterns of speciation in the mallee that are common to many taxa. These patterns may reflect a common history of environmental change that drives speciation, such as aridification and the restriction of dispersal across the Nullarbor Plain. This project concerns the pea-flowered shrubs Templetonia sulcata and T.smithiana, which are partially sympatric, putative cryptic species.

Questions that could be addressed include:

• Are T.sulcata and its apparent sibling species, T.smithiana, genetically distinct from one another?
• How often have leaves been evolutionarily lost? ie. Do the Templetonia species with flattened photosynthetic branchlets belong to a single clade?
• Is there an ecological correlate of leaf loss?

 

Adaptive locomotor morphology and behaviour in coral reef fish

Swimming is a pivotal trait in the evolution and ecology of fishes, given that it can determine how well an individual can find food, mate successfully, and avoid predation. Recent research has shown that variations in swimming morphology and performance can help unravel why coral reef fish display such a huge diversity of ecological patterns of resource use. In this project you will examine whether fish can employ adaptive changes to their swimming morphology, behaviour and/or performance to cope with short-term changes in their environment over space and time. You will learn new techniques in functional morphology, physiology, behavioural ecology and oceanography. The catch is that you need a high level of SCUBA diving qualifications (SSI Rescue or higher) to meet the OH&S requirements of work diving on the Great Barrier Reef.

This project has a February start to align with seasonal fieldwork on the Great Barrier Reef.

Dr. Chris Fulton - christopher.fulton@anu.edu.au

---

Finding the truth behind false negatives: trout predation on native fish larvae

Studies of fish predation are often plagued with the problem of false negatives - observational studies failing to detect fish prey items in a predator's diet. The underlying problem is that fish is often the most rapidly digested prey item (relative to plant material and hard-shelled invertebrates), leading to a disproportionately low frequency of fish prey in studies of predator gut contents. These false negatives have serious consequences for our understanding of aquatic trophic interactions, and in assessing the potential predation pressure imposed by invasive fish on native species. This project you will use direct observations to explore rates of larval fish consumption by invasive trout species. Combined with measurements of digestive physiology, you will provide the first estimates of the full predation pressure exerted by trout in the wild, and highlight how false negatives can be avoided in future field-based observational studies of fish predation.

This project could commence in either February or July.

Dr. Chris Fulton - christopher.fulton@anu.edu.au
Dr. Brendan Ebner - b.ebner@griffith.edu.au
A/Prof. Mark Lintermans - mark.lintermans@canberra.edu.au

---

Radio-tracking freshwater fish: are tags a drag?

Remote radio telemetry is one of the principal techniques used to assess the behavioural ecology of fish. However, we do not know what effect the radio tag may have on the swimming activities of a fish. Are radio tagging results a realistic measure of what fish naturally do in their everyday activities? In this project you will use field and lab-based techniques to determine how anaesthesia, surgery and tag attachment affect the swimming behaviour and performance of freshwater fish. Applying this information to past studies of radio telemetry, you will assess how relevant short-term radio tracking data may be to the activities of untagged fish.

July - to match seasonal activity and availability of the target species.

Dr. Chris Fulton - christopher.fulton@anu.edu.au
Dr. Brendan Ebner - b.ebner@griffith.edu.au

 

 

---

Host social structure and the clonal composition of bacterial populations.

The transmission dynamics of most bacteria is poorly understood. This is even true of well-studied bacterial species such as Escherichia coli inhabiting humans. The Gidgee skink, Egernia stokesii , is a semi-arid species that inhabits rocky outcrops and lives in family groups. Family groups may consist of up to 16 individuals and multiple family groups can occupy the same rock outcrop. Family members defecate at a common location and these scat piles are thought to be used to mark territories.

The goal of this study is to determine if strains of bacteria are more likely to be shared among individuals belonging to the same family group as compared to individuals belonging to different family groups inhabiting the same outcrop or different outcrops.

The research will involve about 4 weeks of fieldwork in South Australia in September. The project will provide the student with experience in the capture and sampling of lizards. Experience with a variety of basic microbiological techniques and molecular techniques for the genetic fingerprinting of bacteria will also be gained. No previous experience with micro-organisms or lizards is required. This project is only suitable for a July start. For more details contact David Gordon (David.Gordon@anu.edu.au).

---

Lactose negative Escherichia coli

The ability to exploit lactose as a growth substrate is a hallmark of the bacterium E. coli and the molecular biology and biochemistry of lactose use in E. coli is thoroughly understood. The lactose operon is normally repressed in the absence of lactose and expression is controlled by the gene lacI. The operon consists of the three genes: lacY, lacZ and lacA, although lacA is not essential for lactose utilisation. Despite being a classic trait, it is one that has been repeatedly lost during the evolution of the genus, for example, among several pathogenic lineages of E. coli collectively known as Shigella. Lactose use has also been lost in strains not known to cause disease and preliminary evidence suggests that the loss may be linked to the ecological niche of the strain. The loss of lacA is also not uncommon.

The proposed research has several aims. To examine the phylogenetic distribution of lactose negative, as well as lacA negative, strains in E. coli. Determine what genetic changes are responsible for the loss of the trait. Determine if the lactose operon is normally repressed in wild type E. coli. Determine if the kinetics of lactose utilisation varies with the phylo-group membership of the strain. The project will exploit a large collection of wild E. coli that have been extensively genetically characterised.

The research will provide the student with experience in a variety of basic microbiological techniques and with enzyme assays and enzyme kinetics. Familiarity with a variety of molecular techniques will be gained, including primer design, PCR-screening and DNA sequencing. Data analysis will involve a variety of phylogenetic and statistical methods.   No previous experience with micro-organisms is required. This project is suitable for a February or July start. For more details contact David Gordon (David.Gordon@anu.edu.au).

---

Microbiota of the Sleepy Lizard, Tiliqua rugosa

As an adult the sleepy lizard is largely herbivorous. No vertebrate is capable of digesting fibres such as cellulose, the main component of plant material. Energy provided through the digestion of plant material results from the actions of microorganisms living in the gastro-intestinal tract of the host. Most vertebrates have modified the morphology of their gastro-intestinal into order to provide a chamber in which the microoganims can carry out fermentation. Unlike the majority of herbivorous vertebrates the sleepy lizard gut possesses no such modifications. Recent studies have characterised the microbial communities of herbivores such as termites and ruminants and the microbial comminties of these groups are very different. However, the microbiota of herbivorous lizards has not been characterised.

The goal of the prosed study is to characterise the microbial community biomass and composition in the sleepy lizard and in a similar-sized carnivorous skink, the blue tongue.

The research will involve about 4 weeks of fieldwork in South Australia in September. The project will provide the student with experience in the capture and sampling of lizards. The student will gain experience in a variety of basic microbiological techniques and become familiar with microbial community fingerprinting techniques, cloning and nucleotide sequencing. Data analysis will involve a variety of recently developed methods for the comparison on microbial communities. No previous experience with micro-organisms is required. This project is only suitable for a July start. For more details contact David Gordon (David.Gordon@anu.edu.au).

---

Biofilm formation in Escherichia coli

The ability of bacterial cells to associate and form complex structures on surfaces is though to enhance their ability to cause disease and persist in the external environment. Biofilm formation protects cells from the host's immune defences, adverse environmental conditions and antibiotics. The physical characteristics of the substrate, temperature and growth media are a few of the many factors known to influence the extent to which a particular strain forms a biofilm. However less is known concerning the degree to which the phylogenetic origin of the strain or the particular genetic makeup of the strain influences both it's ability to form a biofilm and how it responds to different temperatures and growth media.  

The proposed research will focus on the role of iron limitation in biofilm formation and will determine the phylogenetic and gene content factors, particularly those related to iron-acquisition, that explain the extent of biofilm formation in iron-limited and iron-rich media. The project will exploit a large collection of wild E. coli that have been extensively genetically characterised.

The research will provide the student with experience in a variety of basic microbiological techniques and molecular techniques such a PCR screening. Data analysis will involve a variety of phylogenetic and statistical methods. No previous experience with micro-organisms is required. This project could commence in February or July. For more details contact David Gordon (David.Gordon@anu.edu.au).

Rates of molecular evolution in birds

The molecular clock hypothesis, which was proposed in the early 1960s, states that the rate of molecular evolution is constant among organisms. Although it is now widely known that evolutionary rates show significant variation, the patterns of variation have not been characterised in detail.

Over the past year, large amounts of DNA sequence data from the mitochondrial and nuclear genomes has been produced from birds. In addition, at least 90 calibration points, which are needed to estimate rates of molecular evolution, have recently been published for birds. The release of this information provides an excellent opportunity for characterising the patterns of rate variation within a well-defined group of animals. Some particularly interesting questions include:

• Is there a universal molecular clock for birds?
• Do mitochondrial and nuclear genomes show similar patterns of rates?
• To what extent does natural selection affect the patterns of rate variation in coding genes compared with non-coding DNA?

This project can commence in February.

---

Reconstructing populations using ancient DNA

Ancient DNA provides an unparalleled opportunity to look at past populations of animals and plants. Using the latest analytical methods, it is possible to reconstruct the demographic history of extant and extinct species, given sufficient amounts of ancient DNA sequences.

Some ancient DNA data sets have yielded detailed pictures of population history. For example, the analysis of ancient DNA from over 200 North American bison has revealed that the population began to decline at the height of the last glacial cycle, but then suffered a second crash when humans arrived in the Americas. In contrast, analysis of 99 ancient DNA sequences from bowhead whales failed to provide any indication of the impact of sustained whaling over the past few centuries.

This project will investigate the conditions in which ancient DNA will be able to provide informative insights into the demographic history of Pleistocene fauna. In particular, the student will investigate the effects of ancient DNA degradation, sequence variability, population structure, and sampling biases. The work will focus on several organisms of special interest, including bison, brown bears, woolly mammoths, cows, penguins, and horses.

This project can commence in February.

The effect of maternal size and body condition on offspring sex ratios in the mosquitofish Gambusia holbrooki

This project will test whether females adjust their offspring sex ratio in relation to their size and body condition and, if possible, time in the annual breeding season. Gambusia is a prolific, livebearing fish that is a major pest in Australian waterways. The project will involve field collection of fish, and the rearing of offspring in captivity. No special skills are required, other than the ability to think creativity. If possible, the work will also involve experimental manipulation of diet. Sex ratio theory is one of the most interesting areas of behavioral ecology and you will be able to generate some clear predictions that you can test. This project has a major advantage compared to studies of other vertebrates in that it will produce large sample sizes. This is essential for any meaningful test of sex ratio theory. This will allow you to focus on asking a range of question relating offspring sex to brood size, female size and the effect of body size on female fecundity and male mating success.

This project can commence in February 2009.

Background required: Evolutionary and Behavioural Ecology (BIOL3131).

Visual adaptations for foraging in different temporal niches in ants

Supervisors: Dr Heloise Gibb, CSIRO Entomology; Dr Ajay Narendra, Visual Sciences, RSBS, ANU; Dr Paul Cooper, BoZo, ANU

Ants partition their niches temporally, i.e. they restrict their activity to certain times of the day, to avoid threats such as competition or predation, or to exploit specific resources.

In this project, the student will investigate how ant visual systems have adapted to function in different temporal niches in sugar ants, Camponotus. The student will monitor activity patterns of a number of sugar ant species and determine the degree of temporal niche overlap between the different species.

We will then compare the eyes of different species of sugar ants by preparing eye replicas to identify facet size and distribution, and section the eyes to determine the size of the rhabdom. In addition, we will examine the variation in eye structure between different castes, including workers and male and female reproductives (see fig 1), and determine how this relates to their behaviours. The student will receive training in field ecology and in the analysis of eye morphology.

Since ants are most active in the summer months (Nov-Mar), mid year enrolment is necessary. Field work will be carried out at either Black Mountain or the ANU campus and assistants will be available to help with the night-time component of the field work.

Figure 1. Male (left) and female worker (right) of Camponotus consobrinus. Externally, the eyes of the male appear to be bulbous and larger than those of the female worker, but the differences in their eye structure and how it relates to their behaviours is an unexplored topic.

These are examples of the sorts of projects available in my lab. Specific projects will be tailored to student's interests and background.

---

Reproductive ecology of the dioecious shrub Gynatrix pulchella

In some plant species male and female reproductive structures are held on separate individuals rather than on a single plant and within a single flower. This condition is called dioecy. Amongst dioecious species, individuals with male flowers generally allocate fewer resources to reproduction than do individuals with female flowers. This is because the female individuals produce not only flowers but also fruits.

Gynatrix pulchella is an unusual dioecious, wet schlerophyll shrub in which we found that males allocate more resources to reproduction than do females. This initial finding provides basis for further honours research.

For example, we are interested in whether this pattern is found in other populations of G. pulchella growing under a range of conditions and amongst individuals of a wide age range. We are also interested in the impact of this unusual pattern of reproductive allocation on patterns of growth and photosynthetic physiology in males and females. Finally, we don't know what pollinates G. pulchella but pollinator activity is also likely to impact on the reproductive allocation we measure.

---

Plasticity in response to resource availability in the dioecious shrub Dodonaea viscosa

Plants show dramatic and varied responses to resource availability - this variation is called plasticity. In a small proportion of plant species male and female reproductive structures are held of separate individuals rather than on a single plant and within a single flower. This condition is called dioecy. Amongst dioecious species, individuals with male flowers generally allocate fewer resources to reproduction than do individuals with female flowers. This is because the female individuals produce not only flowers but also fruits.

Because they have different patterns of reproductive allocation, the sexes of dioecious species may also have different extents of plasticity in response to resource availability. Dodonaea viscosa is a local dioecious shrub in which females appear to have much higher reproductive allocation than males. We are interested in whether the sexes also show differences in plasticity of response to environmental conditions. This question could be addressed using a combination of glasshouse and field approaches.

---

Variation in leaf shape in Australian Pelargonium species and its effect on photosynthetic physiology

In the genus Pelargonium leaf size and shape are variable both within and among species. This large genus, containing the horticultural geranium, also contains 8 Australian native species. Within species, leaf shape and size depend on growth conditions, including light, temperature and water levels. The size and shape of a leaf influence the thermal properties of the leaf itself, and are therefore likely to have impacts on the photosynthetic physiology of the leaf.

Projects on this system will examine thermal properties of leaves and leaf carbon gain and water relations. New technologies for imaging temperature and photosynthetic traits over the surface of the leaf will be applied.

Orchids are renowned for their diversity of pollination systems. Among the most intriguing is pollination by sexual deception. This predominantly Australian pollination strategy involves the attraction of male pollinators by sex pheromones (e.g. Peakall 1990, Peakall et al. 1997, Peakall et al. 2002). These unique and specialized systems are ideal for exploring a range of evolutionary questions.

My research team is now midway through an exciting 5 year ARC funded research project on Symatric Speciation in Sexually Deceptive Australian Orchids. This is a multidisciplinary project involving the fields of plant reproductive biology, insect ecology, molecular ecology, phylogenetics and chemical ecology.

An important breakthrough for Australian sexually deceptive orchids has been the identification of the compound involved in the chemical mimicry employed by the orchid Chiloglottis trapeziformis. Schiestl et al. (2003) showed that C. trapeziformis mimics a novel single active compound named 'chiloglottone', that comprises the sex pheromone of its pollinator, the thynnine wasp Neozeleboria cryptoides. We have now extended our study of the chemical mimicry to additional Chiloglottis orchid species and their specific male pollinators (Peakall et al. in review). In parallel with the chemical ecology investigations we have also developed a set of informative nuclear DNA microsatellite genetic markers for these orchids (Flanagan et al. 2006) as well as a set of hypervariable chloroplast DNA markers (Ebert et al. in prep). In the field we have established study sites spanning from Tasmania to North New South Wales.

Our substantial progress has opened up a range of exciting opportunities for Honours, PhD and postdoctoral research. All projects offer a mix of laboratory and field work. Some of the possible projects are listed below.

The Peakall Lab, and School of Botany and Zoology at ANU offer superb facilities including a fully equipped molecular laboratory with an in-house ABI Capillary 3100 DNA sequencer, a GC-MS laboratory for chemical ecology and a fleet of 4WD vehicles.

Interested, enthusiastic and highly motivated young scientists are invited to contact Rod Peakall to discuss the possibilities.

---

A Molecular Identification System for Orchid Pollinators

This project would seek to develop molecular methods for rapid identification of orchid pollinators. Presently, the identification of orchid pollinators is hampered by the limited availability of taxonomic specialists and also the discovery of morphologically indistinguishable cryptic species.

A strong background in entomology and molecular ecology is desirable for this project.

---

The Ecology and Population Genetics of Orchid Pollinators

This project would begin the first investigation of the ecology and population genetics of thynnine wasp orchid pollinators. Thynnine wasps are the predominant pollinator of sexually deceptive Australian orchids and represent a large and diverse group of Australasian wasps. No project of this kind has ever been attempted and there is limited knowledge concerning the biology of thynnine wasps in general.

A strong background in entomology and molecular ecology is desirable for this project.

---

Pollen and Gene flow in Sexually Deceptive Orchids

This project would combine field experiments, new DNA based genetic markers and novel statistical approaches. Until now an understanding of gene flow in orchids has been hampered by the unique features of orchid biology.

A strong background in ecology and population genetics is desirable for this project.

Dinosaur extinction and the adaptive radiation of birds and mammals

The fossil record has traditionally been interpreted to support a sudden extinction of dinosaurs and pterosaurs 65 million years ago, coincident with a meteor/comet impact and subsequent rapid evolution of mammals and birds to fill the vacated ecological space. Recent evidence suggests that the extinction of smaller dinosaurs and pterosaurs began many millions of years earlier, and that the origins of many modern mammal and bird groups are also older than previously thought. This project will combine fossil and DNA sequence information to trace the evolution of mammal and bird ecological types (e.g. terrestrial carnivores, arboreal omnivores). The results will allow a number of hypotheses to be tested that concern the interaction of mammals and birds with dinosaurs and pterosaurs.

Background required: A basic understanding of ecology and evolutionary biology. Computer programming skills may be useful, but are not necessary.

---

DNA timescale for the divergence of Australian and New Guinean marsupials

New Guinea and Australia share some marsupial species, such as the rufous spiny bandicoot. Other elements of the New Guinean marsupial fauna (e.g. forest wallabies) are only very distantly related to their closest Australian relatives. This project will gather DNA sequences from a number of closest-relative-pairs of Australian-New Guinean marsupials and use molecular clock methods to infer how long ago the pairs last shared common ancestry. Dates of last common ancestry provide bounds on the timing of dispersal events between Australia and New Guinea. A major question will be whether such bounds cluster around dispersal windows predicted from geotectonic and sea-level data. Moreover, the data will be used to identify differences in evolutionary patterns between Australian and New Guinean marsupial faunas.

Background required: DNA lab skills are desirable, but not necessary.

Comparative phylogeography of log-dwelling invertebrates

Drs Dave Rowell and Paul Sunnucks (LaTrobe) are involved in a major forest conservation genetics and comparative phylogeography project at Tallaganda State Forest, NSW. Specifically, we are looking at organisms that live in decomposing logs on the forest floor. This is a very important habitat and provides food and shelter for a number of invertebrate and vertebrate species.

The major purpose of this study is to establish whether the genetic structure of a selected group of invertebrate taxa is determined by historical factors, limited dispersal or local adaptation. The groups we are targetting include onychophorans (several species), funnelwebs (2 species), terrestrial flatworms and collembolans.

We are using DNA sequence variation and microsatellites to quantify levels of diversity and population structure. There is the opportunity for an honours student to choose one or two of these species to study as a stand-alone project, which could also be incorporated into the overall project.

Inter-individual variation in global gene expression

The genome sequencing projects have resulted in an unprecedented leap in our understanding of the nature, scope and, increasingly, the phenotypic impact of genetic information. An inherent part of this advance has been the development of new genome-wide technologies, permitting global views of the functional genome to be made routinely. While such information represents a tremendous intellectual and practical advance, there is a continuing need to exploit this new data to understand the evolution, organization and function of living systems.

The clear challenge is how to extend the classical question of genotype - phenotype relationship using the new genome-wide approaches? At a fundamental phenotypic level, the question of how genetic variation influences gene expression is also being addressed, taking advantage of the ability to assay mRNA levels on a genome-wide basis using expression microarrays, in combination with high-density genetic maps. Using this approach, the heritability of mRNA levels is now well established, in plants, yeast, lower- and higher-metazoans (including mouse, rat and humans): a field collectively described as expression genetics, systems genetics or eQTL (for “expression quantitative trait loci).

Understanding the influence of genetic variation on gene expression is likely to play a fundamental role in our understanding of how genetic variation influences phenotype, with implications for fields as diverse as human, animal and plant health and disease, behavourial genetics, evolutionary development biology and the emerging field of ecological genomics. Accordingly, this project is focused on developing fundamental new methodology to analyse, understand and exploit the new and powerful datasets arising from the field of expression genetics.

Further reading: Williams RBH, Chan E, Cowley MJ, Little PFR. The influence of genetic variation on gene expression, Genome Research 2007 17(12): 1707-1716.

This project will be located within the Computational and Bioinformatics Unit at JCSMR: comprised of 4 academic staff members (Easteal, Williams, Huttley, Burden) and their research groups, collectively comprising 20 researchers and students. The student will be expected to participate fully in the collective actvites of this Unit, including seminar attendance and a weekly lab meeting/journal club.

Background required: No specific requirements, but some knowledge of genetics, gene expression and basic molecular biology will be invaluable. This project would suite a highly motivated and committed student, who is interested in gaining a serious exposure to computational biology and bioinformatics. Because the project is entirely based on analysis of large scale biological data, and does not involve any experimental work, an interest and commitment to learning relevant material related to statistics and data analysis, as well as computer programming skills (specifically the R language, a programming environment highly tailored to data analysis), is essential for the successful conduct of this project.