Download PROJECT PORTFOLIO LEVELS 4 and 5 MARINE SCIENCE

PROJECT PORTFOLIO
LEVELS 4 and 5
MARINE SCIENCE HONOURS and
MARINE BIOLOGY and COASTAL
MANAGEMENT MASTERS 2016
Available in the Schools of Animal Biology, Earth and
Environment and Plant Biology
Marine Science, Marine Biology and Marine and Coastal Management at
UWA
At UWA, marine topics are taught across three schools in the Faculty of Science: the
School of Animal Biology, the School of Earth and Environment and the School of Plant
Biology. At the undergraduate level, a major in Marine Science is offered within the
Bachelor of Science. This is a three year degree with the possibility of a fourth,
research focused year, Honours, for high performing students. Up to this point, the
degree is broad and covers both biological and physical aspects of the marine
environment.
An increasingly popular alternative to completing an honours year is a masters by
coursework which may include a research project similar to an honours project, but
which also involves additional coursework units. At this level, the degrees become
specialized. Marine students can choose between the Master of Biological Science,
with the Marine Biology specialization, and the Master of Environmental Science with
the Marine and Coastal Management specialization.
To be eligible for Honours or to do a research project within the Masters degree,
student must attain an average of 65% over 4 core subjects at either Level 3 or 4. The
availability of projects will depend very much on the areas in which staff are currently
working and the funding they have available for research. Often, students are asked to
join a research group and work on data already collected. Alternatively, students may
be able to design their own project, set up the experiments and/or observations.
Students should seek a project well in advance of their start date. Research projects
generally run over 1 year, so it is best to have your project settled before the year
starts so you can hit the ground running on Day 1.
This booklet contains a list of potential projects for level 4 and 5 students available for
2016. It is important to realise that this list is not exhaustive; many of the projects are
flexible and can be adjusted to your interests. We strongly suggest you use this booklet
as a guide and contact potential supervisors to discuss the projects and your interests.
Some supervisors do not put up projects, but prefer students to contact them if they are
interested in the general area of research. To this end, we provide a list of potential
supervisors, along with their areas of expertise and contact details.
Use the provided projects to:
1) Gain an idea of the scope of appropriate projects
2) Be introduced to potential supervisors and their fields of study
3) Stimulate ideas about other projects that interest you
If you have further questions, please contact your Honours of Masters’ coordinators
who are Jane Prince ([email protected]) for Marine Science Honours and the
Master of Biological Science (Marine Biology), and Julian
Clifton
([email protected]) for the Master of Environmental Science (Marine and
Coastal Management).
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SUPERVISORS FOR MARINE HONOURS AND MASTERS PROJECTS
MARINE ECOLOGY
Tim Langlois
Jane Prince
Thomas Wernberg
CORAL BIOLOGY
Malcolm McCulloch
Thibaut de Bettignies
MARINE NEUROECOLOGY
Shaun Collin
Kara Yopak
Ryan Kempster
INVERTEBRATE BIOLOGY
Anne Brearley
Tim Langlois
Jane Prince
Thomas Wernberg
SPATIAL ECOLOGY
Renae Hovey
Bryan Boruff
Gary Kendrick
FISH BIOLOGY & ECOLOGY
Tim Langlois
Di McLean
Jane Prince
Jordan Goetze
Todd Bond
Matt Birt
MARINE GEOLOGY
Julian Bourget
OCEANOGRAPHY
Ryan Lowe
Jeff Hansen
Jim Falter
Malcolm McCulloch
SEAGRASS & ALGAE
Renae Hovey
Marion Cambridge
Gary Kendrick
John Stratton
Thomas Wernberg
Thibaut de Bettignies
MARINE RESERVES
Julian Clifton
Jane Prince
Tim Langlois
Di McLean
Jordan Goetze
MARINE MEGA-FAUNA
Mark Meekan
Jessica Meeuwig
Nicola Mitchell
Shaun Collin
Michele Thums
COASTAL PLANNING &
MANAGEMENT
Julian Clifton
Jeff Hansen
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SUPERVISOR LIST
Name
School or Institution
Email
Research interests
Matthew
Birt
Plant Biology
[email protected]
fish ecology, marine reserves
Todd
Bond
Plant Biology
[email protected]
fish ecology, marine reserves
Bryan
Boruff
Earth and Environment
[email protected]
spatial ecology
Julian
Bourget
Earth and Environment
[email protected]
marine geology
Anne
Brearley
Oceans Institute
[email protected]
invertebrate biology
Marion
Cambridge
Oceans Institute
[email protected]
seagrass biology and restoration
Julian
Clifton
Earth and Environment
[email protected]
marine reserves, coastal management
Shaun
Collin
Animal Biology
[email protected]
marine neuro-ecology
Wayne
Davies
Animal Biology
[email protected]
marine neuro-ecology
Thibaut
de Bettignies
Plant Biology
[email protected]
climate change, corals, invertebrate biology
Jim
Falter
Earth and Environment
[email protected]
oceanography
Jordan
Goetze
Plant Biology
[email protected]
fish ecology, marine reserves
Jeff
Hansen
Earth and Environment
[email protected]
coastal processes
Jan
Hemmi
Animal Biology
[email protected]
marine neuro-ecology
Renae
Hovey
Plant Biology
[email protected]
seagrass and kelp ecology, invertebrate ecology, spatial ecology
Gary
Kendrick
Plant Biology
[email protected]
seagrass and kelp ecology
Tim
Langlois
Plant Biology
[email protected]
fish ecology, marine reserves, invertebrate biology and ecology
Ryan
Lowe
Earth and Environment
[email protected]
oceanography
Mark
Meekan
AIMS
[email protected]
marine mega-fauna
Malcolm
McCulloch
Earth and Environment
[email protected]
coral biology, climate change
Dianne
McLean
Plant Biology
[email protected]
fish ecology, marine reserves
Jessica
Meeuwig
Marine futures
[email protected]
fish ecology, marine reserves, marine mega-fauna
Nicki
Mitchell
Animal Biology
[email protected]
marine mega-fauna, climate change
Jane
Prince
Animal Biology
[email protected]
fish ecology, marine reserves, invertebrate biology and ecology
John
Statton
Plant Biology
[email protected]
seagrass ecology and restoration
Michele
Thums
AIMS
[email protected]
marine mega-fauna
Thomas
Wernberg
Plant Biology
[email protected]
kelp and seagrass biology, climate change, invertebrate ecology
Kara
Yopak
Oceans Institute
[email protected]
marine neuroscience
Projects in Coastal Planning and Management
Project: Physical drivers of reef carbonate sediment budgets
Predicting future changes to coastlines fringed by coral reefs requires quantifying
sediment budgets in these environments. To do this we must understand the physical
parameters and biological composition of sediment deposits; the ecology of the
calcifying (production) community; and the dominant sediment transport mechanisms.
This study will examine previously collected datasets (sedimentological, biological,
hydrodynamic, and aerial photographs) from obtained along the Ningaloo Reef coast.
The student will utilize GIS tools to examine both spatial and temporal trends in these
data. These analyses will provide critical data for understanding the link between the
calcifying community of a reef and its sediment reservoir, and in turn, the mechanisms
by which material is transported between regions of the reef. Understanding transport
mechanisms within reef environments will act as the foundation for an improved
understanding of carbonate sediment budgets in fringing coral reefs, which remains a
critical gap in our ability to forecast future resiliency of reef-protected coastlines.
Supervisor/s: Ryan Lowe ([email protected])
Michael Cuttler ([email protected])
Start details: a February start is preferred
Project requirements: None. This project does not involve field work.
Project: Analysis of environmental data collected by the Waterman’s Bay
Marine Observatory
An increasing number of instruments are being deployed off the IOMRC Waterman’s
Bay building to measure atmospheric and oceanic data. A range of projects are
available both relating to the further development of the observatory (e.g.
instrument/software development) or analysis of the collected data. Presently the
observatory consists of a meteorological station and seaward directed video camera,
but will be expanded as to include a shoreline detecting video system and wave/water
temperature observations in the nearshore. Student projects could cover a range of
marine science disciplines from physical oceanography to marine biology. Data
collected by the observatory could be also augmented by additional data streams (e.g.
DOT wave buoys, satellite sea surface temperature). Example projects could include
correlating wind observations with the video derived sea state or the relationship
between shoreline movement and a range of atmospheric variables.
Supervisor/s: Jeff Hansen ([email protected]),
Julian Partridge ([email protected]),
Ryan Lowe ([email protected])
Start details: either February or July
Project requirements: None unless student desires to incorporate fieldwork into the
project.
Projects from the Marine Ecology Group
Project: Tropicalisation of temperate reefs: patterns and mechanisms
This project will investigate different aspects of recent changes in seaweeds, fishes
and corals along the tropical-temperate transition zone in Western Australia. For
example, changes in community structure of invertebrates, growth of seaweeds and
corals, grazing on temperate seaweeds by tropical fish and urchins, and follow-on
consequences of changes in food availability to herbivores
Supervisor/s: Thomas Wernberg – [email protected]
Start Period: February or July
Project requirements: Lab work, aquaria, optional diving with dive qualifications as
per UWA requirements.
Project: Effects of ocean temperature and marine heatwaves on
reproduction, recruitment and growth of seaweeds.
This project will quantify, either in the field or from samples already collected, patterns
of reproduction, recruitment, growth or mortality of marine macroalgae in different
ocean climates. This includes testing the temperature sensitivity and lethal
temperatures of different species.
Supervisor/s Thomas Wernberg – [email protected]
Start Period: February or July
Project requirements: Lab work, aquaria, optional diving with dive qualifications as
per UWA requirements.
Project: Ecophysiology of wide-spread seaweeds and marine
invertebrates.
This project will address the capacity of species to adapt and acclimatise to varied
environmental conditions. The project will test and contrast physiological performance
of species of seaweeds and invertebrates (urchins and gastropods) found across broad
environmental gradients (e.g., temperature, wave exposure, light), and teir
physiological responses to marine heatwaves.
Supervisor/s: Thomas Wernberg – [email protected]
Start Period: February or July
Project requirements: Lab work, aquaria, optional diving with dive qualifications as
per UWA requirements.
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Project: Ecological interactions in the Swan River.
Estuaries such as the Swan River are a focal point for human activities, and they are
therefore vulnerable to a range of stressors. This project will investigate the
interactions between seagrasses, drift algae and invertebrates such as the invasive
mud snail Batillaria.
Supervisor/s: Thomas Wernberg – [email protected]
Start Period: February or July
Project requirements: Both field and lab work required, drivers license and able to
snorkel to UWA standards
Project: Cultivation of juvenile seaweeds: light and temperature
requirements
Large brown seaweeds (Ecklonia and Scytothalia) are major habitat-forming species in
Western Australia that provide shelter and habitat for many organisms. This project will
use culture experiments to test the light and temperature requirements of their juvenile
life stages, including very settlement stages. This will provide critical information for
attempts to culture these species as well as information that will help understand their
ecology and sensitivity to ocean warming.
Supervisor/s: Thomas Wernberg – [email protected]
Start Period: February or July
Project requirements: Primarily laboratory and aquarium-based.
Project: Recent changes in performance and persistence of WA sea
urchins
Sea urchins are notorious for their ability to strip kelp forests from rocky reefs, leaving
nothing behind but barren rock, when their numbers increase. Several species of sea
urchin occur naturally within kelp forests in WA where, in contrast to eastern Australia
and Tasmania, they have little impact on seaweeds. However, preliminary studies
suggest there are changes to abundances of several species, some of which could
lead to over-grazing as it has been seen in Tasmania for the Centrostephanus
rodgersii. This project will investigate patterns of abundance and distribution of sea
urchins on reefs in Western Australia and/or test the influence of temperature and other
environmental conditions on their biology (reproduction, larval performance, feeding
rates etc).
Supervisor/s: Thomas Wernberg – [email protected]
Jane Prince: [email protected]
Start Period: February or July
Project requirements: Lab work, aquaria, optional diving with dive qualifications as
per UWA requirements.
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Project: Reproductive effort and seasonality of high latitude corals
High latitude coral populations were once thought to be pseudo-populations, sustained
by upstream larval sources. However fecund populations at Rottnest Island and the
Houtman Abrolhos Islands suggest this may not be the case. This project will
investigate the reproductive output (eggs per polyp and oocyte diameter) and
reproductive timing of corals in coastal, high latitude regions.
Supervisor/s: Thomas Wernberg – [email protected]
Chenae Tuckett – [email protected]
Start Period: February
Project requirements: Lab work, aquaria, optional diving with dive qualifications as
per UWA requirements.
Project: Spatial and temporal recruitment dynamics of high latitude corals
Recruitment is the measure of the number of juvenile individuals entering an adult
population. In high latitudes it is generally thought that coral recruitment follows peak
spawning periods and is at a lower rate than is seen in the tropics. However there are
few studies confirming this in Western Australia. This project will use recruitment tiles
deployed across temperate Western Australia to determine if this is the case. It will
focus on patterns of recruitment across latitude and across seasons.
Supervisor/s: Thomas Wernberg – [email protected] and
Chenae Tuckett – [email protected]
Start Period: February
Project requirements: Lab work, aquaria, optional diving with dive qualifications as
per UWA requirements.
Project: Effects of heatwaves on kelps and other seaweeds
The project involves an aquaria experiment in the lab. Ecklonia radiata, one of the main
canopy-forming kelps at WA’s coast, shall be collected from two or three different
locations along the coastline (Hamelin Bay, Perth, Jurien Bay). After collection the kelp
will be acclimated in the lab to water conditions and exposed to two simulated marine
heatwaves of different duration or maximum intensity. Possible response
measurements can involve growth, biomass, photosynthetic efficiency and pigment
content.
Supervisor/s: Thomas Wernberg – [email protected] and
Sandra Straub– [email protected]
Start Period: February
Project requirements: Lab work, aquaria, optional diving with dive qualifications as
per UWA requirements.
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Project: Super-invader traits - or just luck? A comparison of traits from
invasive marine seaweeds
Several of the world's most invasive species are seaweeds that belong to a single
genus (Caulerpa). Thousands of studies have been conducted on these Caulerpa
species in the invaded regions but virtually nothing is known about their biology in their
native regions. At least three of these invasive Caulerpa species are native to the Perth
region. The proposed project will study the distribution, ecology, and traits of these
'invasive' Caulerpa species and compare these data to native Caulerpa species that
are not invasive in other places. This project aim to provide new data about the
invasion biology of some of the world's most notorious invaders but with a twist; are
their biology really different from native non-invasive Caulerpa species - or was it just
'luck' that some of the Perth species became invasive?
Supervisor/s: Thomas Wernberg – [email protected] and
Mads Thomsen - [email protected]
Start Period: February or July
Project requirements: Both field and lab work required, drivers license and able to
snorkel to UWA standards. Diving work possible with diving qualifications to UWA
standards.
Project: Contrasting patterns of biodiversity in marine facilitation
cascades can be controlled by seagrass species interactions
Species diversity is often controlled by 'facilitation cascades' - an emergent concept
that suggest positive species interactions are as important as competition and
predation. This project will test if differences in epiphyte communities, as predicted by
the facilitation cascade theory, have cascading effects on the invertebrate communities
living in two types of seagrass beds - and ultimately thereby also modify the fish
communities that feed on these invertebrates. Such differences in invertebrate
communities could also have large implications for marine conservation that
sometimes overlook how different seagrass traits (here epihyte communities) can have
wide implications for biodiversity.
Supervisor/s: Thomas Wernberg – [email protected] and
Mads Thomsen - [email protected]
Start Period: February or July
Project requirements: Lab work, aquaria, optional diving with dive qualifications as
per UWA requirements.
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Project: Ontogenetic shifts in habitat use by marine fishes in northwest
Australia (1)
Baited remote underwater stereo-video (stereo-BRUV) surveys have been conducted
throughout the Exmouth Gulf and offshore across a range of habitats and depths.
The student would be required to analyse this stereo-BRUV video footage which
involves training in EventMeasure software and developing advanced skills in fish
identification. They will then be required to conduct rigorous statistical analyses
assessing the abundance distribution and size of fish, across varying life stages, with
respect to habitat and environmental variables.
Supervisors: Dianne McLean, [email protected]
Timothy Langlois, [email protected]
Todd Bond, [email protected]/
Corey Wakefield (WA Department of Fisheries)
Start period: February or July
Project requirements: See above. This project does not involve field work
Project: Ontogenetic shifts in habitat use by marine fishes in northwest
Australia (2)
Baited remote underwater stereo-video (stereo-BRUV) surveys have been conducted
throughout the northern Pilbara region (Dampier) and offshore across a range of
habitats and depths.
The student would be required to analyse this stereo-BRUV video footage which
involves training in EventMeasure software and developing advanced skills in fish
identification. They will then be required to conduct rigorous statistical analyses
assessing the abundance distribution and size of fish, across varying life stages, with
respect to habitat and environmental variables.
Supervisors: Dianne McLean, [email protected]
Timothy Langlois, [email protected]
Matt Birt, [email protected]/
Corey Wakefield (WA Department of Fisheries)
Start period: February or July
Project requirements: See above. This project does not involve field work
Project: Biogeographic assessment of the abundance distribution of
sharks in northwest Australia
Extensive baited remote underwater stereo-video (stereo-BRUV) surveys have been
conducted in northwest Australia from Gnaraloo to the Dampier Archipelago and
including offshore Islands. The student would be required to analyse stereo-BRUV
video footage which involves training in EventMeasure software and developing
advanced skills in shark identification. They will then be required to conduct rigorous
statistical analyses assessing the abundance distribution and size of sharks across
northwest Australia, with respect to a range of habitat and environmental variables.
Supervisors: Timothy Langlois, [email protected]
Dianne McLean, [email protected]
Jordan Goetze [email protected]
Start period: February or July
Project requirements: See above. This project does not involve field work
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Project: A comparison of juvenile fish assemblages sampled by fish traps
and baited video systems
Baited remote underwater stereo-video (stereo-BRUV) surveys and fish trap collections
have been conducted in the northern Pilbara region in shallow nursery habitats. The
student would be required to analyse this stereo-BRUV video footage which involves
training in EventMeasure software and developing advanced skills in fish identification.
They will then be required to conduct rigorous statistical analyses comparing the
relative abundance, diversity and size of juvenile fishes sampled by stereo-BRUVs and
fish traps, with respect to habitat and environmental variables.
Supervisors: Timothy Langlois, [email protected]
Dianne McLean, [email protected]
Corey Wakefield (WA Department of Fisheries)
Start period: February or July
Project requirements: See above. This project does not involve field work
Project: Can small no-take marine sanctuary zones protect both pelagic
and demersal recreationally targeted fish species?
Ideally, reserves are large and representative of all habitats required to sustain viable
populations of the species to be protected. However, in many cases, large areas are
not available, and what is available cannot adequately provide for all the different life
stages and strategies that some species employ. This is particularly true of migratory
species that typically move large distances between breeding and feeding grounds,
making the area they occupy over their life cycle impossibly large and so difficult to
protect.
Rottnest Island is a popular destination for recreational fishers and is home to many
targeted fish species, including the Western Rock Lobster, which has been shown to
benefit in both numbers and biomass from the establishment of several small no-take
sanctuary zones around the island. The benefits for more mobile species are less
clear. In this study, we intend to concentrate on the migratory Australian Herring and
the more sedentary King George Whiting and try to detect if the no-take areas offer
sanctuary to these species.
Supervisors: Jane Prince: [email protected]
Jordan Goetze: [email protected]
Start period: July only.
Project requirements: This project requires three fieldtrips to Rottnest Island, taking
surveys before, during and after the main tourist/fishing season. Student will need to
demonstrate snorkeling capability to UWA requirements and to hold a manual C-class
driver’s licence.
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Project: Effect of tropical herbivores on seagrass and algal beds at
Rottnest Island
Recent surveys in the shallow bays at Rottnest Island have shown a dramatic increase
in the abundance and distribution of tropical herbivores, in particular the rabbit fish,
Siganus fuscescens, and the parrotfish, Scarus spp, Through their grazing habits,
these species have the potential to impact the turfing and foliose algae and kelp beds
along with the seagrass meadows, which are important habitat for a wide range of
other species of fish and invertebrates.
This project will aim to quantify this impact, looking for evidence of grazing using both
comparative and experimental methods and obtaining robust measures of the
abundance, size structure and behaviour of the fish species.
Supervisors: Jane Prince: [email protected]
Jordan Goetze: [email protected]
Start period: July only.
Project requirements: This project requires a minimum of three fieldtrips to Rottnest
Island. Student will need to demonstrate snorkeling capability to UWA requirements
and to hold a manual C-class driver’s licence.
Project: Underwater imagery as a tool to detect changes in benthic
macrophyte communities
This project will investigate the efficiency of video photography as a tool for detecting
change in macroalgae and seagrass communities in the Kimberley region. Remote
techniques have to be used to monitor benthic communities across large areas that are
not accessible by snorkeling or diving. Video or still photography is a form of nondestructive monitoring that does not require the removal of macrophytes and that can
be done from a ship. It is therefore a valuable tool e.g. to assess environmental
impacts on benthic communities. Video footage can be examined at different scales
and it is important to balance the level of detail achieved and the effort and time it
takes.
You will analyse randomly sampled video frames using the CATAMI classification
scheme. You will compare visual identification and random point counts of macrophyte
cover from video footage to determine the minimum sample size (the number of
randomly sampled video frames) needed to detect change and the minimum
detectable change in cover. The footage will be examined at three scales: transects (m
apart), sites (km apart) and regions (tens of km apart). Skills learned: Video image
analysis, CATAMI classification, identification of macroalgae and seagrasses.
Supervisors: Ylva Olsen, [email protected], 6488 5907, OI Building G10
Andrea Zavala Perez, [email protected]
Gary Kendrick, [email protected], 6488 3998, OI Building
Start period: preferably February
Project requirements: This project will not involve field work and there are no special
requirements
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Project: Reproduction and recruitment in the seagrass Posidonia australis
The seagrass Posidonia australis has been the focus of a 6 year intensive study to
determine the potential of restoration in areas it has been lost. We have found that it
does recruit in great numbers some years but not others. There is a 10-1000 fold
difference in reproduction and seed production among years. This is similar to
observation of seed masting in terrestrial trees like the Oak (Quercus). This thesis will
address reproduction, seed set and recruitment of seedlings for Posidonia for a single
year at Rottnest Island. This data will be used to compare with a decade of
reproduction and seed set data from the island. We will specifically address whether
recruitment success is related to reproductive output.
Supervisors: Gary Kendrick ([email protected]),
Elizabeth Sinclair ([email protected]), and
John Statton ([email protected])
Start period: July start only
Project requirements: Field work and lab work required including SCUBA diving or
snorkeling.
Project: Remote assessment of deepwater corals, kelps and seagrasses
from AUV (marine robotics) deployments 2010 – 2016
A national kelp-monitoring program utilizing Autonomous Underwater Vehicles (AUVs)
has been surveying the central west coast of Western Australia (Rottnest to Houtmans
Abrolhos) annually since 2010. During that time a marine heat wave decimated inshore
kelps and corals. The imagery taken from the AUV represents a unique opportunity to
assess the loss and recovery of the main foundation species in deeper waters, kelps,
seagrass and corals along the WA coastline.
Supervisors: Gary Kendrick: [email protected]
Renae Hovey: [email protected]
Start period: either February or July.
Project requirements: No field work is required.
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Projects from the Marine Neuro-ecology Group
Project: Quantitative measures of brain evolution in bony fishes
Brain and body size relationships have traditionally been used to infer cognitive abilities
across a range of mammals (including humans), providing vital information about life
history traits, behaviour and “intelligence”. This project will apply new methodologies to
accurately assess total neuron number (rather than brain size) and processing power
in bony fishes, using a traditional model species. The goal of this project is to
understand the fundamental selection pressures underlying the evolution of the brain
and its component parts and trace the evolution of cognitive capacity. Techniques will
include isotropic fractionation, flow cytometry, and stereology.
Gabi, M., Collins, C. E., Wong, P., Torres, L. B., Kaas, J. H. and Herculano-Houzel, S.
(2010). "Cellular scaling rules for the brains of an extended number of primate
species." Brain, Behavior, and Evolution 76: 32-44
Herculano-Houzel, S. and Lent, R. (2005). "Isotropic fractionator: A simple, rapid
method for the quantification of total cell and neuron numbers in the brain."
Journal of Neuroscience 25(10): 2518-2521
Supervisors: Shaun Collin: [email protected]
Kara Yopak: [email protected]
Start period: February
Project requirements: Laboratory work
Project: Interspecies variation in the olfactory systems of ancient fishes
Many species combine a myriad of sensory inputs to gain an appreciation of the local
environment. For many organisms (e.g. primates) vision is the primary sense, however,
in other animals sensory systems such as olfaction are critical to their survival.
Compared to vision where a single stimulus (i.e. light) is measured at relatively short
distances, olfaction can detect an array of different olfactory cues (“smells”) over very
long distances. Given the large number of potential molecules that can be detected, it
is not surprising that the number of potential olfactory receptors (ORs) that specifically
recognise these ligands is also numerous. Indeed, in humans alone it is estimated that
there are close to 400 intact OR genes and over 400 OR pseudogenes, thus
representing a very dynamic superfamily of genes. Recently, putative ORs were
identified in one species of lamprey (sea lamprey, Petromyzon marinus; 67 in total) and
a single species of cartilaginous fish (elephant shark, Callorhinchus milii, 2 in total),
thus suggesting that olfaction was important in the ancestors to both the jawless and
jawed vertebrates, respectively. However, the complete repertoire and the degree of
diversity of ORs remain incomplete.
Two projects are on offer to study these species and their close relatives by using
bioinformatics and molecular biology techniques to ascertain the full complement of
ORs (intact and pseudogenised copies) and to study how the repertoire of ORs are
different between species. Such information will be correlated with the behaviour and
habitat of the species under investigation to elucidate the role that the environment
may play in the adaptive evolution of the olfactory system in ancient fishes.
Supervisors: A/Prof Wayne Davies [email protected]
Prof David Hunt [email protected]
Prof Shaun Collin [email protected]
Start details: February
Project requirements: Laboratory work
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Project: Escape responses in fiddler crabs.
How do animals decide when to start their escape dash from an approaching predator?
Understanding the sensory information animals use when making such decisions, will
tell us how they measure risk and how they use visual information to organise their
behaviour to avoid being eaten while still being able to feed and find mates. Fiddler
crabs are highly visual animals that live under constant threat of predation from birds.
Our field experiments have shown that the crabs’ eye limits their ability to measure a
predator’s distance and their direction of movement – a problem they share with many
other small animals. To overcome this deficit, they stage their responses and learn to
ignore certain objects. This project will bring fiddler crabs into the laboratory to test
their escape decisions under controlled conditions. The combination of behavioural
with physiological measurements of visual abilities in the same animals, using
ElectroRetinoGram (ERG), will provide an understanding of the mechanisms
underlying visually guided behaviour in these animals. Animals can be tested in our
artificial mudflat (at UWA) or on a custom made treadmill (e.g. How et al 2012) that
allows us to record the movements of crabs in response to visual stimulation. There
are many possible variations of this project and you will be able to choose in which
direction you want the project to evolve according to your interest and ability.
Hemmi JM & Pfeil A (2010) A multi-stage anti-predator response increases information
on predation risk. Journal of Experimental Biology, 213 1484–1489
Hemmi, JM, & Tomsic, D (2012). The neuroethology of escape in crabs: from sensory
ecology to neurons and back. Current Opinion in Neurobiology, 22, 194–200
How et al. (2012) High e-vector acuity in the polarisation vision system of the fiddler
crab Journal of Experimental Biology 215, 2128-2134
Supervisors: Jan Hemmi [email protected]
Yuri Ogawa [email protected]
Shaun Collin [email protected]
Start period: February
Project requirements: Laboratory work
15
Project: The visual world of fiddler crabs
Australian fiddler crabs are highly visual animals that
inhabit mud and sand-flats. Despite extensive research
into their behaviour and visual ecology, we know
relatively little about their ability to see different colours
and the extent of their ability to see polarised light
(How et al 2012). This project will conduct behavioural,
physiological and or genetic experiments aimed at
measuring the visual capabilities of the crabs’ eyes,
including their ability to see patterns, colour and
polarisation. The measurements will show us the
extent of fiddler crab vision and help us understand
how these animals react to their environment.
Experiments will be conducted using our resident UWA
fiddler crab colony. The crabs are housed in a 4 m2
fully functional artificial mudflat with periodic tidal inundation. You will discover how
sensory information affects animal behaviour, learn how to probe the visual capabilities
of animals and learn genetic (standard molecular biology, qPCR and transcriptome
sequencing (RNA-Seq) ) and electrophysiological recording techniques, as well as UVvis spectrophotometry. This project is flexible and allows the combination of
behavioural, physiological and genetic techniques according to your interest and ability.
Hemmi, JM, & Tomsic, D (2012). The neuroethology of escape in crabs: from sensory
ecology to neurons and back. Current Opinion in Neurobiology, 22, 194–200
How et al. (2012) High e-vector acuity in the polarisation vision system of the fiddler
crab Journal of Experimental Biology 215, 2128-2134
Zeil, J & Hemmi, JM (2006). The visual ecology of fiddler crabs. Journal of
Comparative Physiology A 192, 1–25
Supervisor/s: Jan Hemmi: [email protected]
Yuri Ogawa: [email protected]
Wayne Davies: [email protected]
Start details: February
Project requirements: Laboratory work
16
Project: Eye movements for high resolution in fiddler crabs
The compound eyes of arthropods such insects and crustaceans are well known for
their low spatial resolution. By our visual standards, almost all these animals seem to
have a hopelessly blurry view of the world. This low spatial resolution is due to the
optical design of their eyes: in particular the relatively broad angular sensitivity of the
ommatidia – the individual photoreceptor elements of the eye – and the interommatidial
angle – the way in which each ommatidia’s line of sight differs from that of its
neighbour. If each ommatidium is viewing a large region of visual space, or if each
ommatidium looks in a very different direction, it is inevitable that the whole eye’s view
will lack spatial detail. Unless, that is, arthropods have evolved a way to overcome this
problem.
There is a possibility that this is the
case. In machine vision, a technique
of subpixel interpolation is used to
increase the resolution of an
imaging system or camera. This is
done by taking several images of a
scene but shifting the image sensor
slightly for each image; a bit of
maths then recovers a high
resolution image. If arthropods also
use this technique it is possible that
they can dynamically trade off
temporal resolution (the ability to
see fast moving things) and spatial resolution to see finer detail than would be
anticipated from observing the anatomy of their eyes. To do so, they would have to
move their eyes, or retinas, by tiny amounts. Such movements have been observed in
some crustaceans, but have not been well documented. Fiddler crabs have optimised
the resolution of their eyes along the vertical dimension but have to content with very
limited horizontal resolution (Smolka & Hemmi 2009). These crabs would therefore
particularly benefit from horizontal eye movements. You will use macro high speed
video to investigate whether fiddler crabs move their eyes in a way that would enable
them to employ sub-ommatidial interpolation. You will learn to use computer
programming in Matlab to investigate the potential effect of such interpolation on
images of natural scenes that would be seen by fiddler crabs.
Land M. and Layne, J. (1995) The visual control of behaviour in fiddler crabs I:
Resolution, thresholds and the role of the horizon. J Comp Physiol A 177: 81-90
Smolka, J., & Hemmi, J. M. (2009) Topography of Vision and Behaviour. J Exp Biol
212: 3522–3532
Viollet, S. 2014) Vibrating makes for better seeing: from the fly’s micro-eye movements
to hyperacute visual sensors. Frontiers in Bioengineering and Biotechnology
2(9)1-8 doi: 10.3389/fbioe.2014.00009
Vorobeyv, M., Gumbert, A., Kunze J., Giurfa, M., Menzel, R. (1997) Flowers through
insect eyes Israel Journal of Plant Science 45:93-101
Supervisor/s: Jan Hemmi: [email protected]
Julian Partridge: [email protected]
Start details: February
Project requirements: Laboratory work.
17
Projects in evolutionary biology
Project: Temporal genetic variation in the intertidal snail Bembicium
vittatum
Analysis of variation of genetic traits over time provides valuable information about
stability of genetic structure, effective population size, and contrasting effects of
selection on different traits (e.g., Lessios et al. 1994, Tessier & Bernatchez 1999, Palm
et al. 2003; Charlier et al. 2012). Most studies, however, examine temporal variation
over only a short period of time, even though longer term
comparisons allow much more powerful analyses.
The intertidal snail Bembicium vittatum offers a chance to
examine temporal genetic changes of molecular and
morphological traits over a twenty-year period, representing more
than a dozen generations. This species lacks planktonic larvae,
and is highly genetically subdivided in the Abrolhos Islands, in
ways that reflect patterns of connectivity among populations
(Johnson & Black 1991, 1996, 1998). In addition, populations
differ in their sizes and degrees of isolation, and hence in their
potential for bottlenecks.
Variation of allozyme loci was
examined in 1987 and 1992, and samples for the same sites are
available from 2007 (and from 1997 for some sites). Thus,
analysis of allozymes in the 2007 samples, combined with
comparisons with the previous years, will provide tests of stability
of patterns of genetic subdivision, and specific comparisons
among populations with different characteristics. Alternatively,
more powerful microsatellite DNA markers (Kennington et al.
2012) could be used to examine variation at selected sites, using
samples collected in 1987, 1992, 1997, 2002 and 2007.
These populations also differ in shell shape and colour, which
are adapted to local conditions (Johnson & Black 2000, 2008).
Quantification of temporal variation in these morphological traits will allow testing of the
expectation that they should be less affected by fluctuation in population sizes, and
hence are likely to differ from the allozymes in their amounts and patterns of temporal
variation (e.g., Binks et al. 2007).
This project will involve analysis of allozymes or microsatellite DNA and shell traits
in populations of B. vittatum, to quantify temporal variation, to test effects of population
characteristics and type of trait on genetic structure. The extent and complexity of the
data provide rewarding possibilities for a student willing to take on in-depth analyses.
Background reading
Binks, R.M, Kennington, W.J. & Johnson, M.S. (2007). Rapid evolutionary responses in
a translocated population of intertidal snail (Bembicium vittatum) utilise variation
from different source populations. Conservation Genetics 8: 1421-1429.
Charlier, J., Laikre, L., & Ryman, N. (2012). Genetic monitoring reveals temporal
stability over 30 years in a small, lake-resident brown trout population. Heredity
109: 246-253.
Johnson, M.S., & Black R. (1991). Genetic subdivision of the intertidal snail Bembicium
vittatum (Gastropoda: Littorinidae) varies with habitat in the Houtman Abrolhos
Islands, Western Australia. Heredity 67: 205-213.
Johnson, M.S., & Black R. (1996). Geographic cohesiveness versus associations with
habitat: genetic subdivision of Bembicium vittatum Philippi (Gastropoda:
Littorinidae). in the Houtman Abrolhos Islands. Biol J Linnean Soc 58: 57-74.
18
Johnson, M.S., & Black R. (1998). Increased genetic divergence and reduced genetic
variation in populations of the snail Bembicium vittatum in isolated tidal ponds.
Heredity 80: 163-172.
Johnson, M.S., & Black R. (2000). Associations with habitat versus geographic
cohesiveness: size and shape of Bembicium vittatum Philippi (Gastropoda:
Littorinidae). in the Houtman Abrolhos Islands. Biol J Linnean Soc 71: 563-580.
Johnson, M.S., & Black R. (2008). Adaptive responses of independent traits to the
same environmental gradient in the intertidal snail Bembicium vittatum. Heredity
101: 83-91.
Kennington, W.J., Hevroy, T.H., & Johnson, M.S. (2012). Long-term genetic monitoring
reveals contrasting changes in the genetic composition of newly established
populations of the intertidal snail Bembicium vittatum. Molecular Ecology 21:
3489-3500.
Lessios, H.A., Weinberg, J.R., & Starczak, V.R. (1994). Temporal variation in
populations of the marine isopod Excirolana: how stable are gene frequencies
and morphology? Evolution 48: 549-563.
Palm, S., Laikre, L., Jorde, P.E., & Ryman, N. (2003). Effective population size and
temporal genetic change in stream resident brown trout. Conservation Genetics
4: 249-264.
Tessier, N., & Bernatchez, L. (1999). Stability of population structure and genetic
diversity across generations assessed by microsatellites among sympatric
populations of landlocked Atlantic salmon (Salmo salar L.). Molecular Ecology 8:
169-170.
Supervisor/s: Mike Johnson: [email protected]
Jason Kennington: [email protected]
Start details: February
Project requirements: This project does not involve field work and will suit a student
with a solid background in population genetics and evolution, who is not averse to
tackling complicated multivariate analyses.
19
Project: Phylogenetic relationships among planktonic and directly
developing species within the genus Bembicium (Gastopoda: Littorinidae)
The mode of reproduction can have major effects on population structure and
likelihood of genetic divergence within marine species (Bohonak 1999). Species
without larval dispersal tend to be more subdivided genetically than those with
planktotrophic larvae. Littorine snails of the genus Bembicium include species that
exhibit a planktonic larval stage and species that are direct developers (Johnson and
Black 2006). The genus includes five species, two of which have planktonic dispersal,
B. auratum and B. nanum, and three that are
direct developers, B. vitattum, B. melanostoma
and B. flavescens (Reid 1998).
Allozyme analyses of these five species across
their geographical distributions have been
conducted by Johnson and Black (2006). This
study supported the current taxonomic
treatment of the genus, but failed to resolve
important historical relationships between
species,
which
are
fundamental
to
understanding the origin and evolutionary
significance of modes of reproduction. An
investigation of mitochondrial DNA within
Bembicium will allow finer resolution of genetic
subdivision and provide the essential historical
perspective needed to understand the effects of
modes reproduction on the genetic structure of
this genus. Specifically, the study will (1) test
Bembicium vittatum sitting on a
the hypothesis that direct development evolved
pneumatophore
only once in this genus, (2) allow comparison of
amounts and patterns of genetic divergence in
lineages with different modes of reproduction,
and (3) determine the evolutionary history of populations of the direct developer B.
vittatum, which has disjunct and genetically highly divergent populations over a range
of 4000 km.
Supervisor/s: Jason Kennington: [email protected]
Mike Johnson: [email protected]
Start details: February
Project requirements: This project does not involve field work and will suit a student
with a solid background in population genetics and evolution.
20