Your thesis in 3 minutes

MUBoGS Mini Conference

Although I suggested in my last post that my next one would be about the hierarchical bit of hierarchical models, I am instead taking this opportunity to briefly present a little group called ‘MUBoGS’ and a little conference called ‘The MUBoGS Mini Conference’.

The postgraduate students in The School of Botany, here at Uni Melb, are getting active.  The Melbourne University Botany Graduate Society, affectionately known as MUBoGS, is holding the first Graduate School of Botany Mini Conference.

Our MUBoGS flyer. Note: mini plant (Wow!)

Most postgraduate members from the School (including Hons, Masters and PhDs) across all the lab groups will be presenting their thesis topics in 3 minutes and with the aid of up to 2 (non-animated) slides.

3-minute presentations, or ‘speed talks’ are becoming more frequent, both in conference settings but also within academic institutions. Annually, the University of Queensland runs a very successful 3MT competition that is open to students from many Universities from around the world.

The idea is to give postgrads a chance to practice effective communication of their research to an educated but unspecialised audience (see here for more info and some examples of cool, calm, collected and concise speakers, and here for good advice about preparing for a 3MT comp).

Putting together a 3-minute talk takes a whole lot longer than just 3 minutes.
The aim is to communicate what you’re researching, why you’re doing it and why it’s important.  Often these talks are judged firstly on your communication style, specifically whether you can get a non-specialised audience to understand the significance of your research, but also on how engaging you are.  Condensing the fundamentals of your research into something that can be delivered and understood efficiently is both surprisingly challenging and surprisingly rewarding.

Can you make people understand and care about your research in 3 minutes?

The postgraduate students here in The School of Botany will soon find out.  Our first Mini Conference is shaping up to be an excellent day.  As well as our students presenting, we are having panel discussions of PhD and Postdocs talking about transitions from PhD to ‘Post-PhD-Work’ and sharing some hints about ‘things I wished somebody had told me…’  We are also planning some social trivia and there will be many ‘Mini Plants’ to win throughout the day.

Stay tuned for more Mini Conference news…

And… here’s a photo of Eucalyptus incrassata (+ ants) flowering in the mallee…

Eucalyptus incrassata from Murray Sunset

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‘Model’ refers to…

My blog is titled Freya’s Research, but to date, there has (rather sneakily) been a lack of posts related to what I actually do here in the QAEco lab.   Unfortunately, I don’t just look at orchids and take photos of Acacia.

Caladenia alpina (orchid), Acacia sp. (wattle) and Diuris sp. (orchid)

A large part of my PhD will be building a hierarchical Bayesian model that incorporates plant functional traits as species level predictors of plant growth and reproduction.

In my next couple of posts I will endeavor to explain all these terms (but don’t worry there will also be a few posts about what is flowering around Melbourne). For my first post in this series about my research, I would like to start from the start and try to explain what a model is.

Needless to say, googling “model” gives you mixed results. I found it easier to ask my Supervisor for a good book on modelling.  The result of this was a book, ‘How to Model It, Problem solving for the Computer Age’ by Anthony Starfield, Karl Smith and Andrew Bleloch.

These authors suggest that models are formalisations of the relationships between things.

There are many types of models:

  •  mental models
  • graphical models
  • statistical models
  • mathematical models

A mathematical or statistical model, concerns the relationships between quantifiable things or values. Values that are actively changing are called variables, values that are less likely to change are parameters (these can mediate the effect of variables). Parameters that can’t be changed are called constants.

Hardenbergia violacea (is flowering outside at the moment)

How to model it begins with the authors posing a problem; “how long will it take you to read this book?” A length of time immediately pops into ones head. But, if you go to the trouble of really thinking about it (which the book makes you do), you might find that the time it will take may depend on a few things.

Maybe the time it takes to read the book will depend on how fast I read one page, and then on how many pages there are in the book. Maybe it will depend on the number of tasks I have to do on each page and the time it takes me to do each task (maybe how many things are in flower outside?).

If I take my mental model a bit further, I can formulate a simple equation:

T = pP + wWP

Where:

T = time taken to read the book,
p = time to read one page of the book,
P = number of pages in the book,
W = number of ‘tasks’ per page, and
w = time taken to complete each task

P,  W, and  w changes between different books and so these are variables (because they are actively changing).  p may not change as much from book to book, as everyone probably has an their own average reading time. Therefore, p is a parameter.

The authors of How to model it show that we all make (mental) models all the time.

A model is a purposeful representation of something. Models can be used for synthesising information, for estimating values of important variables, for prediction, decision-making and explanation.  One major benefit of using a formal model is that you’re forced to be explicit about your thought processes. It can be quite challenging and very revealing when you’re confronted with all your assumptions.

In my research I will be a using a type of statistical model called a hierarchical  Bayesian model.  My aim is to model plant growth and reproduction incorporating the influence of species-specific plant functional traits.

Of course, an important consideration should always be what the point of your model is.  Indeed the authors of How to model it suggest you should always ask yourself three questions:

  • What (exactly) am I doing? (I should be able to describe it precisely)
  • Why am I doing it? (How does it fit into the solution)
  • How will it help? (What will I do with the outcome once I have it)

Acacia pycnantha inflorescence

Great questions to ask oneself.  What’s the point?   Why do I want to model plant growth and reproduction?  Why don’t I just spend all my time taking photos of orchids and Acacias?   The answers to all this and more will pop up in a future post or two.

In my next blog, however, I will attempt to give an overview of the ‘hierarchical’ bit of my modelling approach.

Stay tuned…

Ref:

Starfield AM, Smith KA & Bleloch AL (1994) How to model it, problem solving for the computer age.  McGraw Hill, New York.

Thanks to W.K Morris for proof reading.

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The Wattles

Genus: Acacia
Family: Mimosaceae

This time of year (late winter into early spring) is a great time to have eyes and a nose.  One of the main reasons for this, is because it is the flowering time for many Acacias.  For those poor souls who have not been acquainted with, or have not paid much attention to this group of flowering plants, they often look like this (a bright, bright mass of yellow):

A bright mass of sweet smelling yellow

There are many species of Acacia flowering around Melbourne at the moment, and with only a little effort they are relatively straightforward to identify.  For a successful ID of Acacias you need to know something about their foliage and flowers.  A copy of ‘Native trees and shrubs of south-eastern Australia’ by Leon Costerman is also highly recommended.  This comes in a big comprehensive book covering common trees and shrubs of NSW, Vic and SA, but also a very handy smaller field guide ‘Trees of Victoria and adjoining areas’ (‘Mini Costermans’).

Underneath a bipinnate leaf. Note pinnae and pinnules.

Acacias have two broad types of foliage :

Bipinnate leaves  are ‘feathery’ and divided into pinnae. The pinnae further divided into pinnules.  All acacias have bipinnate leaves to start with.
In some species bipinnate leaves are replaced as the plant grows older by leaf like bodies called phyllodes.  Some species have broad, flat phyllodes whilst others can have spiny, needlelike or very slender phyllodes.

For ID in the field, the type of foliage (bipinnate or phyllode) is a good spotting characteristic.  After this, other foliage characteristics such as the number and placement of phyllode veins or the position and number of glands are significant characters for identification.

Different types of phyllodes

Look closely and you might see the individual flowers that make up this globular inflorescence. You can see the number of closed flower buds on the inflorescence on the right.

Individual flowers of Acacia species are tiny.  These tiny flowers are aggregated together to form an inflorescence and Acacias also have two broad inflorescence types: globular or cylindrical.

This division of inflorescence structure is also an important grouping characteristic for ID in the field.  Most Acacia species flower from late winter to early spring.  Time of flowering can be useful to distinguish between some species.

Single globular inflorescence, cylindrical spike and a raceme of globular flower heads.

An Acacia seed pod, a typical pea pod

Finally the fruiting pods are important features.  Size, shape and surface texture are important.

In mini Costermans (which you should put in your pocket before leaving the house, always) the first major groupings occur between :

– Wattles with bipinnate leaves and globular flower heads (go to page 132)
– Wattles with phyllodes and cylindrical inflorescences (go to page 135)
– Wattles with phyllodes and globular flower heads (go to page 138)

Once you have identified one of these broad groups, you can move to another section of the field guide and start looking in more detail at spotting characters such as placement of glands or veins, distribution and flowering times.  Clear drawings with detailed inserts of relevant features such as leaf glands are super helpful and make Acacia ID relatively straightforward.  So give it a go, it is surprisingly satisfying.

For example:

Acacia oxycedrus, photographed July in The Grampians

Acacia oxycedrus (photo left)

Foliage: Stiff green flat phyllodes 2-4 cm long, slightly curved, tapering to a very sharp point, 3-4 raised veins.
Flowers: (Jul-Oct) Yellow, crowded on axis in cylindrical spikes to 3 cm long.

Acacia longifolia (photo below)

Foliage: Flat  green phyllodes, spreading to erect on stiff branches, 2 (-4) main veins, gland near base.
Flowers: (Jul-Oct) Yellow, in spikes.

Acacia longifolia, photographed August at Seaford

 

 

Acacia verticillata (photo below)

Foliage: Green phyllodes mostly in whorls of about 6, often needle-like (or flattened) with sharp point, 8 – 25 mm x 1-2 (-5) cm long.
Flowers: (Jul – Oct) Bright yellow, in soft ovoid or cylindrical spikes 1 – 2 cm long.

Acacia verticillata, photographed in October near Bendigo

Refs

Costermans, L (1994) ‘Native trees and shrubs of south-eastern Australia’.  5th Ed. New Holland Publishers, Australia.

Costermans, L (2006) ‘Trees of Victoria and adjoining areas’.  6th Ed. Costermans Publishing, Australia.

(‘Mini Costermans’ = buy this).

All photos by Me!  For more Acacia love see http://www.flickr.com/photos/cracoo/sets/72157627391145521/with/7970371684/

A baby Acacia displaying both bipinnate leaves and phyllodes

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Trait-based Reading Group

Trait-based approaches to ecology and conservation

I chose the paper for our recent lab Reading Group and we discussed McGill et al.’s (2006) paper on community ecology and functional traits.  General principals in community ecology are notoriously hard to find.  McGill et al. (2006) believe that a focus on functional traits and environmental gradients can lead to a more quantitative, general and predictive science.  The authors propose four broad research themes based on traits, environmental gradients, the ‘interaction milieu’ and performance currencies that are intended to move community ecology beyond simple pairwise species interactions and towards a research agenda focused on a physiological approach with well defined units of measurement.

Overall our group agreed that traits are a powerful way to make generalisations in ecology.  We thought the discussion of big questions and clear future research directions in the paper gave a nice introduction to the field of functional ecology and to future applications of this method.

SLA (Specific Leaf Area) is a commonly used plant functional trait

Our discussion of this general approach led to some questions around the definitions and consistency of use for terms such as ‘functional trait’, ‘life history trait’, ‘functional type’, ‘vital rates’ and ‘attributes’.  This subsequently led to the acknowledgment of different scales in trait based research and questions surrounding levels of variation within traits, between traits, across species as well as between sites, regions and biomes.

We were not entirely clear on the detailed approaches being used to ‘rebuild’ community ecology based on traits, particularly in the face of multiple interactions between large numbers of species, but our attention was drawn to literature (not cited within this paper) that focuses on mechanistic and physiological trait based modelling (reviewed in Kearney and Porter 2006).  We thought that better theory about which traits are important, why, and under which circumstances will make trait-based approaches more applicable to conservation science.  In particular, we concluded that it would be nice to see more quantitative tests of the predictive ability of trait-based research, along the lines of Keith et al. (2007).

Hakea sp. with a different SLA

Within QAECO there are a few Qaecologists who work with functional traits of both plants and animals, with a general focus on applications of trait-based ecology to conservation problems.  See our QAECO blog here for more details.

Keep checking our main lab blog for more of our Reading Group papers (for our discussion on Restoration Ecology, see here).

Refs:

McGill, B.J., Enquist, B.J., Weiher, E., & Westoby, M (2006) Rebuilding community ecology from functional traits. TRENDS in Ecology and Evolution.

Kearney, M., & Porter, W.P (2006) Ecologists have already started rebuilding community ecology from functional traits.  TRENDS in Ecology and Evolution.

Keith, D.A., Holman, L., Rodoreda, S., Lemmon, J., & Bedward, M (2007) Plant functional types can predict decade scale changes in fire prone vegetation.  Journal of Ecology.

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Mallee, where is?

Following on from my last blog post, ‘Mallee, what is?‘, I thought I would briefly introduce some geographic context to my mallee musings with ‘Mallee, where is?‘…

The Mallee is on Earth, in Australia, in Victoria, NSW, SA and WA.

‘Mallee’ is a vegetation that is typically mapped based on the biogeography of dominant ‘mallee’ eucalypts. It is uniquely Australian, with large tracts of open scrub mallee occurring in north west Victoria, south west NSW, south SA and south east WA.

National Parks in and around the Mallee region

In the east of Australia, the mallee  is restricted to sand plains and sand dunes of the  of the Murray basin, and large tracts of remnant mallee vegetation occur across Victoria, NSW and SA.

In Victoria, good places to see mallee type vegetation are The Little Desert, Wyperfeld, Big Desert and Murray Sunset National Parks.

Sometimes referred to as ‘Victoria’s Deserts’ these parks contain a rich diversity of flora and fauna…. as well as quite a bit of sand.

Sand dunes are a prominent feature of the mallee landscape and are clearly visible from satellite imagery.  The Murray Basin has a complex geological history, but broadly speaking many landscape features visible today  were established in the Pliocene and early Holocene due to marine and fluvial deposition, as inland seas expanded and retreated.

Murray Sunset NP and east west sand dune formations, both clearly visible from sat imagery

I will be mainly working in Murray Sunset National Park, which has a diverse vegetation driven by changing soil types across the region.  What does this look like from the ground? Some major plant families in the area include Myrtaceae, Chenopodiaceae and Myoporaceae … stay tuned for more info on these plant families in future posts.

For now, heres a sampler of some of the plants you might see in this region:

From top left: Lomandra leucocephala (Xanthorrhoeaceae), Eremophila sp. (Myoporaceae), Zygophyllum apiculatum (Zgyophyllaceae), Enchylaena tomentosa (Chenopodiaceae), Maireana sp (Chenopodiaceae), Eremophila sp. (Myoporaceae), Scaveola spinescens (Goodeniaceae), Eucalpytus sp. (Mrytaceae) and Goodenia sp. (Goodeniaceae)

References:
  • Noble, J. C. & Bradstock, Ross Andrew. & CSIRO.  (1989).  Mediterranean landscapes in Australia : mallee ecosystems and their management.  East Melbourne, Vic. :  CSIRO.
  • National Mallee Conference. & Noble, J. C. & Joss, P. J. & Jones, G. K. & CSIRO.  (1990).  The Mallee lands : a conservation perspective : proceedings of the National Mallee Conference, Adelaide, April, 1989.  Melbourne :  CSIRO Australia.
  • White, M., A. Oates, et al. (2003). “The vegetation of north-west Victoria: a report to the Wimmera, North Central and Mallee catchment management authorities.” Arthur Rylah Institute for Environmental Research, Melbourne.
  • For mallee related photos: http://www.flickr.com/photos/cracoo/ and Google Earth.
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Mallee, what is?

mal.lee

I am going to be working in the semi arid north western region of Victoria.
This prompted a question: ‘Mallee, what is?’  Not such a simple question…

‘a mallee’ in ‘the mallee’

Deciding what ‘Mallee’ is, takes you on a research path spanning centuries, climates, sea level changes, survival, cultures, egos, pastoral booms, wars, plant physiology, invasive species, drought, pastoral depressions, technological reforms, social reforms, short term decision making,  innovative solutions, community development and ‘antivelopment’ (made up word, like it?).  Not to mention all the social, agricultural and ecological research that goes along with all of these themes.

Mere  dictionary definitions, might lead you to believe the ‘Mallee’ is something along the lines of:

  • a biogeographic region

    Apparently this is a Mallee Fowl, a giant Mallee Fowl!

  • an electoral district
  • a highway
  • a vegetation association
  • any one of ~27ish eucalyptus species
  • a fowl
  • a footy league
  • a community
  • a CMA
  • a growth habit of some eucalypts

But, these dot points don’t really do it for me.  In my search for the answer to:
‘Mallee; what is?’
I came across one definition that seemed appropriate to capture the vast range of anthropogenic and natural histories and narratives that are associated with this ‘M’ word.
‘The Mallee’ isa unifying theme’.  

Perhaps this answer could be up for debate.  The point is, there would be many people with many different perspectives weighing in on this debate.  And thats what makes this ‘M’ word so darn interesting.

After a recent reconnaissance mission to the north west region of Victoria, I am beginning to see how the general notion of ‘the Mallee’ can get under your skin.
Its vast.  In every sense.

Triodia sp. A characteristic mallee species. The common name is ‘Porcupine grass’ and this one even looks like a porcupine!(!)

What I have found to be certain, is that ventures into ‘the Mallee’, whether in a 4WD, a book or behind a screen, definitely requires filling out a risk assessment form, packing extra water, coffee, an epurb, a few maps and some sustenance (watch out for the fruit fly exclusion zone though).

————————————————————–

I will be doing a fair chunk of my field research in ‘the Mallee’, so you can expect a few more mallee related blogs!  I might have some more answers to add to the list in a few years.

For now, theres plenty of reading to do:

  • Noble, J. C. & Bradstock, Ross Andrew. & CSIRO.  (1989).  Mediterranean landscapes in Australia : mallee ecosystems and their management.  East Melbourne, Vic. :  CSIRO.
  • National Mallee Conference. & Noble, J. C. & Joss, P. J. & Jones, G. K. & CSIRO.  (1990).  The Mallee lands : a conservation perspective : proceedings of the National Mallee Conference, Adelaide, April, 1989.  Melbourne :  CSIRO Australia.

The Mallee = Blue + Red






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Introducing… Thelymitra

A very “un-orchid like” orchid

Who is mimicking who? The two Thelymitra species are the mimics.

In my last blog, I introduced the concept of floral mimicry and left you with the tantalizing question: Who are the models and who are the mimics?

I am pleased to introduce you to Thelymitra, an orchid genus packed full of mimics.

Thelymitra ixioides

The genus Thelymitra contains terrestrial deciduous orchids that are widespread across Australasia.

Notable features of Thelymitra include a strongly actinomorphic perianth (all the tepals are the same colour and shape) and that the genus lacks distinct labellum ornamentation that so many other orchid genera possess.

All the tepals of Thelymitra look similar compared to other orchid genera, which tend to have a highly modified main tepal.

It is considered an unusual genus within the Orchidaceae, largely due to the prevalence of this very “un- orchid like” morphology (Dressler 1981).

The distinguishing feature used to characterise between species of Thelymitra relates to the central column structure. The column is produced from the fusion of the style, two staminodes and a single fertile anther.

Thelymitra aristata flower and column structures. P = where the orchid pollen is, S = stigmatic surface. Don’t worry about the other labels. All photos by Freya Thomas.

Most species have flowers that are blue/purple, an unusual colour for terrestrial orchids though a few distinct colour morphs exist such as red and yellow (Jones 2006).

Thelymitra iconically display nastic movements, which has influenced the common name for this genus of ‘Sun Orchids’. The flowers typically open on bright sunny days; the length of time that flowers are open differs between species (Jones 2006).

Thelymitra is a prominent food deceptive genus in the Australian Diuridae and all species are rewardless (Jones 2006). The symmetrical form, together with its lack of reward and close resemblance too many Australian lily-like taxa, suggest that many Thelymitra species are food deceptive mimics of local, co-blooming and pollen rewarding guilds (Bates and Weber 1990).

Thelys

References:

Dressler RL (1981) Biology of the orchid bees (Euglossini). Annual Review of Ecological Systematics 13, 373 – 394.

Bates RJ, Weber JZ (1990) Orchids of South Australia. (South Australia Government Printer: Adelaide).

Jones DL (2006) “A complete guide to native orchids of Australia, including the island territories‟. (Reed New Holland: Sydney).

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