Our research focuses on the population dynamics of plants and how they are influenced by impacts of natural disturbances and global environmental change. We are particularly interested in the interactive effects of fire, grazing and drought in grasslands and woodlands in southern Australia, and how climate change, fragmentation and shrub encroachment affect ecosystems.

Monday, 31 December 2012

Keeping up-to-date in ecological research

It's hard to keep up-to-date with all the new ecology that is being conducted across the globe. Not only is there precious little time to read scientific papers, scan journals for interesting work, and do research, but the sheer volume of material being published means that many interesting research papers will slip by. This is a shame, because it forces us to narrow our search focus when we do read papers.

So, I have started to use Blogs to keep up to date with ecological developments. I started my own Blog because I wanted to communicate about the research we do in my Lab, and to comment on ecology more generally. It's been almost two years since I started, and I've had 15,000 page views. So, I guess someone finds this stuff interesting! Assuming that others share the same philosophy, I started to scan for Blogs that summarised new papers in the general area of Ecology and Evolutionary Biology and came across The EBB and Flow: blogging all things ecology and evolutionary biology. This is a really neat Blog. It's big on reporting about papers that focus on ecological theory (which we should use as the basis for all our investigations) - under the 'Research Focus' tab. The most recent Blog on a new paper by Jonathon Levine about how coexistence theory can help inform community assembly makes a difficult/challenging topic palatable.

EBB and Flow also has excellent sections on 'Conservation Focus', 'Academic Life' (which PhD students will find really informative, 'Career Corner' (ditto), 'Meeting Dispatches', 'Recent Papers of Interest' and the excellent 'Researcher Spotlight' that send the reader off into weird and wonderful (and more importantly, relevant) ecological territory. It's well worth bookmarking!

Happy New Year!

Saturday, 22 December 2012

Ecology Apps.....for Christmas?

I've just upgraded my mobile phone and got myself a smartphone. My Grad Students would perhaps say it's about time I got into the year 2012 (which is not so great given it'll be 2013 in a little over a week). It's not that I don't like technology; rather, I'm a slow adopter. My current phone works fine, and I do hate the idea of consumerism.

But, I've bitten the bullet. One of the reasons was that Nick Bell, a Summer Research Student working on our long-term ecological plots examining alpine vegetation change, recently showed me how useful smartphones can be for the average field ecologist. While he was talking to me about technology stuff that seemed to be based on the English language, he showed me two simple Apps that I might find useful.
Nick talking to John
(thanks to Calvin & Hobbes)

One was an app to help measure tree heights (Smart Measure). Having recently done this with Nick in the field the old fashioned way - tape measure, compasses, pythagoras' calculations - this seemed really simple and effective. Then, he showed me how you could ghost an image on the screen while trying to re-take the same image. This would be awesome for my re-photography work that I am currently undertaking, comparing photos from the 1930s with the current day.

Measuring tree height is easy. Right?
Source: http://www.nativetreesociety.org/measure/tree_measuring_guidelines.htm

I went away and started to do some research. Not on getting a smartphone, but on the apps that I could use in ecology. Very quickly, I was thinking "hmmm, there's a lot of technology available that is cheap, accessible, and that I've totally overlooked".

One of the sites I found was Emilio Bruna's excellent 'Mobile Ecology' webpage. This page lists a bunch of apps for research, teaching and outreach (with a US emphasis, so I guess I'll have to look for the Australian equivalent). If you're interested in such things, it is well worth a look. My favourite was the app called RInstructor - this looks like something that will really facilitate my learning and use of R, particularly how to customise plots.

So, with Christmas coming up, I might just have to treat myself and upload (or is that download) a couple of these apps to see whether my investment in a new phone was actually worth it! In any case, I can see great potential in this technology to help me facilitate my data collection and efficiency in the field.

Merry Christmas, and best of wishes for the New Year. I look forward to writing more about plant ecology in southern Australia in 2013.  JOHN

Friday, 7 December 2012

Fire in south-east Oz - 'new' things to observe

I've just returned from the annual meeting of the Ecological Society of Australia, this year held in my home town of Melbourne. As usual, there was a great mix of student presentations, challenging plenary talks, and ample time for discussion during the breaks.

One thing that struck me was the number of talks I saw on fire. There was a whole symposium dedicated to fire, which was very well-attended. I also saw talks scattered through the programme that dealt with the impacts of individual fires, the regeneration biology of key species, the importance of fire return interval, why fire severity matters, etc, etc.

This is not surprising given that south-eastern Australia is one of the most fire-prone areas on the globe. It is a recurrent feature in many ecosystems, and is projected to increase in frequency because of climate warming over the coming century. Additionally, it is also a contentious issue - the management of bushfire threat in SE Oz revolves around policies that mitigate risk by hazard reduction burning.

Two important issues arise - how often should it occur in an ecosystem (both as a tolerable event and as a desirable disturbance to cue important ecological processes such as seed germination). Second, what type of fire event is likely to have positive or negative impacts on these outcomes.

I've been musing about these questions for the last few weeks, but from a different perspective. And it returns me to one of my favourite pasttimes: observations in ecology.

While fire is a recurrent event throughout much of SE Oz, there are indeed very long fire-free intervals for some parts of the landscape. We intuitively know this. In the rainforests of eastern Victoria, fire is probably fairly rare - perhaps in the order of hundreds of years apart. But what is probably less appreciated is that in the drier, less productive parts of central Victoria, perhaps fire is also equally as rare.

How can I make such a statement?  What evidence do I have for one of the most fire-prone areas of the world having very long fire-free intervals. Well, that is where observation comes in. In the dry, eucalypt-dominated woodlands of north-central Victoria, around Rushworth to Wangaratta, there is a clue on the upper slopes and rocky outcrops. It's a pretty obvious clue when you think about it.

Here, there is a plant that is born to burn (or so it would seem). Grasstrees, in the genus Xanthorrhoea, are arborescent monocots, developing tall stems that allow them to grow to great heights. We know they grow very slowly. Let's focus on X. glauca. For the first 50 yrs, plants consist of leaves but no stem. The stem then emerges and height growth is about 10-25 mm per annum. My old PhD student Peter Curtis measured growth rates over 10 years, so this seems a pretty reasonable estimate. So, a plant 3 m tall might be anywhere up to 350 years old. Each year, the leaves die but are held appressed to the stem rather than shed. In unburnt grasstrees, this 'skirt' can extend all the way along the 'trunk' to the ground. When a fire occurs, the 'skirt' is a ready-made fuel source to rapidly burn the plant - a quick fire where most heat is carried rapidly away from the meristem by convection. Plants generally survive burning, although Peter's work does show that mortality of grasstrees can be quite substantial in the decade after fire. But that is another story..........

Burnt Grasstrees, Rushworth State Forest, October 2012
(Photo: Michele Kohout)
I've been wandering around the bush, observing something recently. In the last few years, many tall grasstrees have been burnt as part of new 'targets' set by the State Government - hazard reduction burns. This, in itself, is notable because many areas of bush being burnt clearly have not been burnt for centuries. How do I know this?

Well, old photos tell us so! Here are some images of grasstrees in the Warby Ranges - taken in the early 1980s by the well-known fire ecologist David Cheal - that are notable for (a) their enormous height (up to 8 m perhaps) and (b) the fact that they have grass skirts that extend all the way to the ground. This suggest that this part of the landscape has not been burnt for upwards of 600 years. Hence, we are not talking about fire suppression since european settlement. And it is not just one or two individuals, but entire slopes, suggesting that fire is very uncommon here. On recent inspection, it is hard now find examples of these great unburnt plants. Low intensity fire has seen to that.

Grasstree in the Warby Ranges, 1983. Note the scale (approx. 1.75 m)
and dead leaves all the way to the ground. The trees in the background
have not been burnt. Rather, they are dying from intense drought.
(Photo: David Cheal)
Grasstrees, all with skirts that indicate long intervals between fires, across a slope at
the Warby Ranges, 1983. Plants are approx. 2.5 m tall.
(Photo: David Cheal)
Long unburnt Grasstrees, Rushworth State Forest, 2012. Scale approx. 40 cm.
(Photo: Michele Kohout)

The lesson here, if there is any, is to observe patterns in nature. The simple observation that grasstrees in some parts of the range (low productivity, rocky) have not experienced frequent fire is probably very important, particularly when thinking about fire return intervals. While low intensity fires may seem ecologically benign, this needs to be put in the context of the fire history of the site.

It also challenges our notion that dry forests burn frequently simply because they occur in a part of the continent where fire is known to occur regularly!

Monday, 5 November 2012

The basics of repeat photography

The photo below, taken in 1979 by La Trobe University botanist Neville Scarlett, is of one of the best remnants of native grassland near Melbourne called Truganina Cemetery. I know this site really well as I did some of my Honours thesis research there, on the recruitment ecology of the Button Wrinklewort.

What is great about old photos is they convey information about the historic state of systems, well before many of us were involved in management and research, and they potentially allow current condition to be compared to prior states. Clearly, this grassland had a high cover of forbs in 1979. The silver coloured vegetation is probably the Lemon Beauty Head (Calocephalus citreus), the yellow flowing daisy is Chrysocephalum apiculatum, while the white sprays are mostly Bracyscome dentata in the background, with Stackhousia (Creamy Candles) in the foreground. While tussock grasses (Themeda triandra) are obvious, they certainly don't dominate. You get the impression this was much closer to a herbfield than a grassland.

Truganina Cemetery, spring 1979
(Photo: Neville Scarlett)

I thought it would be great to take an up-to-date shot of the same location to see how things have changed over the last 30 years. Truganina Cemetery is well-known as an important grassland remnant (it has two nationally endangered species present) and it is managed by irregular burning, while vehicle access is prohibited. Armed with a tripod and digital camera, I went out a few weeks ago to capture the same shot. Below is my effort to replicate Neville's original shot.

Truganina Cemetery, spring 2012
(Photo: John Morgan)

Two things are obvious. Firstly, and probably most obviously, it is clear that much of the colouring afforded by forbs in 1979 has dramatically declined, indicating their cover and abundance has likely diminished by an order of magnitude or more. All four species that I mentioned as obvious in the original shot are still present, so what we are looking at is a dramatic change in species evenness rather than local extinction. We could visualise these changes by constructing a rank-abundance curve, plotting the percent cover of species from most common to least. This would hint that dominance has shifted completely from a multitude of forb species to one native grass, and that forbs are mostly now at very low cover.

Secondly, I found it really hard to re-take the orginal shot. In this case, I don't think it mattered hugely because the magnitude of the change is so great. But, it got me thinking about how I might go about doing this better next time. Using old photos to assess environmental change is becoming increasingly popular in environmental science. Part of this, I suspect, is that old photographs are now being scanned and stored in archives such as the excellent one called TROVE (curated by the National Library of Australia). Hence, how might one go about doing this accurately?

The field is called "repeat photography" or "re-photography". It seems that a pretty common method is indeed just walking out to the same spot and taking the same photo. But then you want to match the conditions as well as possible. There's a lot going on with seasonal variation and time of day in terms of shadow length. Visual parralax is the key to the basic technique; you can get pretty close to the same location by comparing rocks and details that are partially obscured by objects in the foreground... but this does not give you exactly the same picture, just something that is clearly the same viewpoint of the same landscape. Part of the problem here is that an oblique perspective creates a continuously varying scale and this makes it hard to link landscape features in the photograph to absolute spatial co-ordinates.

A good starter is Methods in Re-photography: A Research Method for Amateur Researchers. This has some really excellent background on the scientific relevance and utility of the technique, and a very quick'n'dirty guide to the fundamentals. Apparently the bible on the method is called Repeat Photography: Methods and Applications in the Natural Sciences,edited by Webb et al..

It is pretty clear that matching photos can be a powerful means of comparing local changes in vegetation, particularly when photographs extend well back in time. Aerial photographs are great for the same reason, but most don't extend beyond the 1940s in Australia, so repeat photography has great merit to address small-scale, long-term change. I'll leave you with the nice example below by Roush et al. (2007) that compares the alpine treeline ecotone in Glacier National Park in 1930 with that in 2003. Note the massive invasion of trees across the entire landscape!


Roush, W., Munroe, J.S. and Fagre, D.B. (2007) Development of a spatial analysis method using ground-based repeat photography to detect changes in the alpine treeline ecotone, Glacier National Park, Montana, U.S.A. Arctic, Antarctic and Alpine Research 39, 297-308.

Wednesday, 24 October 2012

Is the tide turning on using locally collected seed for restoration?

Planting Buloke trees on the heavily cleared Wimmera plains
of western Victoria. (Photo: John Morgan)
One of the central tenets that seems to underpin ecological restoration activities in southern Australia, and elsewhere in the world (like the prairies of the USA),  is that propagules should be collected from local populations of the indigenous species that will re-introduced to a site. Defining 'local' has always been a bit of a contentious area because it speaks to the issue of collecting local genotypes and these have largely unknown distributions.  In practice, it roughly translates to collecting seed from close geographic proximity of the planting site.

The two most common explanations that are used to justify / defend this approach are that (i) local seed produces plants that are best adapted to the revegetation site (the 'local adaptation' hypothesis) and (ii) using local seed reduces the risk of causing outbreeding depression (i.e. the introduction of novel genes that will swamp the local genotype). I, too, have tended to use these concepts to underpin my thinking on this issue. But, on reflection, I've started to change my mind on this, for two reasons.

The first is a fairly simple reason. Temperate grasslands in southern Australia have been reduced by more than 95% and hence, the scale of the restoration problem is enormous. Quite frankly, seed availability will constrain our ability to restore this system and we must think more broadly if we want to meaningfully reverse the decline. This means having to collect seed from a wider area (there are simply too few remnants nearby to supply seeds in this severely fragmented landscape) and creating seed orchards to rapidly bulk up seed numbers. Additionally, I have a bit of an ethical dilemma with sourcing local seed off tiny populations; this probably imperils their capacity to survive in the future, and I have grave concerns about this as indirect (maybe even direct) cause of local population decline.

Swainsona spp. are now extremely rare in grasslands.
(Photo: John Morgan)

The second reason I've started to change my mind about the imperative of using local provenance stems from new research that I've been following over the last few years. Two papers caught my eye and I think they are worth sharing.

Hancock et al (2012) experimentally test the idea that plants grown from locally-sourced seed have the advantage of being best adapted to local conditions compared to seeds sourced from further away. Using a common garden experiment, they planted six common species native to woodlands near Sydney, Australia (but with broad distributions down the east coast of Australia) and compared survival, growth and flowering for plants sourced from 'near' and 'far' from the planting sites. After both 7 and 24 months, they found very little evidence that local provenance plants were superior to distant provenances in terms of survival and establishment. Hence, there was little evidence to support the use of local seed, perhaps because these are widespread species with genetically-connected populations. Such an outcome might also relate to the grasslands of southern Australia that were once extensive, connected, and spanned relatively similar climates and soils. Local adaptation is more likely to be important when a species occurs across a strong environmental gradient (such as with altitude). Locally-sourced seed is likely a much more important concept under these circumstances.

Sgro et al (2010) provide a really compelling overview of the concept of building evolutionary resilience into restoration plantings, and why locally collected seed might do more long-term harm than good in the face of rapid climate change. I recommend you read this paper if you are interested in the role of genetics, evolution and adaptation in restoration. It is certainly thought-provoking and one of the most interesting papers I have read this year. You may not agree with it, but it'll certainly challenge you.

A couple of things caught my eye about their paper. Cutting and pasting the crux of the matter, Sgro et al. suggest that:

"The long-term aim of genetic translocations (i.e. use of non-local provenance) is to create populations that harbour the adaptive genetic diversity to enable ongoing adaptation to the environmental changes caused by climate change and other threats. This helps to obviate the need for ongoing intervention and management, ensuring evolutionary resilient populations."

"A ‘local is best’ sourcing practice misses two important points, which may seriously impact restoration or reintroduction outcomes in the face of future climatic changes. The first potential problem with ‘local is best’ recommendations is that there is a risk of encouraging the establishment of populations that do not harbour sufficient genetic variation and evolutionary potential [i.e. establish genetic ghettos]. In addition, strict adherence to ‘local is best’ protocols may encourage the selection of inbred or genetically depauperate seed sources, when genetically healthier sources further afield may produce a more efficacious restoration result. This may serve to perpetuate the number of small inbred populations across highly degraded landscapes that are unlikely to persist in the long term."

Sgro et al. (2010) then provide an interesting recommendation for seed collection protocols to preserve evolutionary resilience by focusing on 'composite provenancing' - the idea that a small amount of seed from distant sources should be included in seed mixes (comprising mostly local seeds) to enhance gene flow that may bring in additional adaptive or beneficial genes.

Recommendations for provenancing based on dispersal distance from parental plant (Figure 3 from Sgro et al. 2010) 
At some levels, this type of discussion makes me think long and hard about what is important regarding conservation of highly modified native ecosystems such as grasslands. Saving the components of the ecosystems (their species) has to assume the highest priority, and if this requires genetic translocations, assisted migrations, and challenging long-held ideas about local provenance, then I am open to this idea. What about you?

Hancock, N., Leishman, M.R. and Hughes, L. (2012) Testing the 'local provenance' paradigm: a common garden experiment in Cumberland Plain woodland, Sydney, Australia. Restoration Ecology doi: 10.1111/j.1526-100X.2012.00931.x

Sgro, C.M., Lowe, A.J. and Hoffmann, A.A. (2010) Building evolutionary resilience for conserving biodiversity under climate change. Evolutionary Applications 4, 326-337.

Sunday, 14 October 2012

Nutrient Network Update

I've just returned from a couple of days in the field (with a sore back and a bad dose of hayfever). But, excitingly, it completed the sixth year of surveying as part of a project that looks to examine the controls on diversity in grassy ecosystems, as part of the global Nutrient Network study.

This project now has >60 sites in grasslands across the globe (see http://nutnet.umn.edu/), with four in Australia: Kinypanial (a semi-arid grassland in southern Australia that I manage), Bogong (alpine grassland managed by Joslin Moore and myself), Mt Caroline in Western Australia (Suzanne Prober) and Burrawan in Queensland (managed by Jennifer Firn and Yvonne Buckley).

Bogong NutNet site
Burrawan NutNet site
Silwood Park NutNet site, England

Our main questions are:
  • 1) what are the relationships between diversity and productivity? This is an old question in ecology, with much hot air generated in the process about humped-back relationships, that we have addressed using our observational data. This resulted in the paper by Adler et al (2011) in Science.
  • 2) are grasslands limited by multiple nutrients or one? This is being addressed by factorial field experiments where we add N, P and K singularly, and in combination. At Kinypanial, productivity is definately co-limited by N and P. Each nutrient, when added alone, has rather minimal impacts on productivity and diversity, but when added together, leads to a profound shift. Indeed, most of these plots (and the NPK plots) have been transformed from a native system to one dominated by the exotic annual grass Avena barbarta after 5 yrs of nutrient addition. Plots sown with N, P and K alone have a remarkable resilience to change. I was not expecting this.
  • 3) is diversity controlled by nutrients (bottom-up processes) or herbivores (top-down processes)? In my sites, it definately seems that bottom-up processes rule, probably because native herbivores have been lost from many Australian grasslands (e.g. kangaroos, bandicoots, wombats) and hence, their current impacts on vegetation are minimal. This is not so true elsewhere in the world where large animals are still part of the natural system and they eat most of the biomass.

Eric Lind, the post-doc on the project, has just been interviewed on the Journal of Ecology Blog and explains the process of running a multi-site, global project with common aims. It's a good explanation of what we are doing and how NutNet can be (potentially) seen as a great model for successfully running such meta-analyse projects with standardised protocols. And the fishtank in the background is a nice touch!

You can see Eric at http://jecologyblog.wordpress.com/2012/10/12/interview-with-eric-lind-on-the-nutrient-network-nutnet/

In the current climate of declining research funding in Australia, multi-site network studies enable me to contribute to some of the big questions in ecology. The opportunity to ask 'big picture' questions, and collaborate with lots of smart people, has really opened my eyes as to the way I do science.

More soon.

Wednesday, 12 September 2012

Wandering the Plains

One of the things I really enjoy is spending time in nature, observing.

And thinking. And observing some more. These are the fundamentals of doing ecology - figuring out the patterns in nature and the mechanisms/processes that underpin them.

And, it's the reason I got interested in ecology in the first place. Long before I knew anything about a GPS, or a Mixed Effects Model, or a molecular phylogeny, or a Powerpoint Presentation, I was interested in plants - their form and function (we'd now think of that as plant functional traits) - and their capacity to grow in interesting patterns (we'd probably call that species coexistence) and the controls of their seedling recruitment (that has always been called the regeneration niche). And, in many ways, that is still what drives my curiousity. Of course, that is now underpinned by ecologial theory and experience.

But the basics remain the same. A few days ago, I spent some time looking at semi-arid woodlands in northern Victoria in an area I'm not all that familar with.  I visited a new Trust for Nature conservation reserve - Wanderer's Plain. And I was struck by how little I knew about the vegetation patterns in this area. There were stark changes from grassland, to woodland, to forest but I wasn't quite sure what was going on.

So, I made some notes and, married with photos, started to unravel the story.

At any new site I visit, I have a little checklist of things I ask myself: how does the topography change? How does the overstorey change? How does the understorey change? How does the soil change? By running through this list, I can start to arrange the components of the landscape into some sort of order. My geomorphologist friend Neville Rosengren calls this 'being able to read the landscape'. While he's looking at rocks and landforms, such a concept is equally applicable to the vegetation.

There were very subtle rises in the landscape, many no more than 100 cm above the surrounding plain, forming ribbon-like bands at semi-regular intervals. Here, the soils were sandy, a sure sign of some aeolian deposition from soils brought from the desert country to the north-west. On top of these rises grew Acacia melvillei (in full flower), but it was largely restricted to this area. Presumably the drainage here is excellent, and the fertility low.

Acacia melvillei in full flower, September 10 2012
(Photo: John Morgan)

Fringing the Acacia is Buloke and tall native grasses
(Photo: John Morgan)

Fringing the Acacia band was an interesting zone of Buloke trees and tall C3 grasses. This occurs at the base of the sandy rises and a short distance into the plains, and I presume is a sort of run-on zone where water and fertility are both more readily available. Soils are likely to be better drained here than on the plain which appears to be composed of clays with very little topographical relief.

Away from the trees are native grasslands - flat and relatively featureless. But there is something going on. The grasslands here were looking spectacular. In large areas, the white-flowered Minuria leptophylla was the dominant herbaceous species. And, in other areas nearby, the yellow flowered annual daisy Hyalosperma semisterile was the dominant species. And rarely was there any co-dominance.
Hyalosperma semisterile - wildflower heaven!
(Photo: John Morgan)
Hyalosperma in the foreground, Minuria in the background
(Photo: John Morgan)
Minuria leptophylla
(Photo: John Morgan)

Why these two species don't co-occur much has been baffling me. Both occur in flat areas with well-developed cryptogamic soil crusts and few tussock grasses. Maybe there are subtle differences in water flows and availability that are not immediately obvious to the eye. Indeed, on inspection of my photos, it looked like Minuria occured in a zone closer to the trees than Hyalosperma. Perhaps soil depth, water and litter flows from the tree zone contribute to this pattern. Or perhaps it's a straight competitive interaction - annuals need an area where resource competition is low to complete their life cycle in four weeks or so here. And so this is, by default, away from the run-on areas dominated by tall grasses.

It suggests the way forward is an experiment. Another of my favourite ecological activities. Perhaps a seed sowing experiment, crossed with resource manipulations, to get to the heart of the patterns I've seen. And, undoubtedly, this will raise even more questions!


Friday, 24 August 2012

Serotiny, undergrads, and generality in fire ecology

Cape Conran, August 2012
(Photo: John Morgan)
I've just spent a delightful four days in coastal vegetation at Cape Conran (about 5 hrs east of Melbourne) with my undergraduate ecology students. Here, there are warm temperate rainforests in deep gullies, tall forests on very old sand dunes, and coastal heaths fringing the margin of the coast. All are subject to fire, but have very different regimes. And fire is being used as a management tool to maintain (perhaps even maximise) plant diversity. This provides an excellent opportunity to ask questions about how plants and plant communities respond to fire.

I find teaching in the field, in small groups, a really satisfying way to train budding plant ecologists. I'm of the opinion that most undergrads learn through their eyes, and by getting their hands dirty! So, last week, I split the students into groups of six, and posed each a research question related to fire ecology. The aim was to make some observations that inform a question, make some predictions, design a study, collect data, collate and interpret that data, and make some statements about what had been found. This is something many of us do every day, but clearly it has to be taught (and learnt!) by students new to the field.

Happy students in recently burned sandplain heath
(Photo: James Shannon)
Surprise, surprise, the students quickly found that ecology isn't as easy as they had thought it might be! And interestingly, the first explanation from an undergrad is "we must have done something wrong" or "because we are undergrads, we are not very good". Nothing could be further from the truth. Undergrads and post-grads often collect meticulous data (down to three decimals points) when the bucket and spade approach would have been fine. Rather than this being an issue about the veracity of the data, it hints about the complexity of nature and our ability to accurately predict/forecast that complexity.

One of the biggest challenges our discipline faces is to develop generalities that might apply across taxa, communities, ecosystems. We've all conducted research where the results are contingent on the study system under examination. Or where opposing results are found across sites due to unknown site history factors. This might be something we accept as the 'norm' and keeps us endlessly asking questions about the natural world. But, it is a major challenge for students trying to understand the contribution they might make to the field, and to managers needing advice about the conservation management and restoration concerns that occupy them daily.

As an example of the challenges faced by my undergrads, one project looked at serotiny in the genus Banksia (Proteaceae) with an eye to thinking about the implications for fire management. Serotiny is the term used for seeds that are stored in fruits for extended periods of time (usually years) and then released spontaneously by an event. Triggers for this release include:
  • Wetting (hygriscence)
  • Warming by the sun (soliscence)
  • Drying atmospheric conditions (xeriscence)
  • Fire (pyriscence)
  • Fire followed by wetting (pyrohydriscence)
Fire is the most common and best studied case of seed release in Banksia and, at Cape Conran, is  likely the trigger for seed release from follicles in three species that exist within close proximity (B. marginata, B. spinulosa, B. serrata). I challenged my students to design an experiment to test the idea that Banksia species have a similar responses to fire with respect to seed release.

This is what happens when you heat Banksia
infructescences at 500 deg C for 2 mins.
From top: B. serrata, B. spinulosa, B. marginata.
(Photo: Susan Hoebee)
Using a muffle furnace, they did a terrific job of teasing out the effects of duration of heating vs. maximumum temperature of heating. What was clear from their impressive data on follicle opening and seed viability was that each species responded in an individualistic manner. Banksia serrata folicles remain 100% closed when heated at 150 deg C for 10 mins while 80% of B. marginata follicles opened under this regime. B. spinulosa was somewhere in between. Hence, while these Banksia are all serotinous, they seem to differ in the type of fire event that will be necessary to ensure follicle opening and hence, seedling recruitment. The implications of this work are clear: three Banksia species at Cape Conran will respond to fire in subtley different ways and hence, we can't assume that one fire type will benefit/disadvantage these species in the same way. Perhaps this is the generality that we can draw from this study?

To me, one way to bridge this 'uncertainty' about data and, why it varies, is to emphasise and adopt proper sampling design in all our studies. This is not a new idea but rather, a call to remember what constitutes sound, evidence-based research. This may reduce some of the uncertainty that is generated by conflicting ecological studies - are the differences due to poor experimental design or real population differences?  I recommend you read the essay by Downes (2010) to brush up on sampling design and its importance in ecology, as well as how to deal with questions that aren't always amenable to experimentation.

Downes, B. (2010) Back to the future: little-used tools and principles of scientific inference can help disentangle effects of multiple stressors on freshwater ecosystems. Freswater Biology 55, Supplement s1, 60-79.

Tuesday, 31 July 2012

What is grazing in native grasslands actually trying to achieve?

In 2003, Josh Dorrough at the Arthur Rylah Institute established the Long-term Ecological Grazing trial (LTEG), a study where three native grasslands across western Victoria - all with a history of grazing by sheep - were selected to examine how manipulating grazing regimes could be used enhance conservation outcomes.

At each site, there were six grazing treatments, each replicated three times. Apart from continuous grazing, and grazing exclosure, the other four treatments tested for the effects of (a) season and (b) duration of grazing. You can read about the results of the initial findings (to 2007) in Zimmer et al. (2010) Forb responses to grazing and rest management in a critically endangered Australian native grassland ecosystem. The Rangeland Journal 32, 187-195.

This grassland is not grazed in spring ('spring rest'), June 2012
(Photo: Michele Kohout)
This grassland is never grazed ('always rested'), June 2012
(Photo: Michele Kohout)
This grassland is always grazed ('never rested'), June 2012
(Photo: Michele Kohout)

I'm lucky enough to be using the study at 10 years after the plots were established to look at longer-term impacts of manipulating grazing regimes on native grasslands (with my new student Kaitlin Wright). The plots are the longest running trials in southern Victoria addressing the question: can strategic grazing  improve/restore threatened native grasslands? At 10 yrs, the plots have been through one of the longest and most intense droughts in Australian history, and plant community dynamics that were not evident in the first 4 yrs (the funding cycle) are likely to be much more apparent now.

My first task is to figure out what indices I would use to describe the changes that have occurred over the last decade.

Traditionally, you would monitor species richness (more correctly, this is species density - the number of species per unit area). Ecologists call this alpha diversity. You might specifically want to know about native species (hopefully they wouldn't go down) and the number of exotic species (hopefully they wouldn't go up). This seems (to me) to be one of the major objectives of the use of conservation management by grazing. So let's state it here: grazing maintains (or enhances) native species richness at the expense of exotic species richness/cover.

But what else matters. How might grazing be used to effect other (positive) change in grasslands?

 It's clear to me that we could enhance the understanding of vegetation change through time by grazing if we consider aspects of spatial heterogenity and spatial and temporal turnover. Do certain grazing regimes enhance spatial heterogenity? If so, you might think that beta diversity might increase. Hence, let's state this hypothesis: grazing (either duration or season) can be used to enhance spatial variability, leading to positive outcomes for native plant diversity because it enhances niche variability. By enhancing variation in structure (with consequent effects on nutrient fluxes, light and moisture), deterministic processes may have greater impacts on species patterning than currently operate on grazed grasslands.

I've been giving some thought about what you'd really try to achieve by shifting regimes or disturbance types. And I've come up with three motivating questions illustrated in the slide below. I can't take credit here - my NutNet collaborators in the USA (Ellen Damschen, Peter Adler and others) are asking similar questions about grassland response to nutrient addition and grazing, but their approach seems relevant to grasslands in western Victoria too! In all cases, I think there is more to be gained than just looking at the number of species. Does continuous grazing homogenise grasslands and can we manipulate aspects of variability (in space and time) to promote positive community responses. If not, why not? Does grazing reduce exotic species cover regardless of richness responses? What do you think is important?

Sunday, 15 July 2012

Population variation in germination of semi-arid shrubs in response to water availability

Staying with the recent theme of seed germination that I have been exploring in recent posts ........  I thought I'd update you on a new project I'm starting.

Germination of semi-arid plants is usually cued to rainfall which is unpredictably distributed across years. Plants must cue their germination to rainfall events that are heavy enough to ensure sufficient moisture for seedling emergence and survival; hence, it is thought that this cue is moisture availability. In variable environments (i.e. drier systems with a large coefficient of variation in mean annual rainfall), it is predicted that a smaller fraction of seeds from a population will germinate at any one timeafter rainfall compared to species whose populations have evolved in more mesic or predictable environments (i.e. systems where the mean is higher and the coefficient of variation is lower). Despite this fairly simple hypothesis, it has not been well studied in Australia, reflecting the gap in fundamental autecological research that exists.

Temporal variability in the environment affects the evolution of life history characters and, as such, leads to population differentiation in traits such as germination. This is called adaptive bet-hedging but this ecological theory has rarely been tested in Australia. Understanding how germination varies with environment within species, and across populations, is also critical for understanding the adaptive potential of species to deal with changing climates in situ and hence, the question of bet-hedging has much applied as well as theoretical interest.

Maireana brevifolia
Maireana decalvans
I am starting a project to determine whether seeds of semi-arid shrubs (in the genera Atriplex and Maireana) sampled from populations in xeric environments have lower germination fractions (at all moisture regimes) than seeds sampled from more mesic populations.

To do this, we will study the lab germination of several populations of semi-arid shrubs that have been collected across a strong climate gradient from southern NSW. This climate gradient represents a temperature, rainfall and evaporation gradient. Seeds will be counted into replicate seed lots and exposed to a range of experimental conditions to see if (a) xeric populations exhibit lower germination fractions than more mesic populations and (b) whether variability in germination is most affected by population differences or is outweighted by environmental conditions.

If you are interested in bet-hedging and seed germination, these paper give a nice entry into the field:

Clauss, M.J. & Venable, D.L. (2000) Seed germination in desert annuals: an empirical test of adaptive bet hedging. The American Naturalist 155: 168-186.

Facelli, J.M., Chesson, P. & Barnes, N. (2005) Differences in seed biology of annual plants in arid lands: a key ingredient of the storage effect. Ecology 86: 2998-3006.

Friday, 29 June 2012

Seeds, germination and climate change - optimums or extremes?

With changing climates, particularly drying and warming, how might plant species respond? If species are to persist in situ, or disperse to new habitats, then the fate of seeds becomes crucial to this outcome. The sensitivity to temperature at the germination phase will likely be one important predictor of a species' ability to respond to a rapidly changing climate.

Seeds come in all shapes and sizes. They are they starting point
for dispersal into new habitats, and the maintenance of plant
populations for many species. Understanding how seeds germinate in response to
climate change will be critical for interpreting their ecological resilience.
(Photo: John Morgan)

The underlying assumption here - about climate change and the temperature sensitivity of seed germination - is, in part, a question about niche breadth.
Species with "narrow" niches are thought to germinate over a narrow range of temperatures and this means that these species are the ones most likely to find a changed world difficult to deal with, particularly in the absence of dispersal. 

By contrast, species with "broader" niches have germination that occurs over a greater range (i.e. the mean has a large standard deviation around it). Hence, if we identify species which possess narrow temperature germination ranges, we may be able to identify those species more susceptible to rapid environmental change.

Seems simple - develop a screening protocol, use a temperature gradient plate to quickly assess germination niche breadth for a large number of species, and identify species with narrow versus broad temperature germination sensitivity.

Niches are, by definition, where R>0 (i.e. births>deaths, regardless of performance). Where R=0, the edge of the niche has been reached, and where R<0, we are outside of the niche. Hence, when assessing seed germination versus temperature, the "optimum" temperature for germination is not actually the most important component of the niche but rather, what happens at the temperature extremes is much more important - identifying whether these species have temperatures where germination is zero defines niche space better than optimums. This is rarely done in most germination studies, partly because scientists are limited in the number of germination cabinets they can use to assess sensivity to temperature at any one time. In my case, I have access to about five growth cabinets. Hence, the value of the temperature gradient plate to assess a large range of temperatures simultaneously!

Temperature Gradient Plate - capable of 192 temperature combinations!

At the edges of the temperature range for germination is where niche expansion is most likely. New sink populations are much more likely to develop from source populations from individuals at the extremes of the niche space (as defined by temperatures) than from optimums. Hence, whilst we might find that species germinate less well at higher (or lower) temperatures than some optimum, the interpretation about temperature extremes for germination should take on more than just statistical significance to us; germination at these extremes of the temperature range is the raw material for future niche expansions. Most authors tend to ignore this and still focus on identifying optimum germination temperatures.

Two papers recently caught my eye and serve as good examples of how we might study fundamental germination processes to help understand potential responses to climate change. The paper by Ooi et al (2009)
Climate change and bet-hedging: interactions between increased soil temperatures and seed bank persistence is one of the few I have seen that explicitly tests whether warmer soils will have implications for germination and the persistence of soil seed banks. It's worth reading if you're interested in how plant population processes underpin responses to climate change. You should also check out the excellent paper by Cochrane et al. (2011) on germination in restricted rocky outcrop species from Western Australia as a good example of narrow versus broad germination strategies, and what this might mean for responding to a warmer world.

Saturday, 16 June 2012

Recent improvements to native grassland conservation

Native grasslands are one of the most endangered ecosystems in Australia. More than a century of agricultural use, coupled with increasing urbanization, has reduced these once abundant ecosystems on fertile soils to distinct rarities. In some areas, much less than 1% of the original system persists.

But this isn't the case everywhere across the range of native grasslands in southern Australia. In the more xeric areas (300-400 mm rainfall), native grasslands are still a feature of the landscape, e.g. the Riverine Plains grasslands of northern Victoria. In part, they survive because agricultural use has been of lower intensity, i.e. sheep grazing has been rather conservative and cropping largely unsuccessful. Additionally, perennial exotic grasses are absent (it's too dry) meaning that the integrity (if not composition) of the native grasslands remains largely intact.

For many years, however, the extent of xeric grasslands in southern Australia was overlooked. The conservation imperative first focused on the mesic C4 grasslands on volcanic soils near Melbourne. Xeric grasslands protection was so poor that  by the early 1990s, none of the ecosystem was under conservation management.

Thankfully, this has changed - reservation has increased the area of xeric native grasslands in the National Reserve System from zero hectares in 1995 to an estate now in excess of 10 000 ha. This is a remarkable achievement. This increase has been driven, to a large extent, by government land purchase coupled with private conservation agreements. I, for one, have much greater hope that grasslands in these areas can now be conserved in a meaningful way. The challenge now will be to manage them for their biodiversity and ecosystem processes in the face of a changing climate. Understanding the factors that affect the resilience of these systems to change is a pressing research need.

I recently undertook a tour of some of the new conservation reserves protecting grasslands in northern Victoria and I thought I'd share some of these sites with you. While it's mid-winter here (and not the best time to see the diversity and colour of grasslands), I was impressed by the scale of grassland protection being achieved.

Chenopod grassland at Boundary Bend, north of Nyah.
Rainfall here is about 320 mm per annum. The grasslands
are dominated by widely-spaced C4  grasses (Sporobolus is common)
as well as scattered chenopod shrubs. Soil crusts - dominated by crustose and foliose 

lichens - are well developed. Black Box can be seen in the background.

Wanderer's Plain, west of Kerang. This is a large grassland (2000 ha)
acquired and managed by the Trust for Nature. Annual rainfall is
approx. 375 mm. Dominant grasses are C4 type, including Sporobolus and
Enteropogon. The grassland plains are often fringed by Buloke and Black Box.

Korrak Korrak grassland, west of Kerang. Another Trust for Nature
grassland, in the 350-375 mm rainfall zone. C4 grasses co-dominate
with C3 grasses (Austrostipa), along with scattered chenopods.
Exotic species are non-existent while native annual forbs are ubiquitous.

In some areas, it is obvious that overgrazing in the past has
led to dramatic soil loss. Large, bare scalds result and there is almost
no recolonization by native species from the surrounding grassland.

Travelling Stock Routes, like this one on the Cobb Hwy near Echuca,
have had minimal disturbance from grazing relative to grazed paddocks. They support many
endangered species that have been grazed out of the broader landscape. Their linear nature, 

however, makes them vulnerable to edge effects

Fabians grassland at Terrick Terrick National Park, an example
of C3 grassland with an intertussock flora dominated by lillies, orchids and
daisies. Rainfall is approx. 400 mm per annum.H ere, the first disturbance
manipulation experiments were conducted in the mid-1990s (the Foreman Plots)
to determine how xeric grasslands respond to fire, grazing exclusion, and soil disturbance.

Thursday, 31 May 2012

Picking a thesis research topic

Late last year, the band REM disbanded after 30 years in the music industry. I don't actually care much for REM's music (sorry!), but I do admire them for their committment to do their own thing over what might be considered their 'working life'. Rather than write music to top the charts, they wrote and performed music that they were really interested in making. This is probably what enabled them to be productive over the long-term - all 20+ albums in REM's case! I like Tim Winton too - the Australian author famous for books such as Cloudstreet and Blueback - for exactly the same reason. He writes about things that interest him (the sea, blokes, curiousity), rather than what will necessarily sell books. And, in some ways, I think students contemplating doing a research thesis could learn a little from them.

No matter what people say, doing ecology is hard! Natural systems are, after all, complex. There are lots of factors that affect ecological processes, and teasing them out can be a challenge. Hence, trying to decide what to study can be a daunting task for any new grad student. Funnily enough, however, modern ecology is not data (or technique or computation) limited – it’s often ideas limited. If you are lucky (like I was), you get to study the "low-hanging fruit" - the questions that need to be answered first before you can move on to deeper understanding. Do grassland plants have soil stored seeds? Is germination stimulated by fire? How big does a gap in the grassland canopy need to be for recruitment of forbs? Once these questions have been picked off, you'll have to think more critically about the next round of obvious things to ask. And this is the challenge.

Hence, when choosing a research project, it's advisable to first read widely, see what’s going on in your field (and related fields), and identify some general question or idea that you can address in your own system? This means being inquisitive and wanting to know where the field is at and how you might contribute meaningfully.

So, how important should this question be?

That is a difficult question to answer. Publishing metrics (Impact Factors, H-scores, etc) and funding trends mean that you should have your eye "on the game" if you want to make ecological research your career. But this doesn't guarantee you'll do good science. Good science involves carefully thought out hypotheses, and well-designed tests of these hypotheses. And to succeed, I think it is critical that you passionately believe in the research you are doing - you own it!  Hence, jumping on the latest "hot topic" in ecology (think the productivity-richness debate) might make your research seem current, but it is just as likely to move quickly on. Good ecological science, however, will stand the test of time.

There are two general observations I'd make when it comes to developing research questions:

First, avoid testing poorly developed hypotheses / theories with data you really don't understand and which wasn’t collected for the purpose. Trying to make your data fit a question isn't good science. That said, the recent surge in meta-analyses shows that when such data do exist, they can provide powerful insights that site by site studies just can't achieve.

Second, selecting a topic based on the choice of tool, not because of the question, is a no-no in my opinion. I’ve seen papers that seem to imply their study is important simply because they used [insert latest fad or bandwagon here]. Bandwagons that depend heavily on technical proficiency might make your research look great, but from my perspective, it is much easier to learn a new skill than to do original, ground-breaking science.

Of course, this is my personal view on the matter and you may disagree. There is no one or right approach here. That said, I'm a question-driven person. Tools are just that: tools! Good luck navigating a research thesis - it really is one the best things you'll ever do - particularly if you find a topic that grabs you and acknowledges those who came before you!!

I'll leave you with a recent comment I saw from Steve Packard (in Ian Lunt's excellent blog) - I thought it was apt (he was talking about the early days of restoration ecology):

"restoration was in the early Wright Brothers stage of flight. We were barely getting off the ground, but we were tackling the most fun and fundamental questions...............in the Wright Brothers’ day, learned academics were also trying to explore flight, but the Wrights made the key discoveries because they had the hammers and wrenches in their own hands and did their own flying."

Friday, 11 May 2012

What have golf balls got to do with grasslands?

Cooper Street grassland, dominated by the C4 grass Themeda triandra
One of the fundamental challenges to grassland management in Victoria is the role of biomass accumulation and the perceived necessity for disturbance regimes that reduce this biomass. In the absence of disturbance (to the vegetation, not the soil), biomass accumulates and smothers intertussock flora, preventing seedling recruitment by native species. In extreme cases, biomass accumulation smothers dominant tussock grasses, leading to their decline and replacement with annual exotic species. For some fauna, dense litter reduces favoured habitat states.

The rate of biomass accumulation, however, varies across the geographic range of native grasslands in southern Australia. Undisturbed Themeda grasslands in mesic regions have relatively high productivity and accumulate large quantities of dead grass, which decomposes very slowly and accounts for the majority of accumulated litter. By contrast, dead grass does not appear to accumulate over long periods in drier grasslands (dominated mainly by Rytidosperma spp., Austrostipa spp.), but instead appears to decay (or blow away) relatively quickly. Thus, low levels of accumulated biomass in xeric grasslands reflect high decomposition rates as well as low productivity rates.

The differences that occur in litter build-up underpin the notion that different types of native grassland need disturbance regimes that differ in their frequency. The frequency of disturbance might be timed to coincide with increasing litter levels that compromise native plant and animal diversity but developing ‘absolute’ disturbance regimes for native grasslands has proved difficult, chiefly because grasslands vary in their rate of litter accumulation. What is needed is a simple, effective assessment tool to quantify levels of biomass accumulation at individual sites upon which management actions can then be implemented.

Since 2006, La Trobe University, in conjunction with Parks Victoria, have been developing a grassy ecosystem biomass monitoring protocol to enable rapid field assessment. The basis premise of this assessment was to use a surrogate measure that would (a) indicate something about absolute levels of biomass in a grassland and (b) the assessment outcomes could be linked to management actions necessary to maintain diversity. This idea builds upon the habitat condition assessment method that identifies the optimum range of grassland structures necessary to maintain the Plains Wanderer, an endangered bird that prefers open-structured grasslands on the riverine plain.

Nick Shultz developed a pilot project to examine the potential value of using surrogates to estimate grassland 'condition'. Briefly, a 1 x 1 m quadrat is located in uniform grassland vegetation and 18 golf balls are dropped into the vegetation (one at a time) from a height of approximately 1.3 m. A photograph is taken of the plot and ‘golf ball visibility’ assessed either from the photo or in the field, and a biomass sample (0.25 m2) is harvested from the plot. The aim of the study was to determine whether the biomass of a grassland could be estimated using the surrogate of ‘golf ball visibility’. The rationale is simple: the fewer golf balls that are observed, the denser the vegetation and the higher its biomass. If the surrogate measure was found to be robust, managers could use the golf ball visibility method to estimate their grassland’s current condition, and plan management interventions based on this information. Essentially, if grassland biomass drives species interactions (negative interactions occur between grassland biomass and plant species diversity, as well as being poor habitat for some grassland fauna), giving managers a tool to estimate biomass is an important step to managing for biodiversity conservation.
Grazed grassland on the Northern Plains. 
How many of the 18 golf balls can you see?
What does this tell us about biomass and the need  for biomass reduction? 
(Photo: John Morgan)

The initial work was promising  but several issues were identified for further study before it could be adopted, including the quantification of the variability in the scoring of the number of golf balls between observers to determine whether this is significant. 

Using Post-Grads as observers, we found that they tended to under-estimate the ball score at low scores, but all observers correctly identified the differences between low biomass (high ball score: 15-18) and high biomass (low ball score: 0-5) .  Hence, it was concluded that despite observer variation, the methodology was repeatable and reliable when trying to identify grassland condition that varies from sparse to dense.

While it is an imprecise method of estimaing biomass in grasslands, the golf ball visibility method does seem useful to inform grassland managers about the existence of grassland 'states' (i.e. low biomass, moderate biomass, high biomass) and the dynamic nature of these states (i.e. how quickly they change from year to year), particularly in response to rainfall. When linked to biodiversity values (such as the existence of Plains Wanderers), the surrogate measure does seem to help managers make decisions about their grassland 'state' and when management actions might be desirable.

The Plains Wanderer
(Photo: http://www.birdway.com.au/pedionomidae/plains_wanderer/index.htm)