Avid followers of this blog (….crickets chirping in the background….) will know that it’s been a while since my last post. Four months to be exact. What I have I been up to? Well, in short, fighting my way through a mass of preparations for leaving Australia and heading to Old Blighty. To York to be exact. Yep, I’ve left the colony and headed back to the old country. I’ll be here for the next two years visiting Prof. Chris Thomas at the University of York and Dr Jenny Hodgson at the University of Liverpool. Chris and Jenny have long standing interests in metapopulation dynamics, and so their respective labs represent a logical place to hone my metapopulation capacities (there’s a masterful in-joke in there if you can spot it…). I’m here courtesy of the Victorian Government, who have packed me off to learn some new skills and extend my professional networks. It is a wonderful opportunity and I’m hugely excited about it!
Last night Diversity and Distributions published our latest paper, in a special issue entitled ‘Risks, Decisions, and Biological Conservation’.
The paper – co-authored by Mick McCarthy, Michael Scroggie, Kirsten Parris and John Baumgartner – describes an occupancy-based approach to metapopulation viability analyses that I think will prove a valuable extension to standard occupancy modelling.
Here’s the back story. In the early 2000’s, Darryl MacKenzie struck ecological gold by developing and publishing an occupancy modelling approach that accounts for imperfect detection. Darryl’s 2003 paper (co-authored with the gurus at the Patuxent Wildlife Research Center) was particularly influential. That paper describes a modelling approach that can be used to estimate the probabilities of extinction and colonisation for a given species using multi-season occupancy data, with the bonus of accounting for imperfect detection. But perhaps most mouth-watering for ecologists was the ability to model the probabilities of extinction and colonisation as functions of site- and landscape-level covariates (things like patch area, quality and connectivity) using standard regression techniques. Doing so allows hypotheses about the drivers of extinction and colonisation to be tested while accounting for imperfect detection.
Our paper builds on this functionality. What we’ve done is effectively tack on the ability to simulate extinction and colonisation dynamics for a given species based on the models of extinction and colonisation that result from Darryl’s approach. That is, we’ve developed a means of running occupancy-based metapopulation viability analyses using these models. We provide code for doing this in the Supplementary Material (see also my Code and data page).
It’s a fairly simple process conceptually. One fits a multi-season occupancy model to their particular dataset, estimates the effects of patch area, quality etc. on the probabilities of extinction and colonisation, extracts the parameters of the extinction and colonisation models, and then simulates the extinction and colonisation dynamics (and hence changes in occupancy) for a particular metapopulation according to these parameters. All that’s required for the simulations are measures of the relevant covariates for each site, and the initial occupancy status of each site.
The cool thing is that one can explore, using these simulations, how the metapopulation will respond to particular management scenarios. You can take away particular patches to represent habitat loss, you can tweak patch characteristics to represent habitat enhancement or degradation, and you can even add in new patches to see how habitat creation affects metapopulation viability. We do just that in the paper – examining the effect of habitat loss and creation on metapopulation viability for the endangered Growling Grass Frog (my particular muse….).
Now, in case Andrew Royle or Marc Kéry are reading, I best now tell you that we in fact used their 2007 Bayesian state-space version of Darryl’s approach. In a move that will surely see them breeze through the pearly gates, Royle and Kéry not only put in the hard-yards developing and publishing the Bayesian approach, but provided code to do it too.
The nifty thing about the Bayesian version is that it provides the opportunity to propagate uncertainty in the effects of patch characteristics on extinction and colonisation through to the simulations. I’ll leave it to the paper to explain how, but what we end up with are probability distributions for the metrics of metapopulation viability that not only encompass uncertainty due to the stochasticity of the modelled dynamics, but also from uncertainty in the parameters of the extinction and colonisation models.
That’s the approach in a nutshell. If you’d like a copy of the paper but can’t get through the paywall, just drop me a line and I’ll email it through. Otherwise, go forth and simulate!
For some time now I’ve been thinking about using this website as a platform for sharing statistical code and data from papers that I’ve published. Well, I’ve finally made a start – take a peak at my imaginatively named new page ‘Code and data’…
I’ve got two primary motivations for uploading code and data from my papers. The first is that I’ve benefited on numerous occasions from the generosity of others who have shared their code with me. From supplementary material in published papers to emails with bits of code I’ve requested, I simply could not have completed some of my research without these generous offerings. I hope to return that favour here.
The second reason is that I want the data I’ve collected to be available to others, either for further dedicated analyses or for use in meta-analyses. The further I go through my career the more I realise just how precious data are. The time, effort and money required to gather field data is perhaps evidence enough. Sadly though, recent experience has taught me just how quickly one’s data can become a vital record of what was once was.
So, swing over to ‘Code and data’ and take a look. I’ll update the page as new papers come out, and work on filling in my back catalogue over the next few months.
Just one request – if you use the code or data presented on this website, please cite the relevant paper, or, if there isn’t one to cite, cite this website instead.
I’m a big fan of the Big Desert. It’s a subtle place. Like a grassland, you have to get up close and personal with it to discover its treasures. It has no towering trees, no roaring waterfalls, no charismatic megafauna. It is miles and miles of rolling sand dunes and Mallee heath. After a fire, it is white sand and black sticks, little else. And yet the Big Desert is a biodiversity wonderland. Ants, scorpions, centipedes, bees, wasps, butterflies, moths, cicadas. The insects hum day and night. As do the reptiles that chase them, and each other…
Just prior to Christmas, Conservation Genetics delivered us a present in the form of acceptance and rapid fire publication of a study we commenced way back in 2004. The publication process never ceases to amaze me. After years of toil collecting data, several more years of painstaking lab work, and finally the rigors of a multi-author drafting process, this paper took just weeks to go from being accepted, through proofing to online-early publication. In fact, to my astonishment, we received proofs a mere five days after the paper was accepted, two days of which were a weekend!
But back to the paper itself. In 2004 I was a shiny new PhD student, champing at the bit to decode the population biology of the growling grass frog. I began a mark-recapture study on the species north of Melbourne, and diligently went about obtaining tissue samples from each frog I captured for a later, prospective, genetics study. Two years and 800 frogs later, the opportunity arose to get that work underway. Josh Hale had just started his own PhD on the conservation genetics of frogs in urbanising landscapes, and was keen to collaborate on the growler project. Josh’s first task was to develop a microsatellite library for the species. He emerged from the lab a year later, gasping for air and 10 kilos lighter, bearing nine new microsatellite loci for our little green friends. You can read about those in another paper, found here. Josh then set about genotyping ~200 growlers from three population clusters that I sampled during my mark-recapture work. These clusters, which I prefer to call metapopulations, were distributed along the Merri Creek at roughly 5 km intervals. Each included pools along the creek, plus neighbouring wetlands such as quarries, swamps and farm dams. Josh used his microsatellite data to assess the pattern of population subdivision in this area, and to test the effect of geographic distance and urban barriers on genetic distance.
So what did we find? In short, remarkable levels of genetic sub-division. Growlers have long been thought to be highly dispersive; vagabonds that wander the landscape in search of optimal conditions. On the contrary, our genetic work indicates that while individual frogs may be able to undertake significant journeys, the majority either can’t or don’t. Josh’s work found strong genetic sub-divisions between each of the wetland clusters I sampled, and even some sub-division within population clusters. The latter is especially interesting because the distances involved are small – 2 km max. Thus, in line with our previous occupancy and mark-recapture work (described here), Josh’s genetic work suggests that the migration rates of growlers are low and strongly distance-limited.
Another important outcome was the fact that populations separated by housing estates, industrial estates or dual-carriage roads displayed relatively high genetic distances. We can infer from this that urbanisation does indeed fragment populations of growlers; something we’ve long suspected but lacked any specific evidence of. It’s not a surprising result – imagine yourself as a little green frog attempting to cross a dual-carriage highway. But it is a vital piece of the puzzle for our understanding of the effects of urbanisation on this species, and for mitigating those effects.
Where to from here? Well, now that you mention it, our molecular work continues. Claire Keely, a PhD student in the QAEG, is working on the broader genetic structure of growlers around Melbourne, the fine-scale determinants of gene flow, and the efficacy of alternate tissue sampling techniques. You can read more about Claire’s great work here. As for Josh and I, we have one more paper to go from our collaboration. It’s a gooden too – a comparison of contemporary genetic diversity in growler populations from the Merri with a now extinct population from the adjacent Plenty River catchment. Think ancient DNA techniques and pickled frogs collected way back in the 1960s. Oh yes, there’s an exciting blog post in that. Stay tuned…
In August 2001, as a whipper-snapper of 22, I met A. John Coventry, Emeritus Curator of Herpetology at Museum Victoria. That day is memorable for more ways than one.
First and foremost, it was the day I met ‘the man’ in Victorian herpetology. AJC had just stepped down from a stint at the Museum spanning 50 years. An incredible length of time, and an incredible contribution to Victorian herpetology. Over that time he had amassed and curated an extraordinarily detailed herpetological collection, discovered several new species, recorded others that were new to the state, and conducted an extensive study of the herptofauna of the Victorian Mallee that laid the ground work for many of the recent ecological studies in this region. But this is just a snippet of AJC’s activities. Peruse the acknowledgements section of just about any herpetological paper, thesis or report with Victorian origins from the second half of last century and there he will be, receiving copious thanks for his time, support and expertise. For a young man besotted with herpetology, you can imagine that meeting AJC was somewhat intimidating.
The second thing that I remember very clearly from that day in 2001 is the sight of AJC catching the biggest and meanest Brownsnake I’ve ever laid eyes on. We were knee deep in grass on a stony knoll adjacent to the Craigieburn Grasslands – prime Brownsnake territory. On this particular day we were working with a crew of Botanists, one of whom suddenly yelped and headed off at break-neck speed. AJC knew exactly what it meant. In flash he had pounced, emerging from long grass with 6ft of writhing, hissing fury. It was a joy to behold.
Over the next six years, courtesy of Peter Robertson, I had the great pleasure of joining AJC on field trips far and wide. AJC was a font of herpetological knowledge, and gave freely of his wisdom. But he was also, quite simply, a fantastic person to be around. His humour was unique – a combination of ancient ‘Dad’ jokes and cheeky boyish naughtiness. Yet he was a statesman too. I would marvel at his inner discipline and resolve. It didn’t matter if he had just spent his fifth night sleeping on a Banana lounge in the middle of nowhere, AJC would be up at the crack, boiling the billy, with a glint in his eye and readiness to lead us off for another day chasing lizards in the sun. And this was after two hip replacements! Incredible stuff.
Fittingly, AJC’s final days were spent in the Mallee doing what he loved. I was there again courtesy of AJC’s great friend and colleague, Peter Robertson. I’ll be eternally grateful to Peter for taking me on that trip. We were searching for Heath Skinks (Liopholis multiscutata) on the tall dunes of the Big Desert. Years before, Peter and AJC had discovered a population of this species in the heart of the Desert, and our objective was to clarify its regional distribution. AJC was in fine form, tearing up and down dunes, leaving me in his wake. We found several new populations, and went home happy with our achievements.
Sadly, not long after arriving home and retiring for the night, AJC’s heart gave out. Peter rang me the next morning with the terrible news, and I bawled and bawled.
But AJC’s legacy lives on. As well as his many scientific contributions, AJC leaves behind a network of Mallee parks whose gazetting sought to protect the biological diversity he played no small part in documenting. Next time you find yourself in the Big Desert marveling at the vista of Mallee heath, think of AJC. If there is a Heaven, his is there, sitting beside a Mallee root fire, with billy boiling and a sea of stars overhead.
This morning, Twitter informed of a recent post on the Early Career Ecologists blog (which you can find here) about the value of photography for ecological research. It’s a great post, and it got me thinking about the plethora of pics I’ve taken over the years during research projects. Some have specific purposes, others are simply to document the process or the beautiful creatures and landscapes I’ve had the fortune to study. It got me thinking: “I should be doing more with this pictorial resource!”.
So here goes folks, the first of a series of blogs sharing these pics with you. Where better to start than with a research project on the endangered (and magnificent!) Inland Carpet Python in Victoria, which I was lucky enough to take part in during 2001…..
Last week I was lucky enough to attend a workshop at the Australian Centre for Ecological Analysis and Synthesis (ACEAS) at the University of Queensland. ACEAS is part of the Terrestrial Ecological Research Network (TERN), funded by the Australian Government. Inspired the famous American version, ACEAS seeks to facilitate the integration, synthesis and modelling of ecosystem data to aid in the development of environmental management strategies.
Our job last week was to collate data on the distribution and demography of several Australian frogs, and to use those data to develop models of population dynamics under climate change. The objective: to assess extinction risks, and identify management options to mitigate those risks. See more on our group page.
Now, here’s the great thing about ACEAS. Autecologists like me are keen to tackle these sorts of projects, but often lack the modelling skills required. On the flip side, ecological modellers interested in these questions are often constrained by their knowledge of the species under study, particularly where to find the information needed to parameterise their models (which frequently hides in Honours or PhD theses, unpublished reports, someone’s hard drive or a dusty filing cabinet). ACEAS brings these two groups together, and harnesses their collective skills to tackle important questions in applied ecology.
Want a workshop of your own? Well, it just so happens that the next round of ACEAS funding is in October. You can enquire with ACEAS direct from here, and find instructions of how to apply here. I can highly recommend it!
I’ll write more about the frog project in blogs to come. For now, let me say a big thanks to Tracey Regan and David Keith for leading the charge and inviting me along, to all the group members for a great week (including our most recent member, Reid Tingley), and to ACEAS for their fantastic hospitality, and their broader efforts to bridge the gap between those with the data, and those with the models.
I’ve never actually pursued it formally, but I’ve got a serious penchant for historical ecology. It’s because I’m a bit of a bleeding heart I suppose, but I long for the environment of the past. In fact, if the Devil presented himself to me tomorrow, carrying a time machine that could whip me off to Murray River circa 1787, I would think very seriously about offering my soul in return. To walk through a Redgum Forest that hasn’t been tainted by a single chainsaw cut; to look into the clear waters of the Murray and know that not one exotic fish swims in her currents; to listen to the cacophony of frogs in a billabong that has never been parched by river regulation; to hear the midnight cry of a Curlew that has no fox to fear…. I could continue like this for pages.
Of course it will never be, unless some miracle of physics takes place in the next 50 years. But last night I found the next best thing, and this post is intended to share that discovery. Folks, let me introduce you to Will Trueman. In this series of YouTube videos, Will explains the origins and outcomes of a research project that has culminated in the most incredible historical account of the native fish fauna of the Murray Darling Basin. Motivated partly by the memory of fishing trips with his old Dad, Will has meticulously pieced together a picture of the native fish community of the southern Murray-Darling prior to its collapse. And what a picture he paints. Let me give you an example.
A little while back, I moved to the town of Kyneton, around 80 km north-west of Melbourne. Kyneton is just on the other side of the Great Dividing Range, and lies in the catchment of the Murray-Darling Basin. Being a keen fisherman, I’ve been exploring the local creeks and rivers chasing some action. One of these ramblings let me to the Campaspe River at Redesdale, just above Lake Eppalock. My first visit in autumn last year revealed a river of great beauty – here the Campaspe runs through a deep basalt gorge, and tumbles over a mix of basalt boulders and mudstone reefs. Add to this crystal clear water and towering Redgums, and I thought I’d found my own fishing utopia. But the fishing itself has been woeful – I’m yet to catch a single native fish here, despite multiple trips and varying techniques. Enter Will Trueman. Through his book, I now know that this section of the Campaspe was once the fishing paradise I thought it should be. Historical accounts suggest this section of the Campaspe was home to Murray Cod, Trout Cod, Macquarie Perch, Silver Perch and Catfish, and that they were there in profusion. What’s more, he provides some proof from the very spot I’ve been fishing. Here it is:
I can’t wait to scour Will’s book over the next few weeks – I’m sure to find many more such historical gems. Who knows, it might just give me the kick I’ve needed to turn whistful dreaming about what was once was, into an active role in ecosystem restoration….
When I first started working on Growling Grass Frogs, I thought of them as the tough guy of the Victorian frog fauna. I already knew them to be a big, voracious predator that would happily scoff just about anything that would fit into their mouths (including each other). But I also thought of them as ‘tough’ in an ecological sense. They seemed pretty general in their habitat requirements, I’d read reports of them being master dispersers, and I presumed them to be long-lived and super fecund. But after a decade of working on Growlers, I’m starting to wise up to the fact that they aren’t so tough after all.
So, from what frailties does the poor old Growler suffer? Here’s the key ones, as I see it:
- Living hard and dying young: If by some quirk of reincarnation you wake up as a Growler tomorrow, don’t be too concerned, because it’s not going to last very long. Despite being one of the largest frogs to grace our good state, it appears that Growlers might be one of the shortest lived. Growler tads metamorphose quickly, taking around 2-3 months to complete the journey. And that’s some journey physiologically – we’re talking growing from a 5 mm grey wriggler to a 110 mm monster taddy, before growing lungs, sprouting legs and losing a tail in the space of a few weeks. And they don’t slow down once they’re out of the water – they hit the ground running, as it were. I once marked a Growler shortly after it metamorphosed and recaptured it at adult size 54 days later. That’s some seriously fast growth by anyone’s measure! With this rapid growth comes early maturation. It appears that most Growlers are able to reproduce in the first breeding season after the one in which they metamorphosed. I’ve recorded this for males, and observed females to reach the required body size within that time frame. It’s just as well they mature so rapidly, because most Growlers are probably dead before their first birthday roles around. Using mark-recapture data collected across northern Melbourne, I’ve estimated that survival rates across a single breeding season may be 13% or lower.
- Habitat specificity: As I said, Growlers are superficially quite general in their habitat requirements. They turn up in a raft of wetlands; from slow-flowing sections of streams, to artificial lakes, old quarries and storm-water wetlands. What’s more, they can often be found in some pretty horrible spots. But the thing is, just because you find a few Growlers in a particular wetland doesn’t mean they are breeding there, nor does it suggest they can persist there for long. Growlers are highly aquatic, and do best in wetlands that permanent or semi-permanent. But they need more than just long hydroperiods – they require diverse aquatic vegetation, and are sensitive to high turbidity, low water temperatures, water pollution and fish predation. When Growler’s turn up at ephemeral wetlands that have recently filled, it’s probably not because they’ve been hunkering down under a rock waiting for the rain (as many of the other resident frogs are likely to have done), it’s because a few have scooted over from a neighbouring wetland that supported a population during the dry. The same is true of Growlers you might find in storm-water wetlands and the like – in many cases I’d bet my bottom dollar that these frogs came from a neighbouring, high quality wetland rather than the putrefying, trolley-ridden waters that ripple before you.
- Relatively poor dispersal capabilities: From the last point, you might be thinking that Growlers are indeed quite the vagabond, roaming widely in search of new opportunities. But my experience is that only a small proportion of Growlers move about, and that the distances these frogs travel are relatively small. During my PhD I marked ~800 Growlers across 19 wetlands in northern Melbourne. Of the 131 that I recaptured, the longest recorded dispersal distance was only 430 m, and the majority stayed pretty close to the spot where I first found them. Now I acknowledge that inferring dispersal rates from mark-recapture has its problems, but this concurs with our occupancy and genetic data. Both suggest that populations separated by more than about 1 km have relatively little interaction with each other. This contrasts markedly with some of the frogs with which Growlers co-occur. Take the Brown Tree Frog and the Common Froglet. Recent genetic work to the east of Melbourne has shown that populations of these frogs display considerable gene flow even when separated by distances of 8 km. It’s quite embarrassing really – here are a couple of frogs that aren’t even half the size of your average Growler, and yet they apparently give Growlers a hiding on the dispersal front.
Clearly, these traits haven’t driven Growlers into decline on their own – the species was abundant historically, and I many of these traits are hard-wired. Instead, these traits represent frailties in the Growler’s ability to cope with the environmental conditions we have thrust upon. My view is that the occurrence of Growlers was probably always quite dynamic at a regional scale. Individual populations would go through booms and busts; the busts would result from wetland drying, changes in wetland condition, or stochastic events that jointly killed off adults and tads, and the booms from colonisation of wetlands that recently filled, or became suitable for some other reason (changes in veg structure etc.). Given enough wetlands in close proximity, and some spatial asynchrony in the local conditions, these systems would have been pretty robust. But the spatial and temporal dependence inherent to such systems (called ‘metapopulations’) gives them an Achilles heel when it comes to human-induced environmental change. Put simply, metapopulations are doubly sensitive to habitat loss, degradation and fragmentation. In the first instance these processes reduce metapopulation size and connectivity, which increases the likelihood that all populations will simultaneously go bust by chance. However, habitat loss and degradation also reduces the diversity of patch conditions, which increases the chance of synchronous local extinctions during widespread perturbations (like drought). It’s no coincidence, in my view, that Growlers disappeared very rapidly from many places across their former range when two big environmental perturbations coalesced in the late 1970s: a severe drought that affected much of south-eastern Australia, and the importation of the renowned frog-killing fungus, Batrachochytrium dendrobatidis. For years we’d being setting Growlers up for a fall through wetland destruction, degradation and fragmentation, and they fell hard when drought and disease arrived in tandem.
So what does this all mean for the conservation of Growlers in contemporary landscapes? For me, it highlights just how important wetland density, diversity and connectivity are for the persistence of this species. It remains commonplace, sadly, for the wetlands upon which this species relies to be destroyed or degraded to make way for urban and agricultural development. Moreover, we continue to isolate wetlands by placing roads and other major barriers between them. History suggests that there is only so much of this that Growlers can withstand. If we don’t learn this lesson soon, we’ll just keep setting the poor old Growler up for a fall, and fall it will when the next perturbation comes along.
Hale, J.M., 2010. Human-induced changes in the population genetic structure of frogs in south-eastern Australia. PhD thesis. University of Melbourne, Melbourne.
Hamer A. J., Lane S. J. & Mahony M. J. (2010) Using probabilistic models to investigate the disappearance of a widespread frog-species complex in high-altitude regions of south-eastern Australia. Animal Conservation 13, 275-85.
Heard, G.W., Scroggie, M.P., and Malone, B.S. (2012). The life history and decline of the threatened Australian frog, Litoria raniformis. Austral Ecology 37, 276-284
Heard, G.W., Scroggie, M.P., and Malone, B.S. (2012). Classical metapopulation theory as a useful paradigm for the conservation of an endangered amphibian. Biological Conservation 148, 156–166.