2016 Herping in review

Between 2013 and 2015, I was lucky enough to embark on an ecological odyssey to the UK. With backing from a Victorian Postdoctoral Research Fellowship, I set off for the University of York and spent a happy two years learning at the knee of Prof. Chris Thomas. Through daily chats with Chris, and the other great folk that called York’s J2 lab home, I gathered a sense of the incredible biodiversity data sets that UK ecologists have at their disposal. The British populace, I soon realised, are just as fanatical about collecting biodiversity data as they are about train spotting, building model aeroplanes and tracking down obscure antiques. From immense observational data sets, to comprehensive, statistically-rigorous monitoring programs, the Brits produce masses of species occurrence and abundance data every year. I was hugely impressed; not just with the British fervor for good, solid data, but the end products too – great ecological science and perhaps an unrivaled capacity to monitor the country’s biodiversity.

Returning to Australia, I had a new found sense of the importance of maintaining records of the species I see in my travels. Specifically, time-stamped occurrence data, the sorts of which are vital to producing species distribution maps and models, and which, in the long-term, can provide insights into population declines, range shifts or even invasions. I’ve been diligently keeping these records ever since, with annual uploads to the Victorian Biodiversity Atlas and the Atlas of Living Australia.

This post will be the first of an annual series sharing those records with you. My intentions are two-fold: i) to share a snippet of the wonderful reptiles and frogs I’ve had the pleasure of meeting each year, and; ii) to encourage you to keep these records too, and to submit them regularly to either a state or national biodiversity atlas.

So, what of 2016? In all, I managed 126 records of 53 species, with observations from the tropical forests of North Queensland, through southern Queensland, New South Wales and into the hills and plains of Victoria. I met numerous new species, including Scrub Python, Jungle Carpet Python, New England Tree Frog, Striped Burrowing Frog, Golden Crowned Snake, Cascade Tree Frog, Sudell’s Frog, Rugose Toadlet and Red-eyed Tree Frog. The full species list can be found in the table that follows, with further details here. I also had the opportunity to photograph many of the species I encountered this year, having finally managed to save enough pennies for a decent digital camera. I’ll leave off with a few of the images I captured (you can head over to my Flickr page if you would like to see more).

Until next year then. Here’s hoping 2017 is just as rewarding…

Species list:

Species Common Name
Amalosia lesueurii Lesueur’s Velvet Gecko
Amphibolurus muricatus Jacky Dragon
Boiga irregularis Brown Tree Snake
Cacophis squamulosus Golden Crowned Snake
Carlia tetradactyla Southern Rainbow Skink
Chelodina longicollis Common Long-necked Turtle
Christinus marmoratus Marbled Gecko
Concinnia martini Martin’s Skink
Crinia parinsignifera Plains Froglet
Crinia signifera Common Froglet
Cryptoblepharus pannosus Ragged Snake-eyed Skink
Ctenotus spaldingi Robust Skink
Ctenotus taeniolatus Copper-tailed Skink
Cyclorana alboguttata Striped Burrowing Frog
Delma impar Striped Legless Lizard
Diporiphora australis Tommy Roundhead
Egernia striolata Tree Skink
Emydura macquarii Murray River Turtle
Eulamprus quoyii Eastern Water Skink
Geocrinia victoriana Victorian Smooth Froglet
Chelonia mydas Green Sea Turtle
Hemidactylus frenatus Asian House Gecko
Hemiergis decresiensis Three-toed Skink
Intellagama lesueurii Eastern Water Dragon
Intellagama lesueurii howittii Gippsland Water Dragon
Lampropholis guichenoti Garden Skink
Land Mullet Bellatorias major
Lerista bouganvilli Bouganville’s Skink
Limnodynastes dumerilii Banjo Frog
Limnodynastes peronii Striped Marsh Frog
Limnodynastes tasmaniensis Spotted Marsh Frog
Liopholis modesta Eastern Ranges Rock Skink
Litoria aurea Green and Golden Bell Frog
Litoria caerulea Green Tree Frog
Litoria chloris Red-eyed Tree Frog
Litoria ewingii Southern Brown Tree Frog
Litoria fallax Eastern Dwarf Tree Frog
Litoria pearsoniana Cascade Tree Frog
Litoria peronii Peron’s Tree Frog
Litoria subglandulosa New England Tree Frog
Litoria verreauxii Whistling Tree Frog
Mixophyse fasciolatus Great Barred Frog
Morethia boulengeri Boulenger’s Skink
Neobatrachus sudelli Common Spade-foot Toad
Parasuta flagellum Little Whip Snake
Pogona barbata Eastern Bearded Dragon
Pseudechis porphyriacus Red-bellied Black Snake
Pseudomoia pagenstecheri Tussock Skink
Pseudonaja textilis Common Brown Snake
Strophurus intermedius Eastern Spiny-tailed Gecko
Tiliqua scincoides Eastern Blue-tongue
Tropidechis carinatus Rough-scaled Snake
Uperoleia rugosa Rugose Toadlet



Cascade Tree Frog (Litoria pearsoniana), Springbrook QLD


Eastern Brown Snake (Pseudonaja textilis), Redesdale VIC


Gippsland Water Dragon (Intellagama lesueurii howittii), Mallacoota VIC


Scrub Python (Morelia kinghorni), Tully QLD


Red-eyed Tree Frog (Litoria chloris), Mt Warning NSW


Lesueur’s Velvet Gecko (Amalosia lesueurii), Retreat NSW

New paper – After the epidemic: ongoing declines, stabilisations and recoveries in chytridiomycosis impacted amphibians

csiro_scienceimage_1392_scanning_electron_micrograph_of_chytrid_fungusWe humans live in perpetual fear of epidemics. Some nasty new bug emerging from the jungle, sweeping across humanity and knocking off millions of us in the process. Or perhaps an existing pathogen that mutates into a superbug capable of spreading like wildfire, transmitted by as little as a dirty look.

While sometimes bordering on irrational (cheers Hollywood), our fear of epidemics is well placed. We’ve had some doozies in the not too distant past. Take Spanish Flu – a disease that killed somewhere between 50 and 100 million people between 1918 and 1920, reducing the world population by up to 5%. What’s more, our spine-bearing brethren give us regular reminders of the ruinous power of pathogens. Examples include white-nose syndrome in bats, avian malaria, Parapoxvirus in squirrels and the recent implosion of Saiga populations on the Eurasian steppe.

In the wildlife realm however, one disease stands head-and-shoulders above the rest as a potent reminder of the destructive capacity of pathogens. Chytridiomycosis, caused by the fungus Batrachochytrium dendrobatidis, has killed literally millions of frogs across the globe over the last four decades, driving thousands of local extinctions and either major decline or global extinction for up to 200 species. A truly remarkable feat for a single pathogen. In Australia, chytrid hit in the late 1970’s, arriving first (we believe) in Brisbane, before heading north and south along the east coast, and skipping across to Western Australia and Tasmania. It left carnage in its wake. Frogs that were formally abundant and readily found simply disappeared. Apart from a few observed die-offs, numerous populations went up in a figurative puff of smoke. Seven species met their doom.

Our most recent paper reviews what happened next. Led by the inimitable Dr Ben Scheele, the paper draws together published and unpublished data to review the fate of Australian frogs impacted by chytridiomycosis following the initial epidemic. We detail the varying responses of these species, ranging from ongoing decline, to stabilisation and even recovery. Furthermore, the review draws together the known mechanisms underpinning these responses, which Australian and international herpetologists have steadily revealed over the last two decades.

The news is mixed. Chytridiomycosis remains the chief threat to several highly endangered frogs in Australia, such as the Southern Corroboree Frog and Baw Baw Frog, both of which may soon no longer persist in the wild. However, others have stabilised and some have even clawed back formerly occupied territory. Encouragingly, the latter may be on-route to full recovery. The review also highlights that we now know enough to trial management options for some species. For example, it may be possible to target reintroduction efforts to habitats with few reservoir hosts of chytrid, or we may be able to manipulate the environment in ways that gives susceptible frogs an epidemiological or demographic edge over the fungus (a topic on which my own research has focused in recent years).

With that, I commend the paper to you. As always, if you’d like to read the paper but can’t get through the paywall, drop me an email and I’ll send it through.

Latest paper: Manipulating wetland hydroperiod to improve occupancy rates by an endangered amphibian

IMG_1047_tweakedWorking on wetland biodiversity takes one to some rather odd places. In my case, it has meant copious hours at the back of industrial estates, in flooded quarry pits and dodging unsavory types around urban backwaters. Hardly Kakadu or the Okavango Delta. But even my haunts are glamorous compared to some. Take the Western Treatment Plant – 11,000 ha of sewage treatment ponds in Melbourne’s south-west that processes half of cities’ effluent (a daily contribution from ~2 million people). I can assure that the WTP looks and smells just like you imagine; hardly the sought of place that should fire the inspiration of wetland ecologists.

And yet it does, because the WTP is wetland of global significance. It even sports a RAMSAR listing to prove it. Twitchers are particularly smitten with the place, flocking on mass to see Brolgas, Bitterns, Red-necked Avocets, Freckled Ducks, Pink-eared Ducks and even the critically-endangered Orange-bellied Parrot. For herpetologists like me, the attraction is frogs. As well as being home to squillions of Melbourne’s more common frogs, the WTP supports arguably the single largest remnant population of Growling Grass Frogs in the country.

Our latest paper focuses on keeping the resident Growler population booming. A collaboration with Andrew Hamer of the Australian Research Centre for Urban Ecology, Ecology Australia P/L and Will Steele of Melbourne Water, the paper uses monitoring data collected by EA over four seasons to update an existing model of the metapopulation dynamics of Growlers in Melbourne, and uses this model to predict how managing the hydroperiod of key wetlands could bolster occupancy rates. Furthermore, it includes a test of this management action in the field, assessing the change in occupancy rate at ponds that received top-up watering in the final year of the study. Encouragingly, occupancy rate increased among these ponds relative to those that didn’t receive top-up watering, suggesting that managing hydroperiod could increase both the range and abundance of Growlers at the WTP.

I’ll sign off here and let you peruse the paper for the juicy details (fire me an email if you can’t get through the paywall). If you’re interested in frogs, wetlands, management experiments, simulations or Bayesian statistics, you should like this one.

Here’s cheers to Parasite Ecology

IMG_1014_tweakedJust before Easter, my old friend Michael Scroggie alerted me to the fact that the good folks over at Parasite Ecology had posted a summary of our Ecology Letters paper on the role of chytridiomycosis in frog metapopulation dynamics. They really nailed the key messages of the paper, and even included a cheeky little cartoon that links our messages around migration to contemporary US politics. Nice!

Three new papers

A quick post to plug three papers that have hit the streets over recent months. The first is a case study of interspecific variation in the phenology of advertisement in frog communities. It was a fun paper to do, drawing together my own monitoring data from across northern Melbourne and coupling it with an extensive dataset collected by Stefano Canessa and Kirsten Parris across the same region in 2009. We built models of calling seasonality and within-season meteorological drivers for the resident frogs, and used these models to assess interspecific variation in peak calling periods. The paper is now published online over at Ecology and Evolution.

The second paper is the culmination of copious hard-work by Claire Keely, whose PhD I co-supervise. After 6 months trudging through the swamps of outer Melbourne searching for Growling Grass Frogs, followed by long hours in the lab genotyping hundreds of individuals, Claire has gained important data on the genetic structure and diversity of this endangered species around the city. It is great to see this work come to fruition. You can find out more about the paper and Claire’s PhD here. The paper itself is freely downloadable from Royal Society Open Science.

Third on the list is the first paper from Lucy Rose’s PhD. Lucy is interested in conservation decision making for freshwater systems in southern Australia, and has used our beloved Growler as a case study for integrating uncertainty in cost-effectiveness analyses. Lucy tackled the rather complex case of how Growlers will respond to urban growth in the Lockerbie Precinct north of Melbourne, working her way through the myriad of conservation options for the species to identify those that not only maximize cost-effectiveness, but minimize uncertainty due to demographic stochasticity and model imprecision. Lucy’s paper is currently online early at Conservation Biology.

New paper: ‘Refugia and connectivity sustain amphibian metapopulations afflicted by disease’

I had to wait until the ripe old age of 16 to see my first Growling Grass Frog. It was under a rock in a disused bluestone quarry in the Plenty Gorge Park, next to a spring-fed and slightly salty wetland. There were many Growlers dotted around the wetland that day; some taking shelter under rocks, others soaking up the sun in a patch of Bullrush. It struck me as odd at the time. I’d already spent an unhealthy proportion of my childhood knee-deep in Melbourne’s wetlands, but had not seen a one. So why were they doing so well in the old quarry? It’s taken me twenty years, but now I know.

Today, Ecology Letters published our latest paper on the spatial epidemiology of chytridiomycosis in remnant Growler populations. The paper – a culmination of 14 years of work – shows that the impact of chytridiomycosis on Growler populations is mediated by wetland microclimate and water chemistry, being considerably lower in warm and saline wetlands. We knew from previous work (on this system and others) that the prevalence and intensity of chytrid infections declines with increasing temperature and salinity (because chytrid is sensitive to both), but our new study is the first to demonstrate that these relationships have important implications for the persistence of frogs threatened by chytrid. Using 11 years of monitoring data, we’ve shown that populations of Growlers in warmer, saltier wetlands have a higher chance of persistence through time because the prevalence of infections is low. Moreover, we’ve shown that some metapopulations of Growlers are unlikely to survive without these warmer, saltier wetlands; that is, without their refuges from disease.

An example of a disease refuge for Growlers: a big, warm and relatively saline quarry wetland

An example of a disease refuge for Growlers: a big, warm and relatively saline quarry wetland

Now, by using ‘some’ in the last sentence, you might think I’m prevaricating. But let me explain, because this leads me on to the next main finding of the study (and, in due course, will take us back to the Plenty Gorge). Both theory and long-term empirical studies tell us that metapopulations are more robust if they are bigger and better connected. Our work shows that these two things also influence metapopulation persistence for Growlers afflicted by chytrid. In short, big, well-connected metapopulations that lack strong refugia can offset higher average rates of population extinction through rescue effects and recolonisations. Think of the extinction of a Growler population as a random event in time, but with a chance that varies between wetlands according to local chytrid prevalence and other factors that stress populations. If this situation prevails, extinctions will be somewhat asynchronous in space and time, and bigger, better connected metapopulations have two advantages. First, in these systems, there is a good chance that declining populations will be rescued by migrants from neighbouring populations before they bite the dust. Second, when a population does succumb, there is a good chance that neighbouring populations persist, which can fire off migrants to recolonise the now vacant wetland. Maybe next year the roles of the rescued and the rescuer will reverse, but the metapopulation will push on regardless.

Of course, for this to work, the benefits of migration need to outweigh the costs of pathogen transmission. Epidemiologists have been concerned about this for decades, using mathematical models to explore how to this trade-off might play out in nature. Our work suggests that for Growlers – and perhaps most frogs that are sensitive to chytrid – there isn’t much to worry about. Growlers just aren’t a major player in spreading the pathogen around. There are seven other frogs in our study area which do that job, and chytrid can travel in various other ways (e.g. though water courtesy of motile zoospores, by riding on the back of crustaceans, and possibly even hitching a ride on ducks feet!). Hence, there is no real trade-off between migration and disease spread for Growlers, and connectivity proves overwhelmingly beneficial.

And with that, back to the Plenty Gorge. What of those frogs today? Well, sadly, they are no more – Growlers haven’t been recorded in the park since 2008. Fundamentally, the local metapopulation was just too small and poorly connected. Populations persisted doggedly in two quarries after chytrid arrived thanks to their environmental leg up, but they blipped out one and then the other when severe drought added an extra layer of stress. Without re-enforcements from more fortunate neighbours, permanent extinction was the only possible outcome. And so it went.

A pool on the Merri Creek that could do with a trim. Lots of shade = cold water = higher chytrid prevalence.

But let’s not finish on doom-and-gloom, because this is not a doom-and-gloom story. In fact, it’s a very positive one, because what we now know about chytrid dynamics for threatened frogs is shovel-ready information (to use a bit of Australian political parlance). Think of the possibilities for enhancing wetlands to give them refugial properties, or creating new wetlands with the right characteristics. Warm wetlands in our study area are big and deep and have minimal shading from overhead canopy and emergent rushes. Slightly salty ones are subject to ground-water influxes. So, considering building a new wetland for Growlers? Well then, make sure it is big and deep, has minimal shading vegetation, and sink a bore to feed it with groundwater. While you are at it, lop the exotic Willows that have overrun the dam next door, and get the back-hoe in and clear out the Phragmites infestations from the adjoining creek. Excellent, excellent. What next? Well, it might be time to download our code and run some simulations. You can estimate the risk of extinction for your newly rejuvenated metapopulation, and test out further habitat management options for reducing that risk. You’ll have a ball, I promise.

Latest paper: Dealing with trade-offs in destructive sampling designs for occupancy surveys

Destructive sampling. It’s a term that makes you squirm a little isn’t it? I feel the same when I think about certain marking techniques or the need to sacrifice specimens for Museum collections. Each presents a dilemma that most ecologists will confront at some point in their careers: the need to do something that is immediately at odds with our core values in pursuit of the greater good for species conservation.

In our latest paper* we tackle the dilemma posed by destructive sampling using a decision-theoretic approach. To be clear, the dilemma here is that some species are very difficult to detect by any other means than pulling apart their favored microhabitats. Hence, gaining the information we need to manage these species is nigh on impossible without some impact on their habitat. We can’t find out how widely they are distributed, we can’t establish the range of habitats on which they rely, and we can’t quantify how they are responding to the management we apply. The focal species of our paper is an excellent example. The Earless Skink (Hemiergis millewae) is an obligate denizen of Spinifex hummocks in the Mallee regions of southern Australia. In Victoria the species is listed as critically endangered, and there is real concern that fuel reduction burning poses a threat to remnant populations. Yet we also don’t know where all the remnant populations are, let alone how persistence relates to fire regimes. To gain that information requires surveys across the Victorian Mallee, but the only practical way of doing those surveys is to prize apart the Spinifex hummocks on which the species relies.

Stefano Canessa took up the challenge of designing surveys for Hemiergis, using a hard-earned survey dataset acquired by Peter Robertson and Ian Sluiter at select sites in the Murray-Sunset National Park. The approach Stef devised finds the number of Spinifex hummocks a surveyor must sample at a site to ensure a threshold detection probability is reached (0.9, 0.95 etc), using a weighting system to reflect a surveyors choice between minimizing the number of hummocks searched and minimizing the quality of hummocks searched. This last bit is important, because Hemiergis don’t use hummocks at random; they like the big ones. So a surveyor can reduce the number of hummocks searched at a site by targeting the biggest ones available, because detection probabilities are higher on a per hummock basis for the bigger ones. But of course this removes the best microhabitats for the species. Instead, a surveyor can target small or medium-sized hummocks and leave the big ones, but this requires removing more hummocks to achieve the desired probability of detection and perhaps leads to greater impacts in the long run (because big hummocks senesce and need to be replaced by adolescent hummocks).

It’s a tricky problem, but Stef’s technique makes the trade-offs and choices clear, and enables repeatable and transparent decisions to be made (as decision theory is intended to do). Stef even provides an Excel worksheet to run the decision analysis, making the approach immediately accessible to managers. But the technique also has wider appeal. Destructive sampling is used to survey a range of species, and the fundamentals of Stef’s approach apply in each case, because all involve a central trade-off between maximizing detection probabilities and minimizing impacts on the focal species’ habitat.

*This link will take you to a post-print version of the paper, rather than the published version, because PLOS completely mangled our figures and refuse to fix them. The published version can be found here.