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.

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.

The Wonders of Convergence

One of the most captivating things about evolution is its propensity to produce identical twins on opposite sides of the globe. Species that are near inseparable morphologically, ecologically and behaviorally, but which have very different DNA. They don’t have common forebears, at least not recent ones. Instead, having been buffeted by equivalent forces over the millennia, and run a parallel race of natural selection, they’ve reached the same evolutionary sweet spot. They’ve been sculpted by the same chisel and converged.

The wonders of convergence were bought home to me again this week while working on a paper I’ve been meaning to write for some time. It concerns the phenology of mate-calling among frogs from my home town of Melbourne, in southern Australia (‘phenology’ being the timing and determinants of periodic biological events). In my ramblings through the literature, I came across a great paper by Daniel Saenz and colleagues on the phenology of mate-calling in a community of frogs from eastern Texas. Texas, that’s roughly 14,000 km from Melbourne, on the other side of the world’s greatest ocean. And yet, what Saenz et al. had to say about the frogs they studied sounded very familiar. Oddly familiar.

And so, with Google’s help, I set to work looking up these Texan amphibians. Surprise, surprise, they are the same frogs I work on 14,000 km away. Quite unrelated phylogenetically, but counterparts nonetheless. Take a look for yourself. In the following pairs of photos, the Australian species is on the left and its Texan analogue on the right. It’s incredible, isn’t it?

Whistling Tree Frog, Litoria verreauxii

Whistling Tree Frog, Litoria verreauxii

Western Chorus Frog, Pseudacris triseriata

Western Chorus Frog, Pseudacris triseriata

 

 

 

 

 

 

Growling Grass Frog, Litoria raniformis

Growling Grass Frog, Litoria raniformis

Common Bullfrog, Rana catesbeiana

Common Bullfrog, Lithobates catesbeiana

 

 

 

 

 

 

 

Common Froglet, Crinia signifera

Common Froglet, Crinia signifera

Northern Cricket Frog, Acris crepitans

Northern Cricket Frog, Acris crepitans

 

 

 

 

 

 

Peron's Tree Frog, Litoria peronii

Peron’s Tree Frog, Litoria peronii

Gray Tree Frog, Hyla versicolor

Gray Tree Frog, Hyla versicolor

 

 

 

 

 

 

Sudell's Frog, Neobatrachus sudelii

Sudell’s Frog, Neobatrachus sudelii

Eastern Spadefoot Toad, Scaphiopus holbrookii

Eastern Spadefoot Toad, Scaphiopus holbrookii

 

 

 

 

 

 

Spotted Marsh Frog, Limnodynastes tasmaniensis

Spotted Marsh Frog, Limnodynastes tasmaniensis

Southern Leopard Frog, Rana sphenocephala

Southern Leopard Frog, Lithobates sphenocephala

 

 

 

 

 

 

 

Photo sources (those not listed are my own):

Western Chorus Frog –  calphotos.berkeley.edu, photographer Todd Pierson.
Common Bullfrog – http://www.discoverlife.org/, photographer unknown.
Northern Cricket Frog – https://www.flickr.com/photos/52463647@N08/, photographer Melville Osborne.
Gray Tree Frog – http://www.californiaherps.com/noncal/misc/miscfrogs/pages/h.versicolor.html, photographer Gary Nafis.
Sudell’s Frog – www.stewartmacdonald.com.au, photographer Stuart MacDonald.
Eastern Spadefoot Toad – http://www.discoverlife.org/, photographer Todd Pierson
Spotted Marsh Frog – http://bwvp.ecolinc.vic.edu.au/fieldguide/fauna/spotted-marsh-frog, photographer Craig Cleeland
Southern Leopard Frog – http://www.frogforum.net/, photographer John Clare

A Natural High

P1000983Tell me this – have you ever taken drugs? Yes? No? The answer depends on one’s definition, but I’ll bet that many of you will admit to dabbling in some form of stimulant. We are, as a society, obsessed with them. Dark aromatic shots of plant extracts; delicate paper tubes delivering wafts of nicotine; colourful vessels of molten sand filled with fermented fruit juice; little polyethylene baggies carrying a fine dust of crystalline tropane alkaloids. We have employed all our ingenuity in search of a high.

Why? Let me give you my theory. I think our craving for stimulants is an attempt to the replace the pulses of endorphins that once accompanied our daily rambling in the wilds. I can honestly say that nature has given me by far the biggest highs of my life. I’ve stood at the edge of Mt Meg’s spectacular granite bluffs, with blood coursing and nostrils flaring, and believed that I could soar off if only I had the courage to jump. I’ve perched atop dunes of the Big Desert and felt my skin tingle with awe. I’ve stood waist deep in the Merri Creek with a full moon overhead and frogs calling all around, and been so fulfilled that if I’d slipped into the murky depths at that very instant, I would have died happy.

My most recent of these experiences was also the most profound. It was March 2011. La Niña had just prized southern Australia loose from El Niños’ grasp, bringing rain and plenty of it. The Murray-Darling catchment, wilting and gasping after ten years of drought, was reborn. Floods spread across every inch of the basin, coalescing at the junction of the Murray and Darling Rivers in Victoria’s north-west. With haste, my old friend Jeremy Tscharke and I packed the car and headed north to glimpse the spectacle. What we found eclipsed even our wildest dreams. 

Land that two years before was literally dying of thirst was now heaving with life. Supposedly long dead Red Gums re-sprouted in effervescent green. Wetlands that we presumed had seen their last flood years before now brimmed with fish and turtles. Frogs reclaimed the flood plain in such numbers that one had to be careful where they placed their feet. It was stunning, and a truly humbling experience.

The climax was a sunset that Jeremy and I will never forget. We’d headed up a flooded Lindsay River in search of ‘Big Red’ – a Red Gum of gargantuan proportions we’d seen previously on aerial imagery. We found her just as the sun dipped below the western horizon. The sky progressed through golden, to pink and eventually to deep violet. As we marveled at this great tree, we talked about the history it had seen. Big Red would already have been a towering giant when Captain Cook sailed up Australia’s eastern seaboard. She could well have sheltered families of Aboriginal people from inclement weather, and her hollow limbs must have once been home to regionally extinct marsupials. Undoubtedly, she has seen scores of floods of the scale of the 2011 epic. This tree was, quite simply, a living piece of history that we could touch and caress and imbibe. We had found our Totem, and returned to camp with a sense of bliss that no substance could ever hope to replicate.

Dwarfed by Big Red

Dwarfed by Big Red. A little shaky, but steady hands are hard to come by under this beauty. Photo: J. Tscharke

Sunset on the Lindsay River I. Photo: J. Tscharke

Bliss I. Photo: J. Tscharke

Sunset on the Lindsay River II. Photo: J. Tscharke

Bliss II. Photo: J. Tscharke

Sunset on the Lindsay River III. Photo: J. Tscharke

Bliss III. Photo: J. Tscharke

Code and data

Picture3For 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.

Enjoy!

Conservation photos, part II: Big Desert

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…

Thick-tailed Gecko, Underwoodisaurus milii

Thick-tailed Gecko, Underwoodisaurus milii

 

 

 

 

 

 

 

 

 

Lined Worm Lizard, Aprasia striolata

Lined Worm Lizard, Aprasia striolata

 

 

 

 

 

 

 

 

 

A sample of Mallee heath

A sample of Mallee heath

 

 

 

 

 

 

 

 

 

Mitchell’s Short-tailed Snake, Parasuta nigriceps

Mitchell’s Short-tailed Snake, Parasuta nigriceps

 

 

 

 

 

 

 

 

 

 

Burton's Legless Lizard, Lialis burtonis

Burton’s Legless Lizard, Lialis burtonis

 

 

 

 

 

 

 

 

 

Marbled-faced Delma, Delma australis

Marbled-faced Delma, Delma australis

 

 

 

 

 

 

 

 

 

Wood Gecko, Diplodactylus vittatus

Wood Gecko, Diplodactylus vittatus

 

 

 

 

 

 

 

 

 

Bardick, Echiopsis curta

Bardick, Echiopsis curta

 

 

 

 

 

 

 

 

 

 

Eastern Spiny-tailed Gecko, Strophurus intermedius

Eastern Spiny-tailed Gecko, Strophurus intermedius

 

 

 

 

 

 

 

 

 

And to finish - sunset, Big Desert style.

And to finish – sunset, Big Desert style.