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.

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

Conservation photos, Part VIII: Skinks

Skinks. Australia is crawling with them, figuratively and literally. At last count we had 339 species. 339 species! And yet the richness of species is only half the story. Australia has a skink for every occasion. Giant skinks and miniature skinks. Skinks that live half of their lives in the alpine deep freeze, and others that toil through the harshest desert heat. Skinks that scale trees in a blistering flash, and others that have lost all but the last vestige of their limbs. Skinks whose days are spent cavorting in tight-knit family units, and others who are murderously territorial. Skinks saturated with colour, and skinks whose camouflage is near impregnable. Skinks whose range extends over hundreds of square kilometers, and others that persist nowhere else but a speck of granite in the Southern Ocean. You would be hard pressed to find a more diverse radiation than the Australian Scincidae…

Eastern Robust Slider, Lerista punctatovittata. Big Desert, Victoria

Eastern Robust Slider, Lerista punctatovittata. Big Desert, Victoria

South-west Crevice Skink, Egernia napoleonis. Albany, Western Australia

South-west Crevice Skink, Egernia napoleonis. Poorongorup NP, Western Australia

Boulenger's Skink, Morethia boulengeri. Mansfield, Victoria

Boulenger’s Skink, Morethia boulengeri. Mansfield, Victoria

White's Skink, Liopholis whitii, Grampians National Park, Victoria

White’s Skink, Liopholis whitii. Grampians NP, Victoria

Ctenotus brachyonyx, Ouyen, Victoria

Ctenotus brachyonyx. Ouyen, Victoria

Tussock Skink, Pseudemoia pagenstecheri. Craigieburn, Victoria

Tussock Skink, Pseudemoia pagenstecheri. Craigieburn, Victoria

Ragged Snake-eyed Skink, Cryptoblepharus pannosus. Murray-Sunset NP, Victoria

Ragged Snake-eyed Skink, Cryptoblepharus pannosus. Murray-Sunset NP, Victoria

Southern Grass Skink, Pseudemoia entrecasteauxii. Mt Baw Baw NP, Victoria

Southern Grass Skink, Pseudemoia entrecasteauxii. Mt Baw Baw NP, Victoria

Conservation photos VII. Weird and wonderful

Evolution crafts some wacky creatures. Birds that can’t fly. Squirrels that can. Mammals that lay eggs. Worms that luminesce. Vampire bats. Goblin fish. Octopus. I must admit that I have a considerable soft spot for these ecological and evolutionary oddities. They are just so fascinating; so mind-bogglingly weird. So indulge me as a list a few more. A few that I’ve had the great joy of seeing in the flesh, and whom I dearly hope to see again. Frogs whose finely textured and brilliantly patterned skin has inspired Aboriginal art for millennia. Dragons that spend their days munching hundreds of tiny, acrid ants, and whose skin not only wards off predators with a litany of devilish thorns, but also pumps water directly to their mouth by capillary action. Miniaturised snakes whose diet is restricted entirely to lizard eggs (that rarest of commodities) and others whose tail so perfectly mimics a grub – in both form and function – that it brings dinner right to their door. Lizards who swim through sand, having long ago cast aside the limbs that hinder their progress. And snakes whose morphology just takes your breath away. Whose beauty you can barely fathom, and whose existence re-affirms why you took up the cause in the first place….

Holy Cross Frog, Notaden bennetti

Holy Cross Frog, Notaden bennetti

Thorny Devil, Moloch horridus

Thorny Devil, Moloch horridus

 

 

 

 

 

 

 

 

 

Black-naped Snake, Neelaps bimaculatus

Black-naped Snake, Neelaps bimaculatus

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Common Death Adder, Acanthophis antarticus

Common Death Adder, Acanthophis antarcticus

 

 

 

 

 

 

 

 

Red-tailed Worm Lizard, Aprasia inaurita

Red-tailed Worm Lizard, Aprasia inaurita

 

 

 

 

 

 

 

 

 

Bandy Bandy, Vermicella vermicella

Bandy Bandy, Vermicella annulata