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.

New paper: ‘A Bayesian model of metapopulation viability, with application to an endangered amphibian’

f1000005.jpgLast 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!