Linking disease, demography and climate

1 08 2010

Last week I mentioned that a group of us from Australia were travelling to Chicago to work with Bob Lacy, Phil Miller, JP Pollak and Resit Akcakaya to make some pretty exciting developments in next-generation conservation ecology and management software. Also attending were Barry Brook, our postdocs: Damien Fordham, Thomas Prowse and Mike Watts, our colleague (and former postdoc) Clive McMahon, and a student of Phil’s, Michelle Verant. At the closing of the week-long workshop, I thought I’d share my thoughts on how it all went.

In a word, it was ‘productive’. It’s not often that you can spend 1 week locked in a tiny room with 10 other geeks and produce so many good and state-of-the-art models, but we certainly achieved more than we had anticipated.

Let me explain in brief why it’s so exciting. First, I must say that even the semi-quantitative among you should be ready for the appearance of ‘Meta-Model Manager (MMM)’ in the coming months. This clever piece of software was devised by JP, Bob and Phil to make disparate models ‘talk’ to each other during a population projection run. We had dabbled with MMM a little last year, but its value really came to light this week.

We used MMM to combine several different models that individually fail to capture the full behaviour of a population. Most of you will be familiar with the individual-based population viability (PVA) software Vortex that allows relatively easy PVA model building and is particular useful for predicting extinction risk of small populations. What you most likely don’t know exists is what Phil, Bob and JP call Outbreak – an epidemiological modelling software based on the classic susceptible-exposed-infectious-recovered framework. Outbreak is also an individual-based model that can talk directly to Vortex, but only through MMM. Read the rest of this entry »





Mega-meta-model manager

24 07 2010

As Barry Brook just mentioned over at BraveNewClimate.com, I’ll be travelling with him and several of our lab to Chicago tomorrow to work on some new aspects of linked climate, disease, meta-population, demographic and vegetation modelling. Barry has this to say, so I won’t bother re-inventing the wheel:

… working for a week with Dr Robert LacyProf Resit Akcakaya and collaborators, on integrating spatial-demographic ecological models with climate change forecasts, and implementing multi-species projections (with the aim of improving estimates of extinction risk and provide better ranking of management and adaptation options). This work builds on a major research theme at the global ecology lab, and consequently, a whole bunch of my team are going with me — Prof Corey Bradshaw (lab co-director), my postdocs Dr Damien FordhamDr Mike Watts and Dr Thomas Prowse and Corey’s and my ex-postdoc, Dr Clive McMahon. This builds on earlier work that Corey and I had been pursuing, which he described on ConservationBytes last year.

The ‘mega-meta-model manager’ part is a clever piece of control-centre software that integrates these disparate ecological, climate and disease dynamic inputs. Should be some good papers coming out of the work soon.

Of course, I’ll continue to blog over the coming week. I’m not looking forward to the 30-hour travel tomorrow to Chicago, but it should be fun and productive once I get there.

CJA Bradshaw

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Fanciful mathematics and ecological fantasy

3 05 2010

© flickr/themadlolscientist

Bear with me here, dear reader – this one’s a bit of a stretch for conservation relevance at first glance, but it is important. Also, it’s one of my own papers so I have the prerogative :-)

As some of you probably know, I dabble quite a bit in population dynamics theory, which basically means examining the mathematics people use to decipher ecological patterns. Why is this important? Well, most models predicting extinction risk, estimating optimal harvest rates, determining minimum viable population size and metapopulation dynamics for species’ persistence rely on good mathematical abstraction to be realistic. Get the maths wrong, and you could end up overharvesting a species (e.g., 99.99 % of fisheries management), underestimating extinction risk from habitat degradation, and getting your predictions wrong about the effects of invasive species. Expressed as an equation itself, (conservation) ecology = mathematics.

A long-standing family of models known as ‘phenomenological’ models (i.e., because they deal with the phenomenon of population size which is an emergent property of the mechanisms of birth, death and immigration) has been used to estimate everything from maximum sustainable yield targets, temporal abundance patterns, wildlife management interventions, extinction risk to epidemiological patterns. The basic form of the model describes the growth response, or the relationship between the population’s rate of change (growth) and its size. The simplest form (known as the Ricker), assumes a linear decline in population growth rate (r) as the number of individuals increases, which basically means that populations can’t grow indefinitely (i.e., they fluctuate around some carrying capacity if unperturbed). Read the rest of this entry »





Inbreeding does matter

29 03 2010

I’ve been busy with Bill Laurance visiting the University of Adelaide over the last few days, and will be so over the next few as well (and Bill has promised us a guest post shortly), but I wanted to get a post in before the week got away on me.

I’ve come across what is probably the most succinct description of why inbreeding depression is an important aspect of extinctions in free-ranging species (see also previous posts here and here) by Mr. Conservation Genetics himself, Professor Richard Frankham.

Way back in the 1980s (oh, so long ago), Russ Lande produced a landmark paper in Science arguing that population demography was a far more important driver of extinctions than reduced genetic diversity per se. He stated:

“…demography may usually be of more immediate importance than population genetics in determining the minimum viable size of wild populations”

We now know, however, that genetics in fact DO matter, and no one could put it better than Dick Frankham in his latest commentary in Heredity.

I paraphrase some of his main points below:

  • Controversy broke out in the 1970 s when it was suggested that inbreeding was deleterious for captive wildlife, but Ralls and Ballou (1983) reported that 41/44 mammal populations had higher juvenile mortality among inbred than outbred individuals.
  • Crnokrak and Roff (1999) established that inbreeding depression occurred in 90 % of the datasets they examined, and was similarly deleterious across major plant and animal taxa.
  • They estimated that inbreeding depression in the wild has approximately seven times greater impact than in captivity.
  • It is unrealistic to omit inbreeding depression from population viability analysis models.
  • Lande’s contention was rejected when Spielman et al. (2004) found that genetic diversity in 170 threatened taxa was lower than in related non-threatened taxa

Lande might have been incorrect, but his contention spawned the entire modern discipline of conservation genetics. Dick sums up all this so much more eloquently than I’ve done here, so I encourage you to read his article.

CJA Bradshaw

ResearchBlogging.orgFrankham, R. (2009). Inbreeding in the wild really does matter Heredity, 104 (2), 124-124 DOI: 10.1038/hdy.2009.155

Lande, R. (1988). Genetics and demography in biological conservation Science, 241 (4872), 1455-1460 DOI: 10.1126/science.3420403

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A magic conservation number

15 12 2009

Although I’ve already blogged about our recent paper in Biological Conservation on minimum viable population sizes, American Scientist just did a great little article on the paper and concept that I’ll share with you here:

Imagine how useful it would be if someone calculated the minimum population needed to preserve each threatened organism on Earth, especially in this age of accelerated extinctions.

A group of Australian researchers say they have nailed the best figure achievable with the available data: 5,000 adults. That’s right, that many, for mammals, amphibians, insects, plants and the rest.

Their goal wasn’t a target for temporary survival. Instead they set the bar much higher, aiming for a census that would allow a species to pursue a standard evolutionary lifespan, which can vary from one to 10 million years.

That sort of longevity requires abundance sufficient for a species to thrive despite significant obstacles, including random variation in sex ratios or birth and death rates, natural catastrophes and habitat decline. It also requires enough genetic variation to allow adequate amounts of beneficial mutations to emerge and spread within a populace.

“We have suggested that a major rethink is required on how we assign relative risk to a species,” says conservation biologist Lochran Traill of the University of Adelaide, lead author of a Biological Conservation paper describing the projection.

Conservation biologists already have plenty on their minds these days. Many have concluded that if current rates of species loss continue worldwide, Earth will face a mass extinction comparable to the five big extinction events documented in the past. This one would differ, however, because it would be driven by the destructive growth of one species: us.

More than 17,000 of the 47,677 species assessed for vulnerability of extinction are threatened, according to the latest Red List of Threatened Species prepared by the International Union for Conservation of Nature. That includes 21 percent of known mammals, 30 percent of known amphibians, 12 percent of known birds and 70 percent of known plants. The populations of some critically endangered species number in the hundreds, not thousands.

In an effort to help guide rescue efforts, Traill and colleagues, who include conservation biologists and a geneticist, have been exploring minimum viable population size over the past few years. Previously they completed a meta-analysis of hundreds of studies considering such estimates and concluded that a minimum head count of more than a few thousand individuals would be needed to achieve a viable population.

“We don’t have the time and resources to attend to finding thresholds for all threatened species, thus the need for a generalization that can be implemented across taxa to prevent extinction,” Traill says.

In their most recent research they used computer models to simulate what population numbers would be required to achieve long-term persistence for 1,198 different species. A minimum population of 500 could guard against inbreeding, they conclude. But for a shot at truly long-term, evolutionary success, 5,000 is the most parsimonious number, with some species likely to hit the sweet spot with slightly less or slightly more.

“The practical implications are simply that we’re not doing enough, and that many existing targets will not suffice,” Traill says, noting that many conservation programs may inadvertently be managing protected populations for extinction by settling for lower population goals.

The prospect that one number, give or take a few, would equal the minimum viable population across taxa doesn’t seem likely to Steven Beissinger, a conservation biologist at the University of California at Berkeley.

“I can’t imagine 5,000 being a meaningful number for both Alabama beach mice and the California condors. They are such different organisms,” Beissinger says.

Many variables must be considered when assessing the population needs of a given threatened species, he says. “This issue really has to do with threats more than stochastic demography. Take the same rates of reproduction and survival and put them in a healthy environment and your minimum population would be different than in an environment of excess predation, loss of habitat or effects from invasive species.”

But, Beissinger says, Traill’s group is correct for thinking that conservation biologists don’t always have enough empirically based standards to guide conservation efforts or to obtain support for those efforts from policy makers.

“One of the positive things here is that we do need some clear standards. It might not be establishing a required number of individuals. But it could be clearer policy guidelines for acceptable risks and for how many years into the future can we accept a level of risk,” Beissinger says. “Policy people do want that kind of guidance.”

Traill sees policy implications in his group’s conclusions. Having a numerical threshold could add more precision to specific conservation efforts, he says, including stabs at reversing the habitat decline or human harvesting that threaten a given species.

“We need to restore once-abundant populations to the minimum threshold,” Traill says. “In many cases it will make more economic and conservation sense to abandon hopeless-case species in favor of greater returns elsewhere.





Raise targets to prevent extinction

12 11 2009

I know I’ve blogged recently about this, but The Adelaidean did a nice little article that I thought I’d reproduce here. The source can be found here.

Adelaidean story Nov 2009





Susceptibility of sharks, rays and chimaeras to global extinction

10 11 2009
tiger shark

© R. Harcourt

Quite some time ago my colleague and (now former) postdoctoral fellow, Iain Field, and I sat down to examine in gory detail the extent of the threat to global populations of sharks, rays and chimaeras (chondrichthyans). I don’t think we quite realised the mammoth task we had set ourselves. Several years and nearly a hundred pages later, we have finally achieved our goal.

Introducing the new paper in Advances in Marine Biology entitled Susceptibility of sharks, rays and chimaeras to global extinction by Iain Field, Mark Meekan, Rik Buckworth and Corey Bradshaw.

The paper covers the following topics:

  • Chondrichthyan Life Historyangel shark
  • Niche breadth
  • Age and growth
  • Reproduction and survival
  • Past and Present Threats
  • Fishing
  • Beach meshing
  • Habitat loss
  • Pollution and non-indigenous species
  • Chondrichthyan Extinction Risk
  • Drivers of threat risk in chondrichthyans and teleosts
  • Global distribution of threatened chondrichthyan taxa
  • Ecological, life history and human-relationship attributes
  • Threat risk analysis
  • Relative threat risk of chondrichthyans and teleosts
  • Implications of Chondrichthyan Species Loss on Ecosystem Structure, Function and Stability
  • Ecosystem roles of predators
  • Predator loss in the marine realm
  • Ecosystem roles of chondrichthyans
  • Synthesis and Knowledge Gaps
  • Role of fisheries in future chondrichthyan extinctions
  • Climate change
  • Extinction synergies
  • Research needs

common skateAs mentioned, quite a long analysis of the state of sharks worldwide. Bottom line? Well, as most of you might already know sharks aren’t doing too well worldwide, with around 52 % listed on the IUCN’s Red List of Threatened Species. This compares interestingly to bony fishes (teleosts) that, although having only 8 % of all species Red-Listed, are generally in higher-threat Red List categories. We found that body size (positively) and geographic range (negatively) correlated with threat risk in both groups, but Red-Listed bony fishes were still more likely to be categorised as threatened after controlling for these effects.

blue sharkIn some ways this sort of goes against the notion that sharks are inherently more extinction-prone than other fish – a common motherhood statement seen at the beginning of almost all papers dealing with shark threats. What it does say though is that because sharks are on average larger and less fecund than your average fish, they tend to bounce back from declines more slowly, so they are more susceptible to rapid environmental change than your average fish. Guess what? We’re changing the environment pretty rapidly.

We also determined the spatial distribution of threat, and found that Red-Listed species are clustered mainly in (1) south-eastern South America; (2) western Europe and the Mediterranean; (3) western Africa; (4) South China Sea and South East Asia and (5) south-eastern Australia.

shark market, Indonesia

© W. White

Now, what are the implications for the loss of these species? As I’ve blogged recently, the reduction in predators in general can be a bad thing for ecosystems, and sharks are probably some of the best examples of ecosystem structural engineers we know (i.e., eating herbivores; ‘controlling’ prey densities, etc.). So, we should be worried when sharks start to disappear. One thing we also discovered is that we still have a rudimentary understanding of how climate change will affect sharks, the ways in which they structure ecosystems, and how they respond to coastal development. Suffice it to say though that generally speaking, things are not rosy if you’re a shark.

We end off with a recommendation we’ve been promoting elsewhere – we should be managing populations using the minimum viable population (MVP) size concept. Making sure that there are a lot of large, well-connected populations around will be the best insurance against extinction.

CJA Bradshaw

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ResearchBlogging.orgI.C. Field, M.G. Meekan, R.C. Buckworth, & C.J.A. Bradshaw (2009). Susceptibility of Sharks, Rays and Chimaeras to Global Extinction Advances in Marine Biology, 56, 275-363 : 10.1016/S0065-2881(09)56004-X





October Issue of Conservation Letters

18 10 2009

The second-to-last issue in 2009 (October) of Conservation Letters is now out. Click here for full access.

cl2-5

Household goods made of non-timber forest products. © N. Sasaki

Papers in this issue:





Managing for extinction

9 10 2009

ladderAh, it doesn’t go away, does it? Or at least, we won’t let it.

That concept of ‘how many is enough?’ in conservation biology, the so-called ‘minimum viable population size‘, is enough to drive some conservation practitioners batty.

How many times have we heard the (para-) phrase: “It’s simply impractical to bring populations of critically endangered species up into the thousands”?

Well, my friends, if you’re not talking thousands, you’re wasting everyone’s time and money. You are essentially managing for extinction.

Our new paper out online in Biological Conservation entitled Pragmatic population viability targets in a rapidly changing world (Traill et al.) shows that populations of endangered species are unlikely to persist in the face of global climate change and habitat loss unless they number around 5000 mature individuals or more.

After several meta-analytic, time series-based and genetic estimates of the magic minimum number all agreeing, we can be fairly certain now that if a population is much less than several thousands (median = 5000), its likelihood of persisting in the long run in the face of normal random variation is pretty small.

We conclude essentially that many conservation biologists routinely underestimate or ignore the number of animals or plants required to prevent extinction. In fact, aims to maintain tens or hundreds of individuals, when thousands are actually needed, are simply wasting precious and finite conservation resources. Thus, if it is deemed unrealistic to attain such numbers, we essentially advise that in most cases conservation triage should be invoked and the species in question be abandoned for better prospects

A long-standing idea in species restoration programs is the so-called ‘50/500’ rule; this states that at least 50 adults are required to avoid the damaging effects of inbreeding, and 500 to avoid extinctions due to the inability to evolve to cope with environmental change. Our research suggests that the 50/500 rule is at least an order of magnitude too small to stave off extinction.

This does not necessarily imply that populations smaller than 5000 are doomed. But it does highlight the challenge that small populations face in adapting to a rapidly changing world.

We are battling to prevent a mass extinction event in the face of a growing human population and its associated impact on the planet, but the bar needs to be a lot higher. However, we shouldn’t necessarily give up on critically endangered species numbering a few hundred of individuals in the wild. Acceptance that more needs to be done if we are to stop ‘managing for extinction’ should force decision makers to be more explicit about what they are aiming for, and what they are willing to trade off, when allocating conservation funds.

CJA Bradshaw

(with thanks to Lochran Traill, Barry Brook and Dick Frankham)

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This post was chosen as an Editor's Selection for ResearchBlogging.orgResearchBlogging.org

Traill, L.W., Brook, B.W., Frankham, R.R., & Bradshaw, C.J.A. (2009). Pragmatic population viability targets in a rapidly changing world Biological Conservation DOI: 10.1016/j.biocon.2009.09.001





Wobbling to extinction

31 08 2009

crashI’ve been meaning to highlight for a while a paper that I’m finding more and more pertinent as a citation in my own work. The general theme is concerned with estimating extinction risk of a particular population, species (or even ecosystem), and more and more we’re finding that different drivers of population decline and eventual extinction often act synergistically to drive populations to that point of no return.

In other words, the whole is greater than the sum of its parts.

In other, other words, extinction risk is usually much higher than we generally appreciate.

This might seem at odds with my previous post about the tendency of the stochastic exponential growth model to over-estimate extinction risk using abundance time series, but it’s really more of a reflection of our under-appreciation of the complexity of the extinction process.

In the early days of ConservationBytes.com I highlighted a paper by Fagan & Holmes that described some of the few time series of population abundances right up until the point of extinction – the reason these datasets are so rare is because it gets bloody hard to find the last few individuals before extinction can be confirmed. Most recently, Melbourne & Hastings described in a paper entitled Extinction risk depends strongly on factors contributing to stochasticity published in Nature last year how an under-appreciated component of variation in abundance leads to under-estimation of extinction risk.

‘Demographic stochasticity’ is a fancy term for variation in the probability of births deaths at the individual level. Basically this means that there will be all sorts of complicating factors that move any individual in a population away from its expected (mean) probability of dying or reproducing. When taken as a mean over a lot of individuals, it has generally been assumed that demographic stochasticity is washed out by other forms of variation in mean (population-level) birth and death probability resulting from vagaries of the environmental context (e.g., droughts, fires, floods, etc.).

‘No, no, no’, say Melbourne & Hastings. Using some relatively simple laboratory experiments where environmental stochasticity was tightly controlled, they showed that demographic stochasticity dominated the overall variance and that environmental variation took a back seat. The upshot of all these experiments and mathematical models is that for most species of conservation concern (i.e., populations already reduced below to their minimum viable populations size), not factoring in the appropriate measures of demographic wobble means that most people are under-estimating extinction risk.

Bloody hell – we’ve been saying this for years; a few hundred individuals in any population is a ridiculous conservation target. People must instead focus on getting their favourite endangered species to number at least in the several thousands if the species is to have any hope of persisting (this is foreshadowing a paper we have coming out shortly in Biological Conservationstay tuned for a post thereupon).

Melbourne & Hastings have done a grand job in reminding us how truly susceptible small populations are to wobbling over the line and disappearing forever.

CJA Bradshaw

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Not-so-scary maths and extinction risk

27 08 2009
© P. Horn

© P. Horn

Population viability analysis (PVA) and its cousin, minimum viable population (MVP) size estimation, are two generic categories for mathematically assessing a population’s risk of extinction under particular environmental scenarios (e.g., harvest regimes, habitat loss, etc.) (a personal plug here, for a good overview of general techniques in mathematical conservation ecology, check out our new chapter entitled ‘The Conservation Biologist’s Toolbox…’ in Sodhi & Ehrlich‘s edited book Conservation Biology for All by Oxford University Press [due out later this year]). A long-standing technique used to estimate extinction risk when the only available data for a population are in the form of population counts (abundance estimates) is the stochastic exponential growth model (SEG). Surprisingly, this little beauty is relatively good at predicting risk even though it doesn’t account for density feedback, age structure, spatial complexity or demographic stochasticity.

So, how does it work? Well, it essentially calculates the mean and variance of the population growth rate, which is just the logarithm of the ratio of an abundance estimate in one year to the abundance estimate in the previous year. These two parameters are then resampled many times to estimate the probability that abundance drops below a certain small threshold (often set arbitrarily low to something like < 50 females, etc.).

It is simple (funny how maths can become so straightforward to some people when you couch them in words rather than mathematical symbols), and rather effective. This is why a lot of people use it to prescribe conservation management interventions. You don’t have to be a modeller to use it (check out Morris & Doak’s book Quantitative Conservation Biology for a good recipe-like description).

But (there’s always a but), a new paper just published online in Conservation Letters by Bruce Kendall entitled The diffusion approximation overestimates extinction risk for count-based PVA questions the robustness when the species of interest breeds seasonally. You see, the diffusion approximation (the method used to estimate that extinction risk described above) generally assumes continuous breeding (i.e., there are always some females producing offspring). Using some very clever mathematics, simulation and a bloody good presentation, Kendall shows quite clearly that the diffusion approximation SEG over-estimates extinction risk when this happens (and it happens frequently in nature). He also offers a new simulation method to get around the problem.

Who cares, apart from some geeky maths types (I include myself in that group)? Well, considering it’s used so frequently, is easy to apply and it has major implications for species threat listings (e.g., IUCN Red List), it’s important we estimate these things as correctly as we can. Kendall shows how several species have already been misclassified for threat risk based on the old technique.

So, once again mathematics has the spotlight. Thanks, Bruce, for demonstrating how sound mathematical science can pave the way for better conservation management.

CJA Bradshaw

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Vortex of travel to RAMAStan

9 06 2009




Just a short post to say that the frequency of posts might decline somewhat over the coming weeks. I’m currently travelling in the US on a mixture of leave and work.

From the work side of things, I’ll be heading shortly to Harvard University in Boston to spend some time with colleague Navjot Sodhi of the National University of Singapore who’s finishing up a year-long Hrdy Fellowship there. We’ll be joined by my close friend and colleague, Barry Brook, and Resit Akçakaya of RAMAS fame. We’ll be working on a few ideas regarding extinction dynamics, modelling and climate change projections for species distributions and risk.

We’ll be heading next to visit Bob Lacy of VORTEX fame at the Chicago Zoological Society. We’ll be joined by Phil Miller of the IUCN‘s Species Survival Commission (SSC) Conservation Breeding Specialist Group, JP Pollak of Cornell University, and maybe Jon Ballou of the Smithsonian National Zoological Park. We’re hoping to help take the next generation of species vulnerability software into a more realistic framework that accounts for the complexities of climate change.

I’m looking forward to the trip and meeting new colleagues.

CJA Bradshaw