Western Australia’s moronic shark cull

4 07 2014

another stupid politicianA major media release today coordinated by Jessica Meeuwig in Western Australia makes the (obvious) point that there’s no biological justification to cull sharks.

301 Australian and International Scientists experts have today provided their submission to the Western Australia Environmental Protection Authority (EPA), rejecting the scientific grounds for the proposed three-year drum-line programme.

Coordinating scientist, Professor Jessica Meeuwig from the University of Western Australia said:

“To have over 300 researchers, including some of the world’s top shark specialists and marine ecologists, all strongly agreeing that there is no scientific basis for the lethal drum-line programme, tells you how unjustified the government’s proposal is. If the EPA and the Federal Minister for the Environment are using science for decisions, the drum-line proposal should not be approved.”

The experts agree that the proposal presents no evidence that the lethal drum-line programme, as implemented, will improve ocean safety. It ignores evidence from other hook-based programs in Hawaii and Queensland that have been shown to be ineffective in reducing shark attacks on humans.

Dr. Christopher Neff from the University of Sydney stated:

“There is no evidence that drum lines reduce shark bites. The Western Australia EPA now faces a question of science versus politics with global implications because it is considering establishing a new international norm that would allow for the killing of protected white sharks.”

The drum lines are ineffective and indiscriminate, with 78% of the sharks captured not considered ‘threatening’ to humans. Yet, scientifically supported, non-lethal alternatives such as the South African ‘Shark Spotter’ and Brazil’s ‘Tag and Remove’ programmes are not adequately assessed as viable options for Western Australia. Read the rest of this entry »





Ecological processes depend on …

14 05 2014
© Cagan Sekercioglu

© Cagan Sekercioglu

I have been known to say (ok – I say it all the time) that ecologists should never equivocate when speaking to the public. Whether it’s in a media release, blog post, television presentation or newspaper article, just stick to ‘yes’ or ‘no’. In other words, don’t qualify your answer with some horrid statistical statement (i.e., in 95% of cases …) or say something like “… but it really depends on …”. People don’t understand uncertainty – to most people, ‘uncertainty’ means “I don’t know” or worse, “I made it all up”.

But that’s only in the movies.

In real ‘ecological’ life, things are vastly different. It’s never as straightforward as ‘yes’ or ‘no’, because ecology is complex. There are times that I forget this important aspect when testing a new hypothesis with what seem like unequivocal data, but then reality always hits.

Our latest paper is the epitome of this emergent complexity from what started out as a fairly simple question using some amazing data. What makes birds change their range1? We looked at this question from a slightly different angle than had been done before because we had access to climate data, life-history data and most importantly, actual range change data. It’s that latter titbit that is typically missing from studies aiming to understand what drives species toward a particular fate; whether it’s a species distribution model predicting the future habitat suitability of some species as a function of climate change, or the past dynamics of some species related to its life history pace, most often the combined dynamics are missing. Read the rest of this entry »





We’re sorry, but 50/500 is still too few

28 01 2014

too fewSome of you who are familiar with my colleagues’ and my work will know that we have been investigating the minimum viable population size concept for years (see references at the end of this post). Little did I know when I started this line of scientific inquiry that it would end up creating more than a few adversaries.

It might be a philosophical perspective that people adopt when refusing to believe that there is any such thing as a ‘minimum’ number of individuals in a population required to guarantee a high (i.e., almost assured) probability of persistence. I’m not sure. For whatever reason though, there have been some fierce opponents to the concept, or any application of it.

Yet a sizeable chunk of quantitative conservation ecology develops – in various forms – population viability analyses to estimate the probability that a population (or entire species) will go extinct. When the probability is unacceptably high, then various management approaches can be employed (and modelled) to improve the population’s fate. The flip side of such an analysis is, of course, seeing at what population size the probability of extinction becomes negligible.

‘Negligible’ is a subjective term in itself, just like the word ‘very‘ can mean different things to different people. This is why we looked into standardising the criteria for ‘negligible’ for minimum viable population sizes, almost exactly what the near universally accepted IUCN Red List attempts to do with its various (categorical) extinction risk categories.

But most reasonable people are likely to agree that < 1 % chance of going extinct over many generations (40, in the case of our suggestion) is an acceptable target. I’d feel pretty safe personally if my own family’s probability of surviving was > 99 % over the next 40 generations.

Some people, however, baulk at the notion of making generalisations in ecology (funny – I was always under the impression that was exactly what we were supposed to be doing as scientists – finding how things worked in most situations, such that the mechanisms become clearer and clearer – call me a dreamer).

So when we were attacked in several high-profile journals, it came as something of a surprise. The latest lashing came in the form of a Trends in Ecology and Evolution article. We wrote a (necessarily short) response to that article, identifying its inaccuracies and contradictions, but we were unable to expand completely on the inadequacies of that article. However, I’m happy to say that now we have, and we have expanded our commentary on that paper into a broader review. Read the rest of this entry »





Cleaning up the rubbish: Australian megafauna extinctions

15 11 2013

diprotodonA few weeks ago I wrote a post about how to run the perfect scientific workshop, which most of you thought was a good set of tips (bizarrely, one person was quite upset with the message; I saved him the embarrassment of looking stupid online and refrained from publishing his comment).

As I mentioned at the end of post, the stimulus for the topic was a particularly wonderful workshop 12 of us attended at beautiful Linnaeus Estate on the northern coast of New South Wales (see Point 5 in the ‘workshop tips’ post).

But why did a group of ecological modellers (me, Barry Brook, Salvador Herrando-Pérez, Fréd Saltré, Chris Johnson, Nick Beeton), ancient DNA specialists (Alan Cooper), palaeontologists (Gav Prideaux), fossil dating specialists (Dizzy Gillespie, Bert Roberts, Zenobia Jacobs) and palaeo-climatologists (Michael Bird, Chris Turney [in absentia]) get together in the first place? Hint: it wasn’t just the for the beautiful beach and good wine.

I hate to say it – mainly because it deserves as little attention as possible – but the main reason is that we needed to clean up a bit of rubbish. The rubbish in question being the latest bit of excrescence growing on that accumulating heap produced by a certain team of palaeontologists promulgating their ‘it’s all about the climate or nothing’ broken record.

Read the rest of this entry »





Don’t blame it on the dingo

21 08 2013

dingo angelOur postdoc, Tom Prowse, has just had one of the slickest set of reviews I’ve ever seen, followed by a quick acceptance of what I think is a pretty sexy paper. Earlier this year his paper in Journal of Animal Ecology showed that thylacine (the badly named ‘Tasmanian tiger‘) was most likely not the victim of some unobserved mystery disease, but instead succumbed to what many large predators have/will: human beings. His latest effort now online in Ecology shows that the thylacine and devil extinctions on the Australian mainland were similarly the result of humans and not the scapegoat dingo. But I’ll let him explain:

‘Regime shifts’ can occur in ecosystems when sometimes even a single component is added or changed. Such additions, of say a new predator, or changes such as a rise in temperature, can fundamentally alter core ecosystem functions and processes, causing the ecosystem to switch to some alternative stable state.

Some of the most striking examples of ecological regime shifts are the mass extinctions of large mammals (‘megafauna’) during human prehistory. In Australia, human arrival and subsequent hunting pressure is implicated in the rapid extinction of about 50 mammal species by around 45 thousand years ago. The ensuing alternative stable state was comprised of a reduced diversity of predators, dominated by humans and two native marsupial predators ‑ the thylacine (also known as the marsupial ‘tiger’ or ‘wolf’) and the devil (which is now restricted to Tasmania and threatened by a debilitating, infectious cancer).

Both thylacines and devils lasted on mainland Australia for over 40 thousand years following the arrival of humans. However, a second regime shift resulted in the extinction of both these predators by about 3 thousand years ago, which was coincidentally just after dingoes were introduced to Australia. Dingoes are descended from early domestic dogs and were introduced to northern Australia from Asia by ancient traders approximately 4 thousand years ago. Today, they are Australia’s only top predator remaining, other than invasive European foxes and feral cats. Since the earliest days of European settlement, dingoes have been persecuted because they prey on livestock. During the 1880s, 5614 km of ‘dingo fence’ was constructed to protect south-east Australia’s grazing rangelands from dingo incursions. The fence is maintained to this day, and dingoes are poisoned and shot both inside and outside this barrier, despite mounting evidence that these predators play a key role in maintaining native ecosystems, largely by suppressing invasive predators.

Perhaps because the public perception of dingoes as ‘sheep-killers’ is so firmly entrenched, it has been commonly assumed that dingoes killed off the thylacines and devils on mainland Australia. People who support this view also point out that thylacines and devils persisted on the island of Tasmania, which was never colonised by dingoes (although thylacines went extinct there too in the early 1900s). To date, most discussion of the mainland thylacine and devil extinctions has focused on the possibility that dingoes disrupted the system by ‘exploitation competition’ (eating the same prey), ‘interference competition’ (wasting the native predators’ precious munching time), as well as ‘direct predation’ (dingoes actually eating devils and thylacines). Read the rest of this entry »





Fast-lane mesopredators

29 07 2013

Another post from Alejandro Frid (a modified excerpt from a chapter of his forthcoming book).

I fall in love easy. Must be my Latino upbringing. Whatever it is, I have no choice on the matter. So for five years and counting, I have been passionate about lingcod (Ophiodon elongatus) and rockfish (Sebastes spp.), upper- and mid-level predatory fishes on rocky reefs of the Northeast Pacific.

Lingcod are beautiful and fierce. Rockfish are cosmic. Both taste mighty good and—surprise, surprise—have been overfished to smithereens throughout much of their range. Howe Sound, my field site near Vancouver, British Columbia, is no exception, although new protective legislation might be starting to give them some slack.

Our dive surveys1 and earlier studies, in combination, have pieced together a story of ecosystem change. In the Howe Sound of today, lingcod rarely exceed body lengths of 80 cm. But up to 30 years ago, when overfishing had yet to inflict the full extent of its current damage, lingcod with lengths of 90 to 100 cm had been common in the area. There is nothing unique about this; most fisheries target the biggest individuals, ultimately reducing maximum body size within each species of predatory fish.

As predators shrink, the vibrant tension of predation risk slips away. The mechanism of change has a lot to do with mouth size. Predatory fishes swallow prey whole, usually head or tail first, so it is impossible for them to eat prey bigger than the width and height of their open jaws. And bigger fishes have bigger jaws, which makes them capable not only of consuming larger prey, but also of scaring bigger prey into using antipredator behaviours, such as hiding in rocky crevices. As predators shrink, big prey enter a size refuge and only small prey remain at risk, which can alter trophic cascades and other indirect species interactions. Read the rest of this entry »





Saving world’s most threatened cat requires climate adaptation

23 07 2013
© CSIC Andalusia Audiovisual Bank/H. Garrido

© CSIC Andalusia Audiovisual Bank/H. Garrido

The Iberian lynx is the world’s most threatened cat, with recent counts estimating only 250 individuals surviving in the wild. Recent declines of Iberian lynx have been associated with sharp regional reductions in the abundance of its main prey, the European rabbit, caused mainly by myxomatosis virus and rabbit haemorrhagic disease. At present, only two Iberian lynx populations persist in the wild compared with nine in the 1990s.

Over €90 million has been spent since 1994 to mitigate the extinction risk of this charismatic animal, mainly through habitat management, reduction of human-caused mortality and, more recently, translocation. Although lynx abundance might have increased in the last ten years in response to intensive management, a new study published in Nature Climate Change warns that the ongoing conservation strategies could buy just a few decades before the species goes extinct.

The study led by Damien Fordham from The Environment Institute (The University of Adelaide) and Miguel Araújo from the Integrative Biogeography and Global Change Group (Spanish Research Council) shows that climate change could lead to a rapid and severe decrease in lynx abundance in coming decades, and probably result in its extinction in the wild within 50 years. Current management efforts could be futile if they do not take into account the combined effects of climate change, land use and prey abundance on population dynamics of the Iberian Lynx.

Read the rest of this entry »





Software tools for conservation biologists

8 04 2013

computer-programmingGiven the popularity of certain prescriptive posts on ConservationBytes.com, I thought it prudent to compile a list of software that my lab and I have found particularly useful over the years. This list is not meant to be comprehensive, but it will give you a taste for what’s out there. I don’t list the plethora of conservation genetics software that is available (generally given my lack of experience with it), but if this is your chosen area, I’d suggest starting with Dick Frankham‘s excellent book, An Introduction to Conservation Genetics.

1. R: If you haven’t yet loaded the open-source R programming language on your machine, do it now. It is the single-most-useful bit of statistical and programming software available to anyone anywhere in the sciences. Don’t worry if you’re not a fully fledged programmer – there are now enough people using and developing sophisticated ‘libraries’ (packages of functions) that there’s pretty much an application for everything these days. We tend to use R to the exclusion of almost any other statistical software because it makes you learn the technique rather than just blindly pressing the ‘go’ button. You could also stop right here – with R, you can do pretty much everything else that the software listed below does; however, you have to be an exceedingly clever programmer and have a lot of spare time. R can also sometimes get bogged down with too much filled RAM, in which case other, compiled languages such as PYTHON and C# are useful.

2. VORTEX/OUTBREAK/META-MODEL MANAGER, etc.: This suite of individual-based projection software was designed by Bob Lacy & Phil Miller initially to determine the viability of small (usually captive) populations. The original VORTEX has grown into a multi-purpose, powerful and sophisticated population viability analysis package that now links to its cousin applications like OUTBREAK (the only off-the-shelf epidemiological software in existence) via the ‘command centre’ META-MODEL MANAGER (see an examples here and here from our lab). There are other add-ons that make almost any population projection and hindcasting application possible. And it’s all free! (warning: currently unavailable for Mac, although I’ve been pestering Bob to do a Mac version).

3. RAMAS: RAMAS is the go-to application for spatial population modelling. Developed by the extremely clever Resit Akçakaya, this is one of the only tools that incorporates spatial meta-population aspects with formal, cohort-based demographic models. It’s also very useful in a climate-change context when you have projections of changing habitat suitability as the base layer onto which meta-population dynamics can be modelled. It’s not free, but it’s worth purchasing. Read the rest of this entry »





Want to work with us?

22 03 2013
© Beboy-Fotolia

© Beboy-Fotolia

Today we announced a HEAP of positions in our Global Ecology Lab for hot-shot, up-and-coming ecologists. If you think you’ve got what it takes, I encourage you to apply. The positions are all financed by the Australian Research Council from grants that Barry Brook, Phill Cassey, Damien Fordham and I have all been awarded in the last few years. We decided to do a bulk advertisement so that we maximise the opportunity for good science talent out there.

We’re looking for bright, mathematically adept people in palaeo-ecology, wildlife population modelling, disease modelling, climate change modelling and species distribution modelling.

The positions are self explanatory, but if you want more information, just follow the links and contacts given below. For my own selfish interests, I provide a little more detail for two of the positions for which I’m directly responsible – but please have a look at the lot.

Good luck!

CJA Bradshaw

Job Reference Number: 17986 & 17987

The world-leading Global Ecology Group within the School of Earth and Environmental Sciences currently has multiple academic opportunities. For these two positions, we are seeking a Postdoctoral Research Associate and a Research Associate to work in palaeo-ecological modelling. Read the rest of this entry »





Food for sex

18 03 2013
Quercus_KakFeed Photo
Kakapo are unique among the ~ 400 parrot species (Psittaciformes) for being flightless, nocturnal and extremely long-lived (up to 100 years!). Additionally, they are herbivorous (seeds, fruits, polen, plants), males can weigh up to 2-4 kg (40% heavier than females), and females lay their eggs on the ground or cavities – i.e., 3 eggs in a single clutch annually, although 2 clutches might occur if the nest fails at the beginning of the reproductive season or if the eggs are taken for artificial incubation.Native to New Zealand, kakapo once inhabited the subalpine fringes of forest and scrub. Polynesians (1000 years ago) and Europeans (mostly in the XIX Century) arrived in the archipelago accompanied by dogs, cats, rats and mustelids that cornered kakapo populations in the Fiordland region (south-west of the South Island) where it was declared extinct in 1989. In 1977, a population of some 200 individuals was found on Stewart Island - this population was already in decline to the claws and jaws of feral cats. By the 1980s, the failure of captive breeding programs prompted the transfer of 60 individuals from Steward to carnivore-free islands. The global (known) population ‘rocketed’ from 50 individuals in 1999 to 126 in the 2012 censuses and, consequently, the kakapo’s IUCN status changed in 2000 from ‘Extinct in the Wild’ to ‘Critically Endangered’. Under the management of the Kakapo Recovery Programme, kakapo are now present on the islands of CodfishAnchor and Little Barrier.

Inbreeding, system shocks caused by fire or cyclones (for example), or demographic stochasticity (by which two or more outcomes are possible) such as how many males and females will be born in a single year, are all factors that threaten the persistence of small and fragmented populations. They can, however, be reverted by conservation actions.

If you have ever taken dancing classes, you will be familiar with the scarcity of male partners and how this can jeopardize group learning. When reproduction, rather than salsa pirouettes, is at stake, a biased sex ratio can compromise the persistence of species. For instance, when females are unable to find males (or vice versa), fertility rates can collapse as a result – a well-known cause of an Allee effect (1). Curiously, natural selection can promote such bias by favouring a species’ investment in litters dominated by one of the two genders. The evolutionary formulation of such scenario is that females can adjust the sex ratio of their offspring depending on the amount of available resources (2) – see contrasting cross-taxa studies on this subject (3-5). Thus, when resources abound (e.g., food), mothers can afford the offspring’s gender requiring more resources to reach adulthood or once adulthood is reached, is less likely to reproduce successfully (6). This predisposition to one gender or another can be key to the conservation of endangered species (7).

The kakapo case

At the end of the 1990s, the New Zealand Department of Conservation placed dispensers of supplementary food in the territories of some kakapo (a rather enormous, flightless parrot Strigops habroptilus) to encourage their reproduction. Back then, only 60 individuals were left of the entire species . Unfortunately, those females with access to the supplemental food conceived 67% of male chicks (so exacerbating the fact that kakapo populations are naturally male-biased), while those females without extra feeding had 71% of female chicks (8). Something wasn’t working. Read the rest of this entry »





Science immortalised in cartoon

1 02 2013

Well, this is a first for me (us).

I’ve never had a paper of ours turned into a cartoon. The illustrious and brilliant ‘First Dog on the Moon‘ (a.k.a. Andrew Marlton) who is chief cartoonist for Australia’s irreverent ‘Crikey‘ online news magazine just parodied our Journal of Animal Ecology paper No need for disease: testing extinction hypotheses for the thylacine using multispecies metamodels that I wrote about a last month here on ConservationBytes.com.

Needless to say, I’m chuffed as a chuffed thing.

Enjoy!

Stripey





No need for disease

7 01 2013

dead or alive thylacineIt’s human nature to abhor admitting an error, and I’d wager that it’s even harder for the average person (psycho- and sociopaths perhaps excepted) to admit being a bastard responsible for the demise of someone, or something else. Examples abound. Think of much of society’s unwillingness to accept responsibility for global climate disruption (how could my trips to work and occasional holiday flight be killing people on the other side of the planet?). Or, how about fishers refusing to believe that they could be responsible for reductions in fish stocks? After all, killing fish couldn’t possibly …er, kill fish? Another one is that bastion of reverse racism maintaining that ancient or traditionally living peoples (‘noble savages’) could never have wiped out other species.

If you’re a rational person driven by evidence rather than hearsay, vested interest or faith, then the above examples probably sound ridiculous. But rest assured, millions of people adhere to these points of view because of the phenomenon mentioned in the first sentence above. With this background then, I introduce a paper that’s almost available online (i.e., we have the DOI, but the online version is yet to appear). Produced by our extremely clever post-doc, Tom Prowse, the paper is entitled: No need for disease: testing extinction hypotheses for the thylacine using multispecies metamodels, and will soon appear in Journal of Animal Ecology.

Of course, I am biased being a co-author, but I think this paper really demonstrates the amazing power of retrospective multi-species systems modelling to provide insight into phenomena that are impossible to test empirically – i.e., questions of prehistoric (and in some cases, even data-poor historic) ecological change. The megafauna die-off controversy is one we’ve covered before here on ConservationBytes.com, and this is a related issue with respect to a charismatic extinction in Australia’s recent history – the loss of the Tasmanian thylacine (‘tiger’, ‘wolf’ or whatever inappropriate eutherian epithet one unfortunately chooses to apply). Read the rest of this entry »





Individuals a population to conserve make

28 11 2012
Unique in its genus, the saiga antelope inhabits the steppes and semi-desert environments in two sub-species split between Kazakhstan (Saiga tatarica tatarica, ~ 80% of the individuals) and Mongolia (Saiga tatarica mongolica). Locals hunt them for their meat and the (attributed) medicinal properties of male horns. Like many ungulates, the population is sensitive to winter severity and summer drought (which signal seasonal migrations of herds up to 1000 individuals). But illegal poaching has reduced the species from > 1 million in the 1970s to ~ 50000 currently (see RT video). The species has gone extinct in China and Ukraine, and has been IUCN “Critically Endangered” from 2002. The photo shows a male in The Centre for Wild Animals, Kalmykia, Russia (courtesy of Pavel Sorokin).

In a planet approaching 7 billion people, individual identity for most of us goes largely unnoticed by the rest. However, individuals are important because each can promote changes at different scales of social organisation, from families through to associations, suburbs and countries. This is not only true for the human species, but for any species (1).

It is less than two decades since many ecologists started pondering the ways of applying the understanding of how individuals behave to the conservation of species (2-9), which some now refer to as ‘conservation behaviour’ (10, 11). The nexus seems straightforward. The decisions a bear or a shrimp make daily to feed, mate, move or shelter (i.e., their behaviour) affect their fitness (survival + fertility). Therefore, the sum of those decisions across all individuals in a population or species matters to the core themes handled by conservation biology for ensuring long-term population viability (12), i.e., counteracting anthropogenic impacts, and (with the distinction introduced by Cawley, 13) reversing population decline and avoiding population extinction.

To use behaviour in conservation implies that we can modify the behaviour of individuals to their own benefit (and mostly, to the species’ benefit) or define behavioural metrics that can be used as indicators of population threats. A main research area dealing with behavioural modification is that of anti-predator training of captive individuals prior to re-introduction. Laden with nuances, those training programs have yielded contrasting results across species, and have only tested a few instances of ‘success’ after release into the wild (14). For example, captive black-tailed prairie dogs (Cynomys ludovicianus) exposed to stuffed hawks, caged ferrets and rattlesnakes had higher post-release survival than untrained individuals in the grasslands of the North American Great Plains (15). A clear example of a threat metric is aberrant behaviour triggered by hunting. Eleanor Milner-Gulland et al. (16) have reported a 46 % reduction in fertility rates in the saiga antelope (Saiga tatarica) in Russia from 1993-2002. This species forms harems consisting of one alpha male and 12 to 30 females. Local communities have long hunted this species, but illegal poaching for horned males from the early 1990s (17) ultimately led to harems with a female surplus (with an average sex ratio up to 100 females per male!). In them, only a few dominant females seem to reproduce because they engage in aggressive displays that dissuade other females from accessing the males. Read the rest of this entry »





Global Ecology postgraduate opportunities

12 08 2012

I should have published these ages ago, but like many things I have should have done earlier, I didn’t.

I also apologise for a bit of silence over the past week. After coming back from the ESP Conference in Portland, I’m now back at Stanford University working with Paul Ehrlich trying to finish our book (no sneak peaks yet, I’m afraid). I have to report that we’ve completed about about 75 % it, and I’m starting to feel like the end is in sight. We hope to have it published early in 2013.

So here they are – the latest 9 PhD offerings from us at the Global Ecology Laboratory. If you want to get more information, contact the first person listed as the first supervisor at the end of each project’s description.

1. Optimal survey and harvest models for South Australian macropods (I’ve advertised this before, but so far, no takers):

The South Australia Department of Environment, Water and Natural Resources (DEWNR) is custodian of a long-term macropod database derived from the State’s management of the commercial kangaroo harvest industry. The dataset entails aerial survey data for most of the State from 1978 to present, annual population estimates, quotas and harvests for three species: red kangaroo (Macropus rufus), western grey kangaroo (Macropus fuliginosus), and the euro (Macropus robustus erubescens).

DEWNR wishes to improve the efficiency of surveys and increase the precision of population estimates, as well as provide a more quantitative basis for setting harvest quotas.

We envisage that the PhD candidate will design and construct population models:

  • to predict population size/densities with associated uncertainty, linking fluctuations to environmental variability (including future climate change projections)
  • to evaluate the efficiency of spatially explicit aerial surveys
  • to estimate demographic parameters (e.g., survival rate) from life tables and
  • to estimate spatially explicit sustainable harvest quotas

 Supervisors: me, A/Prof. Phill Cassey, Dr Damien Fordham, Dr Brad Page (DEWNR), Professor Michelle Waycott (DEWNR).

2. Correcting for the Signor-Lipps effect

The ‘Signor-Lipps effect’ in palaeontology is the notion that the last organism of a given species will never be recorded as a fossil given the incomplete nature of the fossil record (the mirror problem is the ‘Jaanusson effect’, where the first occurrence is delayed past the true time of origination). This problem makes inference about the timing and speed of mass extinctions (and evolutionary diversification events) elusive. The problem is further complicated by the concept known as the ‘pull of the recent’, which states that the more time since an event occurred, the greater the probability that evidence of that event will have disappeared (e.g., erased by erosion, hidden by deep burial, etc.).

In a deep-time context, these problems confound the patterns of mass extinctions – i.e., the abruptness of extinction and the dynamics of recovery and speciation. This PhD project will apply a simulation approach to marine fossil time series (for genera and families, and some individual species) covering the Phanerozoic Aeon, as well as other taxa straddling the K-T boundary (Cretaceous mass extinction). The project will seek to correct for taphonomic biases and assess the degree to which extinction events for different major taxa were synchronous.

The results will also have implications for the famous Sepkoski curve, which describes the apparent logistic increase in marine species diversity over geological time with an approximate ‘carrying capacity’ reached during the Cenozoic. Despite recent demonstration that this increase is partially a taphonomic artefact, a far greater development and validation/sensitivity analysis of underlying statistical models is needed to resolve the true patterns of extinction and speciation over this period.

The approach will be to develop a series of models describing the interaction of the processes of speciation, local extinction and taphonomic ‘erasure’ (pull of the recent) to simulate how these processes interact to create the appearance of growth in numbers of taxa over time (Sepkoski curve) and the abruptness of mass extinction events. The candidate will estimate key parameters in the model to test whether the taphonomic effect is strong enough to be the sole explanation of the apparent temporal increase in species diversity, or whether true diversification accounts for this.

Supervisors: me, Prof. Barry Brook

3. Genotypic relationships of Australian rabbit populations and consequences for disease dynamics

Historical evidence suggests that there were multiple introduction events of European rabbits into Australia. In non-animal model weed systems it is clear that biocontrol efficacy is strongly influenced by the degree of genetic diversity and number of breed variants in the population.

The PhD candidate will build phylogenetic relationships for Australian rabbit populations and develop landscape genetic models for exploring the influence of myxomatosis and rabbit haemorrhagic disease virus (RHDV) on rabbit vital rates (survival, reproduction and dispersal) at regional and local scales. Multi-model synthesis will be used to quantify the relative roles of environment (including climate) and genotype on disease prevalence and virulence in rabbit populations.

Supervisors: A/Prof Phill Cassey, Dr Damien Fordham, Prof Barry Brook Read the rest of this entry »





Conservation catastrophes

22 02 2012

David Reed

The title of this post serves two functions: (1) to introduce the concept of ecological catastrophes in population viability modelling, and (2) to acknowledge the passing of the bloke who came up with a clever way of dealing with that uncertainty.

I’ll start with latter first. It came to my attention late last year that a fellow conservation biologist colleague, Dr. David Reed, died unexpectedly from congestive heart failure. I did not really mourn his passing, for I had never met him in person (I believe it is disingenuous, discourteous, and slightly egocentric to mourn someone who you do not really know personally – but that’s just my opinion), but I did think at the time that the conservation community had lost another clever progenitor of good conservation science. As many CB readers already know, we lost a great conservation thinker and doer last year, Professor Navjot Sodhi (and that, I did take personally). Coincidentally, both Navjot and David died at about the same age (49 and 48, respectively). I hope that the being in one’s late 40s isn’t particularly presaged for people in my line of business!

My friend, colleague and lab co-director, Professor Barry Brook, did, however, work a little with David, and together they published some pretty cool stuff (see References below). David was particularly good at looking for cross-taxa generalities in conservation phenomena, such as minimum viable population sizes, effects of inbreeding depression, applications of population viability analysis and extinction risk. But more on some of that below. Read the rest of this entry »





Better SAFE than sorry

30 11 2011

Last day of November already – I am now convinced that my suspicions are correct: time is not constant and in fact accelerates as you age (in mathematical terms, a unit of time becomes a progressively smaller proportion of the time elapsed since your birth, so this makes sense). But, I digress…

This short post will act mostly as a spruik for my upcoming talk at the International Congress for Conservation Biology next week in Auckland (10.30 in New Zealand Room 2 on Friday, 9 December) entitled: Species Ability to Forestall Extinction (SAFE) index for IUCN Red Listed species. The post also sets a bit of the backdrop to this paper and why I think people might be interested in attending.

As regular readers of CB will know, we published a paper this year in Frontiers in Ecology and the Environment describing a relatively simple metric we called SAFE (Species Ability to Forestall Extinction) that could enhance the information provided by the IUCN Red List of Threatened Species for assessing relative extinction threat. I won’t go into all the detail here (you can read more about it in this previous post), but I do want to point out that it ended up being rather controversial.

The journal ended up delaying final publication because there were 3 groups who opposed the metric rather vehemently, including people who are very much in the conservation decision-making space and/or involved directly with the IUCN Red List. The journal ended up publishing our original paper, the 3 critiques, and our collective response in the same issue (you can read these here if you’re subscribed, or email me for a PDF reprint). Again, I won’t go into an detail here because our arguments are clearly outlined in the response.

What I do want to highlight is that even beyond the normal in-print tête-à-tête the original paper elicited, we were emailed by several people behind the critiques who were apparently unsatisfied with our response. We found this slightly odd, because many of the objections just kept getting re-raised. Of particular note were the accusations that: Read the rest of this entry »





Sustainable kangaroo harvests

10 11 2011

When I first started this blog back in 2008, I extolled the conservation virtues of eating kangaroos over cattle and sheep. Now I want to put my academic money where my mouth is, and do some kangaroo harvest research.

Thanks to the South Australia Department of Environment and Natural Resources  (DENR) and the commercial kangaroo harvest industry, in conjunction with the University of Adelaide, I’m pleased to announce a new scholarship for a PhD candidate to work on a project entitled Optimal survey and harvest models for South Australian macropods based at the University of Adelaide’s School of Earth and Environmental Sciences.

DENR is custodian of a long-term macropod database derived from the State’s management of the commercial kangaroo harvest industry. The dataset entails aerial survey data for most of the State from 1978 to present, annual population estimates, quotas and harvests for three species: red kangaroo (Macropus rufus), western grey kangaroo (Macropus fuliginosus), and the euro (Macropus robustus erubescens). Read the rest of this entry »





Oceans need their giants

2 11 2011

Another great post from Salvador Herrando Pérez.

from adsown.blogspot.com

Commercial and sport fishing establish minimum body sizes for catches of many species to preserve fish stocks. Recent work reveals that sustainable fisheries also depend on the regulation of the harvest of the biggest fish, at least in long-lived species.

Growing up in Spain in the 1980s, I was taken by a Spanish television spot featuring a shoal of little fish sucking colourful dummies, and at the same time (how they managed, I never questioned) singing the motto Little fish? No, thanks. The then Ministry of Agriculture, Fishery and Food created this media campaign to create awareness among consumers not to buy immature fish at local markets – “…a 60-gram hake will only weigh 2 kg after two years” the add stated.

Indeed, the regulation of fish harvest by age classes is substantial to any fishery. In particular, the protection of younger fish has been a beacon of fishery policy and management that dates back to the 19th century when, among others, the British ichthyologist Ernst Holt concluded that: “…it is desirable that fish should have a chance of reproducing their species at least once before they are destroyed” 1. Very much in line with such principles, conventional fish stock management has in practice neglected the mature age classes2, other than for the fact that they are the end point of extraction and what we consumers eat on the table. Read the rest of this entry »





Where the sick buffalo roam

28 10 2011

It’s been some time coming, but today I’m proud to announce a new paper of ours that has just come out in Journal of Applied Ecology. While not strictly a conservation paper, it does provide some novel tools for modelling populations of threatened species in ways not available before.

The Genesis

A few years ago, a few of us (Bob LacyPhil Miller and JP Pollak of Vortex fame, Barry Brook, and a few others) got together in a little room at the Brookfield Zoo in the suburban sprawl of Chicago to have a crack at some new modelling approaches the Vortex crew had recently designed. The original results were pleasing, so we had a follow-up meeting last year (thanks to a few generous Zoo benefactors) and added a few post-docs and students to the mix (Damien FordhamClive McMahon, Tom Prowse, Mike Watts, Michelle Verant). The great population modeller Resit Akçakaya also came along to assist and talk about linkages with RAMAS.

Out of that particular meeting a series of projects was spawned, and one of those has now been published online: Novel coupling of individual-based epidemiological and demographic models predicts realistic dynamics of tuberculosis in alien buffalo.

The Coupling

So what’s so novel about modelling disease in buffalo, and why would one care? Well, here’s the interesting part. The buffalo-tuberculosis example was a great way to examine just how well a new suite of models – and their command-centre module – predicted disease dynamics in a wild population. The individual-based population modelling software Vortex has been around for some time, and is now particularly powerful for predicting the extinction risk of small populations; the newest addition to the Vortex family, called Outbreak, is also an individual-based epidemiological model that allows a population of individuals exposed to a pathogen to progress over time (e.g., from susceptible, exposed, infectious, recovered/dead). Read the rest of this entry »





生态学 = ‘Ecology’ in China

13 05 2011

I’m just heading home after a very inspiring workshop organised by Fangliang He at Sun Yat-sen University in Guangzhou, China (I’m writing this from the Qantas Club in the Hong Kong airport).

Before I proceed to regale you with the salient details of the ‘International Symposium for Biodiversity and Theoretical Ecology‘, I am compelled to state publicly that I offer my sincerest condolences to Fangliang and his family; unfortunately Fangliang’s brother passed away while we were at the workshop and so Fangliang wasn’t able to spend much time reaping the fruits of his organisational labour. If you know Fangliang, please send him a supporting email.

That sad note aside, I am delighted to say that the workshop was compelling, challenging and also rather fortuitous. I was one of many overseas invitees, and I must say that I was at times overwhelmed by the size of the brains they managed to pack into the auditorium. Many colleagues I didn’t know attended, and I hope that many will become collaborators. The international invitees were: Read the rest of this entry »








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