Species-area & species-accumulation curves not the same

30 05 2016

IBI’ve just read an elegant little study that has identified the main determinants of differences in the slope of species-area curves and species-accumulation curves.

That’s a bit of a mouthful for the uninitiated, so if you don’t know much about species-area theory, let me give you a bit of background for why this is an important new discovery.

Perhaps one of the only ‘laws’ in ecology comes from the observation that as you sample from larger and larger areas of any habitat type, the number of species tends to increase. This of course originates from MacArthur & Wilson’s classic book, The Theory of Island Biography (1967), and while simple in basic concept, it has since developed into a multi-headed Hydra of methods, analysis, theory and jargon.

One of the most controversial aspects of generic species-area relationships is the effect of different sampling regimes, a problem I’ve blogged about before. Whether you are sampling once-contiguous forest of habitat patches in a ‘matrix’ of degraded landscape, a wetland complex, a coral reef, or an archipelago of true oceanic islands, the ‘ideal’ models and the interpretation thereof will likely differ, and in sometimes rather important ways from a predictive and/or applied perspective. Read the rest of this entry »





Homage to Hanski

21 05 2016

qaecology's avatarThe Quantitative & Applied Ecology Group

Hanski06A tribute from QAECO

Ecology lost a giant last week. It was with great sadness that we at QAECO heard of Professor Ilkka Hanski’s passing after a long illness. Ilkka’s career profoundly affected us. From metapopulation theory, through expansive empirical research, to conservation planning, Ilkka’s research stood as an exemplar that focused our minds and spurred us on. He delivered not just a framework for understanding the complex world of spatial population dynamics, but set a bench mark of rigour that lifted our own aspirations.

Looking back at Ilkka’s career takes one on a fascinating journey. It begins in the fields of Finland, where Ilkka spent long hours of his youth collecting butterflies, bees and beetles. In his own words, it left a lasting impression (Hanski 1999), searing two key elements of population dynamics onto his mind: the importance of habitat patchiness to species distributions, and the changeability of species…

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Australia pisses away the little water it has

9 05 2016

cow_drinking_australia_dryWater, water nowhere, with little left to drink.

Australians are superlative natural resource wasters, but living in the driest inhabited continent on the planet, you’d think we’d be precious about our water use.

You’d be wrong.

On the contrary, Australia has a huge water footprint (defined as “the total volume of freshwater that is used to produce the goods and services consumed by the people of the nation”). For internal domestic use (i.e., not including agricultural and industrial uses, or water imported directly or within other goods), Australians use about 341000 litres per person per year (data from 1997–2001), which is six times the global average of 57000 litres per person per year (1).

Agricultural production is one of the chief consumers of freshwater around the world. For example, the global average virtual water content of rice (paddy) is 2.29 million litres/tonne produced, and for wheat it is 1.33 litres/tonne. Growing crops for biofuel in particular has a huge water footprint — depending on the crop in question, it takes an average of 1400–20000 litres of water to produce just one litre of biofuel (2). If an agricultural product comes from livestock — say, meat, leather, or wool — the water content is typically much higher because of the feed required to keep the animal alive. For example, it takes about three years to raise beef cattle to slaughtering age, with an average of 200 kg of boneless beef produced per animal. This requires about 1,300 kg of grains, 7200 kg of pasture or hay, and 31000 litres of water for drinking and cleaning. This means that the total amount of water required to produce 1 kg of beef is about 15340 litres (1). For Australia, which has over 20 million or so cattle at any one moment, the water footprint alone should at least be cause for concern the next time you tuck into a steak dinner. Read the rest of this entry »





One-two carbon punch of defaunation

30 04 2016

1-2 punchI’ve just read a well-planned and lateral-thinking paper in Nature Communications that I think readers of CB.com ought to appreciate. The study is a simulation of a complex ecosystem service that would be nigh impossible to examine experimentally. Being a self-diagnosed fanatic of simulation studies for just such purposes, I took particular delight in the results.

In many ways, the results of the paper by Osuri and colleagues are intuitive, but that should never be a reason to avoid empirical demonstration of a suspected phenomenon because intuition rarely equals fact. The idea itself is straightforward, but takes more than a few logical steps to describe: Read the rest of this entry »





Shadow of ignorance veiling society despite more science communication

19 04 2016

imagesI’ve been thinking about this post for a while, but it wasn’t until having some long, deep chats today with staff and students at Simon Fraser University‘s Department of Biological Sciences (with a particular hat-tip to the lovely Nick Dulvy, Isabelle Côté & John Reynolds) that the full idea began to take shape in my brain. It seems my presentation was a two-way street: I think I taught a few people some things, and they taught me something back. Nice.

There’s no question at all that science communication has never before been so widespread and of such high quality. More and more scientists and science students are now blogging, tweeting and generally engaging the world about their science findings. There is also an increasing number of professional science communication associations out there, and a growing population of professional science communicators. It is possibly the best time in history to be involved in the generation and/or communication of scientific results.

Why then is the public appreciation, acceptance and understanding of science declining? It really doesn’t make much sense if you merely consider that there has never been more good science ‘out there’ in the media — both social and traditional. For the source literature itself, there has never before been as many scientific journals, articles and even scientists writing. Read the rest of this entry »





Sensitive numbers

22 03 2016
toondoo.com

A sensitive parameter

You couldn’t really do ecology if you didn’t know how to construct even the most basic mathematical model — even a simple regression is a model (the non-random relationship of some variable to another). The good thing about even these simple models is that it is fairly straightforward to interpret the ‘strength’ of the relationship, in other words, how much variation in one thing can be explained by variation in another. Provided the relationship is real (not random), and provided there is at least some indirect causation implied (i.e., it is not just a spurious coincidence), then there are many simple statistics that quantify this strength — in the case of our simple regression, the coefficient of determination (R2) statistic is a usually a good approximation of this.

In the case of more complex multivariate correlation models, then sometimes the coefficient of determination is insufficient, in which case you might need to rely on statistics such as the proportion of deviance explained, or the marginal and/or conditional variance explained.

When you go beyond this correlative model approach and start constructing more mechanistic models that emulate ecological phenomena from the bottom-up, things get a little more complicated when it comes to quantifying the strength of relationships. Perhaps the most well-known category of such mechanistic models is the humble population viability analysis, abbreviated to PVA§.

Let’s take the simple case of a four-parameter population model we could use to project population size over the next 10 years for an endangered species that we’re introducing to a new habitat. We’ll assume that we have the following information: the size of the founding (introduced) population (n), the juvenile survival rate (Sj, proportion juveniles surviving from birth to the first year), the adult survival rate (Sa, the annual rate of surviving adults to year 1 to maximum longevity), and the fertility rate of mature females (m, number of offspring born per female per reproductive cycle). Each one of these parameters has an associated uncertainty (ε) that combines both measurement error and environmental variation.

If we just took the mean value of each of these three demographic rates (survivals and fertility) and project a founding population of = 10 individuals for 1o years into the future, we would have a single, deterministic estimate of the average outcome of introducing 10 individuals. As we already know, however, the variability, or stochasticity, is more important than the average outcome, because uncertainty in the parameter values (ε) will mean that a non-negligible number of model iterations will result in the extinction of the introduced population. This is something that most conservationists will obviously want to minimise.

So each time we run an iteration of the model, and generally for each breeding interval (most often 1 year at a time), we choose (based on some random-sampling regime) a different value for each parameter. This will give us a distribution of outcomes after the 10-year projection. Let’s say we did 1000 iterations like this; taking the number of times that the population went extinct over these iterations would provide us with an estimate of the population’s extinction probability over that interval. Of course, we would probably also vary the size of the founding population (say, between 10 and 100), to see at what point the extinction probability became acceptably low for managers (i.e., as close to zero as possible), but not unacceptably high that it would be too laborious or expensive to introduce that many individuals. Read the rest of this entry »





Higher biodiversity imparts greater disease resistance

12 03 2016

fungal infection

Is biodiversity good for us? In many ways, this is a stupid question because at some point, losing species that we use directly will obviously impact us negatively — think of food crops, pollination and carbon uptake.

But how much can we afford to lose before we notice anything bad is happening? Is the sort of biodiversity erosion we’re seeing today really such a big deal?

One area of research experiencing a surge in popularity is examining how variation in biodiversity (biowealth1) affects the severity of infectious diseases, and it is particularly controversial with respect to the evidence for a direct effect on human pathogens (e.g., see a recent paper here, a critique of it, and a reply).

Controversy surrounding the biodiversity-disease relationship among non-human species is less intense, but there are still arguments about the main mechanisms involved. The amplification hypothesis asserts that a community with more species has a greater pool of potential hosts for pathogens, so pathogens increase as biodiversity increases. On the contrary, the dilution hypothesis asserts that disease prevalence decreases with increasing host species diversity via several possible mechanisms, such as more host species reducing the chance that a given pathogen will ‘encounter’ a suitable host, and that in highly biodiverse communities, an infected individual is less likely to be surrounded by the same species, so the pathogen cannot easily be transmitted to a new host (the so-called transmission interference hypothesis).

So I’ve joined the ecological bandwagon and teamed up yet again with some very clever Chinese collaborators to test these hypotheses in — if I can be so bold to claim — a rather novel and exciting way.

Our new paper was just published online in EcologyWarming and fertilization alter the dilution effect of host diversity on disease severity2. Read the rest of this entry »





Environmental Arsehats

3 03 2016

arsehatI’m starting a new series on ConservationBytes.com — one that exposes the worst environmental offenders on the planet.

I’ve taken the idea from an independent media organisation based in Australia — Crikey — who has been running the Golden Arsehat of the Year awards since 2008. It’s a hilarious, but simultaneously maddening, way of shaming the worst kinds of people.

So in the spirit of a little good fun and environmental naming-and-shaming, I’d like to put together a good list of candidates for the inaugural Environmental Arsehat of the Year awards.

So I’m keen to receive your nominations, either privately via e-mail, the ConservationBytes.com message service, or even in the comments stream of this post. Once I receive a good list of candidates, I’ll do separate posts on particularly deserving individuals, followed by an online poll where you can vote for your (least) favourite Arsehat.

There are a few nomination rules, however. Read the rest of this entry »





Disadvantages of marine protected areas

29 02 2016

 

 

 

Stop wasting time

Stop wasting time





Biowealth

24 02 2016

frogWhile I’ve blogged about this before in general terms (here and here), I thought it wise to reproduce the (open-access) chapter of the same name published in late 2013 in the unfortunately rather obscure book The Curious Country produced by the Office of the Chief Scientist of Australia. I think it deserves a little more limelight.

As I stepped off the helicopter’s pontoon and into the swamp’s chest-deep, tepid and opaque water, I experienced for the first time what it must feel like to be some other life form’s dinner. As the helicopter flittered away, the last vestiges of that protective blanket of human technological innovation flew away with it.

Two other similarly susceptible, hairless, clawless and fangless Homo sapiens and I were now in the middle of one of the Northern Territory’s largest swamps at the height of the crocodile-nesting season. We were there to collect crocodile eggs for a local crocodile farm that, ironically, has assisted the amazing recovery of the species since its near-extinction in the 1960s. Removing the commercial incentive to hunt wild crocodiles by flooding the international market with scar-free, farmed skins gave the dwindling population a chance to recover.

redwoodConservation scientists like me rejoice at these rare recoveries, while many of our fellow humans ponder why we want to encourage the proliferation of animals that can easily kill and eat us. The problem is, once people put a value on a species, it is usually consigned to one of two states. It either flourishes as do domestic crops, dogs, cats and livestock, or dwindles towards or to extinction. Consider bison, passenger pigeons, crocodiles and caviar sturgeon.

As a conservation scientist, it’s my job not only to document these declines, but to find ways to prevent them. Through careful measurement and experiments, we provide evidence to support smart policy decisions on land and in the sea. We advise on the best way to protect species in reserves, inform hunters and fishers on how to avoid over-harvesting, and demonstrate the ways in which humans benefit from maintaining healthy ecosystems. Read the rest of this entry »





How to rank journals

18 02 2016

ranking… properly, or at least ‘better’.

In the past I have provided ranked lists of journals in conservation ecology according to their ISI® Impact Factor (see lists for 2008, 2009, 2010, 2011, 2012 & 2013). These lists have proven to be exceedingly popular.

Why are journal metrics and the rankings they imply so in-demand? Despite many people loathing the entire concept of citation-based journal metrics, we scientists, our administrators, granting agencies, award committees and promotion panellists use them with such merciless frequency that our academic fates are intimately bound to the ‘quality’ of the journals in which we publish.

Human beings love to rank themselves and others, the things they make, and the institutions to which they belong, so it’s a natural expectation that scientific journals are ranked as well.

I’m certainly not the first to suggest that journal quality cannot be fully captured by some formulation of the number of citations its papers receive; ‘quality’ is an elusive characteristic that includes inter alia things like speed of publication, fairness of the review process, prevalence of gate-keeping, reputation of the editors, writing style, within-discipline reputation, longevity, cost, specialisation, open-access options and even its ‘look’.

It would be impossible to include all of these aspects into a single ‘quality’ metric, although one could conceivably rank journals according to one or several of those features. ‘Reputation’ is perhaps the most quantitative characteristic when measured as citations, so we academics have chosen the lowest-hanging fruit and built our quality-ranking universe around them, for better or worse.

I was never really satisfied with metrics like black-box Impact Factors, so when I started discovering other ways to express the citation performance of the journals to which I regularly submit papers, I became a little more interested in the field of bibliometrics.

In 2014 I wrote a post about what I thought was a fairer way to judge peer-reviewed journal ‘quality’ than the default option of relying solely on ISI® Impact Factors. I was particularly interested in why the new kid on the block — Google Scholar Metrics — gave at times rather wildly different ranks of the journals in which I was interested.

So I came up with a simple mean ranking method to get some idea of the relative citation-based ‘quality’ of these journals.

It was a bit of a laugh, really, but my long-time collaborator, Barry Brook, suggested that I formalise the approach and include a wider array of citation-based metrics in the mean ranks.

Because Barry’s ideas are usually rather good, I followed his advice and together we constructed a more comprehensive, although still decidedly simple, approach to estimate the relative ranks of journals from any selection one would care to cobble together. In this case, however, we also included a rank-placement resampler to estimate the uncertainty associated with each rank.

I’m pleased to announce that the final version1 is now published in PLoS One2. Read the rest of this entry »





Bad science

10 02 2016

Head in HandsIn addition to the surpassing coolness of reconstructing long-gone ecosystems, my new-found enthusiasm for palaeo-ecology has another advantage — most of the species under investigation are already extinct.

That might not sound like an ‘advantage’, but let’s face it, modern conservation ecology can be bloody depressing, so much so that one sometimes wonders if it’s worth it. It is, of course, but there’s something marvellously relieving about studying extinct systems for the simple reason that there are no political repercussions. No self-serving, plutotheocratic politician can bugger up these systems any more. That’s a refreshing change from the doom and gloom of modern environmental science!

But it’s not all sweetness and light, of course; there are still people involved, and people sometimes make bad decisions in an attempt to modify the facts to suit their creed. The problem is when these people are the actual scientists involved in the generation of the ‘facts’.

As I alluded to a few weeks ago with the publication of our paper in Nature Communications describing the lack of evidence for a climate effect on the continental-scale extinctions of Australia’s megafauna, we have a follow-up paper that has just been published online in Proceedings of the Royal Society B — What caused extinction of the Pleistocene megafauna of Sahul? led by Chris Johnson of the University of Tasmania.

After our paper published earlier this month, this title might seem a bit rhetorical, so I want to highlight some of the reasons why we wrote the review. Read the rest of this entry »





It’s not always best to be the big fish

3 02 2016

obrien_fish_2Loosely following the theme of last week’s post, it’s now fairly well established that humans tend to pick on the big species first.

From fewer big trees, declines of big carnivores, elephant & rhino poaching, to fishing down the web, big species tend to cop it hardest when it comes to human-caused ecological disturbance.

While there are a lot of different combinations of traits that make some species more vulnerable to extinction than others (see examples for legumes, amphibians, sharks & teleosts, and mammals), one of the main ones is species size.

Generally speaking, larger species tend to produce fewer offspring and breed later in life than smaller species. This means that despite larger species tending to live longer than their smaller counterparts, their ‘slow’ reproductive output means that they are generally more susceptible to rapid environmental change (mainly via human intervention). In other words, their capacity for self-replacement is often too low to counteract the offtake from direct exploitation or habitat loss.

Despite a reasonable scientific understanding of this extinction-risk principle, the degree to which human disturbance affects species’ distributions is much less well quantified, and this is especially true for marine species.

I’m proud to announce another fascinating paper led by my postdoc, Camille Mellin, that has just come out online in Nature CommunicationsHumans and seasonal climate variability threaten large-bodied coral reef fish with small ranges.

With the world’s largest combined dataset of coral reef fish surveys for the entire Indo-Pacific (including the coral reef fish biodiversity hotspot — the Coral Triangle), we examined which conditions best described the distribution of fishes over a range of body sizes. Read the rest of this entry »





No evidence climate change is to blame for Australian megafauna extinctions

29 01 2016

bw spear throwingLast July I wrote about a Science paper of ours demonstrating that there was a climate-change signal in the overall extinction pattern of megafauna across the Northern Hemisphere between about 50,000 and 10,000 years ago. In that case, it didn’t have anything to do with ice ages (sorry, Blue Sky Studios); rather, it was abrupt warming periods that exacerbated the extinction pulse instigated by human hunting.

Contrary to some appallingly researched media reports, we never claimed that these extinctions arose only from warming, because the evidence is more than clear that humans were the dominant drivers across North America, Europe and northern Asia; we simply demonstrated that warming periods had a role to play too.

A cursory glance at the title of this post without appreciating the complexity of how extinctions happen might lead you to think that we’re all over the shop with the role of climate change. Nothing could be farther from the truth.

Instead, we report what the evidence actually says, instead of making up stories to suit our preconceptions.

So it is with great pleasure that I report our new paper just out in Nature Communications, led by my affable French postdoc, Dr Frédérik SaltréClimate change not to blame for late Quaternary megafauna extinctions in Australia.

Of course, it was a huge collaborative effort by a crack team of ecologists, palaeontologists, geochronologists, paleo-climatologists, archaeologists and geneticists. Only by combining the efforts of this diverse and transdisciplinary team could we have hoped to achieve what we did. Read the rest of this entry »





Getting your conservation science to the right people

22 01 2016

argument-cartoon-yellingA perennial lament of nearly every conservation scientist — at least at some point (often later in one’s career) — is that the years of blood, sweat and tears spent to obtain those precious results count for nought in terms of improving real biodiversity conservation.

Conservation scientists often claim, especially in the first and last paragraphs of their papers and research proposals, that by collecting such-and-such data and doing such-and-such analyses they will transform how we manage landscapes and species to the overall betterment of biodiversity. Unfortunately, most of these claims are hollow (or just plain bullshit) because the results are either: (i) never read by people who actually make conservation decisions, (ii) not understood by them even if they read the work, or (iii) never implemented because they are too vague or too unrealistic to translate into a tangible, positive shift in policy.

A depressing state of being, I know.

This isn’t any sort of novel revelation, for we’ve been discussing the divide between policy makers and scientists for donkey’s years. Regardless, the whinges can be summarised succinctly: Read the rest of this entry »





Outright bans of trophy hunting could do more harm than good

5 01 2016

In July 2015 an American dentist shot and killed a male lion called ‘Cecil’ with a hunting bow and arrow, an act that sparked a storm of social media outrage. Cecil was a favourite of tourists visiting Hwange National Park in Zimbabwe, and so the allegation that he was lured out of the Park to neighbouring farmland added considerable fuel to the flames of condemnation. Several other aspects of the hunt, such as baiting close to national park boundaries, were allegedly done illegally and against the spirit and ethical norms of a managed trophy hunt.

In May 2015, a Texan legally shot a critically endangered black rhino in Namibia, which also generated considerable online ire. The backlash ensued even though the male rhino was considered ‘surplus’ to Namibia’s black rhino populations, and the US$350,000 generated from the managed hunt was to be re-invested in conservation. Together, these two incidents have triggered vociferous appeals to ban trophy hunting throughout Africa.

These highly politicized events are but a small component of a large industry in Africa worth > US$215 million per year that ‘sells’ iconic animals to (mainly foreign) hunters as a means of generating otherwise scarce funds. While to most people this might seem like an abhorrent way to generate money, we argue in a new paper that sustainable-use activities, such as trophy hunting, can be an important tool in the conservationist’s toolbox. Conserving biodiversity can be expensive, so generating money is a central preoccupation of many environmental NGOs, conservation-minded individuals, government agencies and scientists. Making money for conservation in Africa is even more challenging, and so we argue that trophy hunting should and could fill some of that gap. Read the rest of this entry »





Influential conservation papers of 2015

25 12 2015

most popularAs I did last year and the year before, here’s another arbitrary, retrospective list of the top 20 influential conservation papers of 2015 as assessed via F1000 Prime.

Read the rest of this entry »





Death of the question

17 12 2015
Zombie apocalypse

Zombie apocalypse

It’s something I’ve noticed over the years going to scientific conferences and seminars — the number of questions, and more importantly their quality, have declined.

Sure, it’s anecdotal and it might just be that my perspective has changed, but I’d bet my left testicle that it’s true.

But why? There are possibly many contributing factors, such as increasingly jam-packed conferences with multiple concurrent sessions, a massive and increasing number of participants and less time for each of us to present our work. However, I think the main reason is that we’re now all glued to our electronic devices.

Yes, I’m talking about the Twitteratti, but also the tablet-tossers, laptop-layabouts and the iPhone-idiots. We have a saying in our family when we spot a smartphone zombie oblivious to oncoming traffic that she/he looks like a “… spastic fingering a sandwich” (not my quote, but I am particularly fond of using it).

Read the rest of this entry »





Bee informed: Quick pollination facts about our most important pollinators

27 11 2015

if we die

If bees were to disappear, humans will disappear within a few years.

Albert Einstein

I find it interesting that so much is said about bees (including here on this blog), yet many of the ‘facts’ that one hears mentioned in any variety of news sources, public presentations and even scientific articles aren’t very well sourced and at times highly suspect.

For your fact-finding benefit then, I present to you some of the established facts about bees: Read the rest of this entry »





When science is ignored: Mauritius starts culling 18,000 threatened fruit bats

8 11 2015

JS7D2844aRrHere’s a depressing emergency post by Fabiola Monty.

I started working on this article to discuss how useful science is being ignored in Mauritius.

The Mauritian government has decided to implement a fruit bat cull as an ‘urgent response’ to the claims of huge economic losses by fruit farmers, a decision not supported by scientific evidence. We have now received confirmation in Mauritius through a local press communiqué that on 7 November 2015, The Mauritian Ministry of Agro Industry and Food Security in collaboration with the local Police Department and Special Mobile Force will start the culling of 18,000 bats in their natural habitats “with a view to reducing the extent of damages caused to fruits by bats”.

Tackling human-wildlife conflicts can indeed be challenging, but can the culling of 18,000 endemic Mauritian flying fox (Pteropus niger) resolve ‘human-wildlife conflict’ in the land of the dodo? In the case of Mauritius, scientific evidence not only demonstrates that the situation has been exaggerated, but that there are alternatives to bat culling that have been completely brushed aside by policy makers.

JS7D3726aRrAre the Mauritius fruit bats agricultural pests?

While fruit bats are being labelled as serious pests, scientific evidence shows instead that their impacts have been exaggerated. A recent (2014) study indicates that bats damage only 3-11% of fruit production, with birds also contributing to 1-8% of fruit loss. Rats are also probable contributors to fruit damage, but the extent remains unquantified. Interestingly, more fruits are lost (13-20%) because they are not collected in time and are left to over-ripen.

While the results of the study were communicated to legislators a few months before they made the decision to cull, it is clear that these were ignored in favour of preconceived assumptions.

Are there too many fruit bats? Read the rest of this entry »